1dce

CRYSTAL STRUCTURE OF RAB GERANYLGERANYLTRANSFERASE FROM RAT BRAIN

Method: X-RAY DIFFRACTION D_max: 142.6 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT)

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–567	Non-standard monomer：Yes (specific site not provided by mmCIF)	PROTEIN (RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT) × 1 （Q08603） ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.00 Å R-free 0.263
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–567	Non-standard monomer：Yes (specific site not provided by mmCIF)	PROTEIN (RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT) × 1 （Q08603） ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.00 Å R-free 0.263

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1DCE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1LTX Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid Deposited 2002-05-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–567（567 aa）	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1 FAR FARNESYL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；20% PEG 3350, 100mM KSCN, 100mM Namalonate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.70 Å R-free 0.272
3C72 Engineered RabGGTase in complex with a peptidomimetic inhibitor Deposited 2008-02-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–236（236 aa） Chain A 353–441（89 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 CX1 N-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-L-tyrosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2 M Ca-Acetate, 0.1 M HEPES, cocrystallization with 5 mM inhibitor, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.30 Å R-free 0.256
3DSS Crystal structure of RabGGTase(DELTA LRR; DELTA IG) Deposited 2008-07-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：PFTA domains, UNP residues 1-237 and 353-441 Chain A 353–441（89 aa） Fragment：PFTA domains, UNP residues 1-237 and 353-441	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.80 Å R-free 0.194
3DST Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with geranylgeranyl pyrophosphate Deposited 2008-07-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：PFTA domains, UNP residues 1-237 and 353-441 Chain A 353–441（89 aa） Fragment：PFTA domains, UNP residues 1-237 and 353-441	Not recorded	GRG GERANYLGERANYL DIPHOSPHATE × 1 ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.90 Å R-free 0.220
3DSU Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with farnesyl pyrophosphate Deposited 2008-07-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：PFTA domains, UNP residues 1-237 and 353-441 Chain A 353–441（89 aa） Fragment：PFTA domains, UNP residues 1-237 and 353-441	Not recorded	FPP FARNESYL DIPHOSPHATE × 1 ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.90 Å R-free 0.215
3DSV Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with mono-prenylated peptide Ser-Cys-Ser-Cys(GG) derivated from Rab7 Deposited 2008-07-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：PFTA domains, UNP residues 1-237 and 353-441 Chain A 353–441（89 aa） Fragment：PFTA domains, UNP residues 1-237 and 353-441	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 GER GERAN-8-YL GERAN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.10 Å R-free 0.211
3DSW Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with mono-prenylated peptide Ser-Cys(GG)-Ser-Cys derivated from Rab7 Deposited 2008-07-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：PFTA domains, UNP residues 1-237 and 353-441 Chain A 353–441（89 aa） Fragment：PFTA domains, UNP residues 1-237 and 353-441	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 GER GERAN-8-YL GERAN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.15 Å R-free 0.232
3DSX Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with di-prenylated peptide Ser-Cys(GG)-Ser-Cys(GG) derivated from Rab7 Deposited 2008-07-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：PFTA domains, UNP residues 1-237 and 353-441 Chain A 353–441（89 aa） Fragment：PFTA domains, UNP residues 1-237 and 353-441	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 GER GERAN-8-YL GERAN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 2.5% (v/v)DMSO, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.10 Å R-free 0.229
3HXB Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 6) Deposited 2009-06-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：RabGGTase ALPHA-subunit Chain A 353–441（89 aa） Fragment：RabGGTase ALPHA-subunit	Mutation：DELTA LRR; DELTA IG Mutation：DELTA LRR; DELTA IG	BD5 N-[(benzyloxy)carbonyl]-D-tyrosyl-L-phenylalanyl-L-tyrosine × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.25 Å R-free 0.278
3HXC Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 8) Deposited 2009-06-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：RabGGTase ALPHA-subunit Chain A 353–441（89 aa） Fragment：RabGGTase ALPHA-subunit	Mutation：DELTA LRR; DELTA IG Mutation：DELTA LRR; DELTA IG	ZN ZINC ION × 1 CA CALCIUM ION × 1 BD6 N-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-N-hydroxy-L-tryptophanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.95 Å R-free 0.218
3HXD Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 9) Deposited 2009-06-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：RabGGTase ALPHA-subunit Chain A 353–441（89 aa） Fragment：RabGGTase ALPHA-subunit	Mutation：DELTA LRR; DELTA IG Mutation：DELTA LRR; DELTA IG	ZN ZINC ION × 1 CA CALCIUM ION × 1 BD7 N-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-N-hydroxy-L-tyrosinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.95 Å R-free 0.222
3HXE Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 37) Deposited 2009-06-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：RabGGTase ALPHA-subunit Chain A 353–441（89 aa） Fragment：RabGGTase ALPHA-subunit	Mutation：DELTA LRR; DELTA IG Mutation：DELTA LRR; DELTA IG	ZN ZINC ION × 1 CA CALCIUM ION × 1 BD8 N-undecanoyl-L-histidyl-L-phenylalanyl-N-methyl-N-(2-pyridin-2-ylethyl)-L-tyrosinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.95 Å R-free 0.215
3HXF Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 32) Deposited 2009-06-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：RabGGTase ALPHA-subunit Chain A 353–441（89 aa） Fragment：RabGGTase ALPHA-subunit	Mutation：DELTA LRR; DELTA IG Mutation：DELTA LRR; DELTA IG	ZN ZINC ION × 1 CA CALCIUM ION × 1 BD9 N-undecanoyl-L-histidyl-L-histidyl-N-methyl-N-(2-pyridin-2-ylethyl)-L-tyrosinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.90 Å R-free 0.212
3PZ1 Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3 Deposited 2010-12-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：Fusion of residues 1-237 and 353-441 with linker AGSG Chain A 353–441（89 aa） Fragment：Fusion of residues 1-237 and 353-441 with linker AGSG	Not recorded	3PZ (3R)-3-benzyl-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-7-carbonitrile × 1 ZN ZINC ION × 1 CA CALCIUM ION × 1 DMS DIMETHYL SULFOXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.95 Å R-free 0.232
3PZ2 Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3 and lipid substrate GGPP Deposited 2010-12-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：UNP residues 1-237 and 353-441 Chain A 353–441（89 aa） Fragment：UNP residues 1-237 and 353-441	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 3PZ (3R)-3-benzyl-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-7-carbonitrile × 1 GRG GERANYLGERANYL DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.35 Å R-free 0.256
3PZ3 Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS-analogue 14 Deposited 2010-12-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：UNP residues 1-237 and 353-441 Chain A 353–441（89 aa） Fragment：UNP residues 1-237 and 353-441	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 PZ3 4-({(3R)-7-(5-formylfuran-2-yl)-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-3-yl}methyl)phenyl benzylcarbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.00 Å R-free 0.224
4EHM RabGGTase in complex with covalently bound Psoromic acid Deposited 2012-04-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Chain A 353–441（89 aa）	Not recorded	PJA 4-formyl-3-hydroxy-8-methoxy-1,9-dimethyl-11-oxo-11H-dibenzo[b,e][1,4]dioxepine-6-carboxylic acid × 1 ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；285 K；20mM Hepes pH7.2, 100mM NaCl, 2mM DTT, 15% PEG 3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 2.20 Å R-free 0.251
4GTS Engineered RabGGTase in complex with BMS analogue 16 Deposited 2012-08-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：residues 1-237 and 353-441 linked with AGSG Chain A 353–441（89 aa） Fragment：residues 1-237 and 353-441 linked with AGSG	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 7TP 5-{(3R)-3-(4-hydroxybenzyl)-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-7-yl}furan-2-carbaldehyde × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；285 K；RabGGTase in 20mM Hepes pH7.2, 100mM NaCl and 2mM DTT was mixed with 15% PEG3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2. The obtained crystals was soaked with 20% PEG3350, 0.2M Ca Acetate, 5% Glycerol in the presence of 1mM inhibitor for 12 hour, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 2.45 Å R-free 0.248
4GTT Engineered RabGGTase in complex with BMS analogue 12 Deposited 2012-08-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：residues 1-237 and 353-441 linked with AGSG Chain A 353–441（89 aa） Fragment：residues 1-237 and 353-441 linked with AGSG	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 7TQ 4-({(3R)-7-cyano-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-3-yl}methyl)phenyl benzylcarbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；285 K；RabGGTase in 20mM Hepes pH7.2, 100mM NaCl and 2mM DTT was mixed with 15% PEG3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2. The obtained crystals was soaked with 20% PEG3350, 0.2M Ca Acetate, 5% Glycerol in the presence of 1mM inhibitor for 12 hour., VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 2.05 Å R-free 0.233
4GTV Engineered RabGGTase in complex with BMS analogue 13 Deposited 2012-08-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–237（237 aa） Fragment：residues 1-237 and 353-441 linked with AGSG Chain A 353–441（89 aa） Fragment：residues 1-237 and 353-441 linked with AGSG	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 7TR 4-({(3R)-7-cyano-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-3-yl}methyl)phenyl diethylcarbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；285 K；RabGGTase in 20mM Hepes pH7.2, 100mM NaCl and 2mM DTT was mixed with 15% PEG3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2. The obtained crystals was soaked with 20% PEG3350, 0.2M Ca Acetate, 5% Glycerol in the presence of 1mM inhibitor for 12 hour, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.95 Å R-free 0.211

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PGTA_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–567； UniProt 1–567 Author chain C； PDBConstruct 1–567； UniProt 1–567

PROTEIN (RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT)

OrganismNot specified

UniProt Q08603

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–331	Not recorded	PROTEIN (RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT) × 1 （Q08602） ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.00 Å R-free 0.263
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–331	Not recorded	PROTEIN (RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT) × 1 （Q08602） ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.00 Å R-free 0.263

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1DCE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1LTX Structure of Rab Escort Protein-1 in complex with Rab geranylgeranyl transferase and isoprenoid Deposited 2002-05-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–331（331 aa）	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1 FAR FARNESYL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；20% PEG 3350, 100mM KSCN, 100mM Namalonate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.70 Å R-free 0.272
3C72 Engineered RabGGTase in complex with a peptidomimetic inhibitor Deposited 2008-02-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–331（331 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 CX1 N-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-L-tyrosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2 M Ca-Acetate, 0.1 M HEPES, cocrystallization with 5 mM inhibitor, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.30 Å R-free 0.256
3DSS Crystal structure of RabGGTase(DELTA LRR; DELTA IG) Deposited 2008-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–331（331 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.80 Å R-free 0.194
3DST Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with geranylgeranyl pyrophosphate Deposited 2008-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–331（331 aa）	Not recorded	GRG GERANYLGERANYL DIPHOSPHATE × 1 ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.90 Å R-free 0.220
3DSU Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with farnesyl pyrophosphate Deposited 2008-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–331（331 aa）	Not recorded	FPP FARNESYL DIPHOSPHATE × 1 ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.90 Å R-free 0.215
3DSV Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with mono-prenylated peptide Ser-Cys-Ser-Cys(GG) derivated from Rab7 Deposited 2008-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–331（331 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 GER GERAN-8-YL GERAN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.10 Å R-free 0.211
3DSW Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with mono-prenylated peptide Ser-Cys(GG)-Ser-Cys derivated from Rab7 Deposited 2008-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–331（331 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 GER GERAN-8-YL GERAN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.15 Å R-free 0.232
3DSX Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with di-prenylated peptide Ser-Cys(GG)-Ser-Cys(GG) derivated from Rab7 Deposited 2008-07-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–331（331 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 GER GERAN-8-YL GERAN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 2.5% (v/v)DMSO, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.10 Å R-free 0.229
3HXB Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 6) Deposited 2009-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–331（331 aa） Fragment：RABGGTase BETA-subunit	Not recorded	BD5 N-[(benzyloxy)carbonyl]-D-tyrosyl-L-phenylalanyl-L-tyrosine × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.25 Å R-free 0.278
3HXC Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 8) Deposited 2009-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–331（331 aa） Fragment：RABGGTase BETA-subunit	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 BD6 N-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-N-hydroxy-L-tryptophanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.95 Å R-free 0.218
3HXD Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 9) Deposited 2009-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–331（331 aa） Fragment：RABGGTase BETA-subunit	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 BD7 N-[(benzyloxy)carbonyl]-L-histidyl-N-methyl-L-phenylalanyl-N-hydroxy-L-tyrosinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.95 Å R-free 0.222
3HXE Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 37) Deposited 2009-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–331（331 aa） Fragment：RABGGTase BETA-subunit	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 BD8 N-undecanoyl-L-histidyl-L-phenylalanyl-N-methyl-N-(2-pyridin-2-ylethyl)-L-tyrosinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.95 Å R-free 0.215
3HXF Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 32) Deposited 2009-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–331（331 aa） Fragment：RABGGTase BETA-subunit	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 BD9 N-undecanoyl-L-histidyl-L-histidyl-N-methyl-N-(2-pyridin-2-ylethyl)-L-tyrosinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.90 Å R-free 0.212
3PZ1 Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3 Deposited 2010-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–331（330 aa） Fragment：UNP residues 10-339	Not recorded	3PZ (3R)-3-benzyl-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-7-carbonitrile × 1 ZN ZINC ION × 1 CA CALCIUM ION × 1 DMS DIMETHYL SULFOXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 1.95 Å R-free 0.232
3PZ2 Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS3 and lipid substrate GGPP Deposited 2010-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–331（330 aa） Fragment：UNP residues 10-339	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 3PZ (3R)-3-benzyl-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-7-carbonitrile × 1 GRG GERANYLGERANYL DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.35 Å R-free 0.256
3PZ3 Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS-analogue 14 Deposited 2010-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–331（330 aa） Fragment：UNP residues 10-339	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 PZ3 4-({(3R)-7-(5-formylfuran-2-yl)-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-3-yl}methyl)phenyl benzylcarbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；284 K；14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K	Resolution 2.00 Å R-free 0.224
4EHM RabGGTase in complex with covalently bound Psoromic acid Deposited 2012-04-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–331（330 aa）	Not recorded	PJA 4-formyl-3-hydroxy-8-methoxy-1,9-dimethyl-11-oxo-11H-dibenzo[b,e][1,4]dioxepine-6-carboxylic acid × 1 ZN ZINC ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；285 K；20mM Hepes pH7.2, 100mM NaCl, 2mM DTT, 15% PEG 3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 2.20 Å R-free 0.251
4GTS Engineered RabGGTase in complex with BMS analogue 16 Deposited 2012-08-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–331（330 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 7TP 5-{(3R)-3-(4-hydroxybenzyl)-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-7-yl}furan-2-carbaldehyde × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；285 K；RabGGTase in 20mM Hepes pH7.2, 100mM NaCl and 2mM DTT was mixed with 15% PEG3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2. The obtained crystals was soaked with 20% PEG3350, 0.2M Ca Acetate, 5% Glycerol in the presence of 1mM inhibitor for 12 hour, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 2.45 Å R-free 0.248
4GTT Engineered RabGGTase in complex with BMS analogue 12 Deposited 2012-08-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–331（330 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 7TQ 4-({(3R)-7-cyano-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-3-yl}methyl)phenyl benzylcarbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；285 K；RabGGTase in 20mM Hepes pH7.2, 100mM NaCl and 2mM DTT was mixed with 15% PEG3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2. The obtained crystals was soaked with 20% PEG3350, 0.2M Ca Acetate, 5% Glycerol in the presence of 1mM inhibitor for 12 hour., VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 2.05 Å R-free 0.233
4GTV Engineered RabGGTase in complex with BMS analogue 13 Deposited 2012-08-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–331（330 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 7TR 4-({(3R)-7-cyano-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-3-yl}methyl)phenyl diethylcarbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；285 K；RabGGTase in 20mM Hepes pH7.2, 100mM NaCl and 2mM DTT was mixed with 15% PEG3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2. The obtained crystals was soaked with 20% PEG3350, 0.2M Ca Acetate, 5% Glycerol in the presence of 1mM inhibitor for 12 hour, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.95 Å R-free 0.211

20 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PGTB_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–331； UniProt 1–331 Author chain D； PDBConstruct 1–331； UniProt 1–331

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dce
Deposition date deposition_date	1999-11-04
Structure title title	CRYSTAL STRUCTURE OF RAB GERANYLGERANYLTRANSFERASE FROM RAT BRAIN
Keywords keywords	RAB GERANYLGERANYLTRANSFERASE, 2.0 A RESOLUTION, N-FORMYLMETHIONINE, ALPHA SUBUNIT, BETA SUBUNIT, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	43.16 Å
Radius of gyration Rg (electron density) rg_electron	42.81 Å
Forward intensity I(0) i0	607054000.00
Molecular weight molecular_weight	201580.0 kDa
Excluded volume excluded_volume	251730 Å³
Envelope volume envelope_volume	336780 Å³
Hydration-shell volume shell_volume	65564 Å³
Envelope diameter envelope_diameter	139.6 Å
Shell Rg shell_rg	47.74 Å
Envelope Rg envelope_rg	42.11 Å
Shape Rg shape_rg	42.82 Å
Total Rg total_rg	43.03 Å
Total atoms total_atoms	14153
Residues n_residues	1790
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	142.6 Å
Rg (real space) rg_real	43.15 Å
Rg uncertainty (real space) rg_real_error	1.18 Å
I(0) (real space) i0_real	6.0710e+08
I(0) uncertainty (real space) i0_real_error	1.0450e+07
Rg (reciprocal space) rg_reciprocal	43.16 Å
I(0) (reciprocal space) i0_reciprocal	607100000.0000
Solution quality estimate total_estimate	0.8973
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.2 Å
Skewness Skewness skewness	0.278
Kurtosis Kurtosis kurtosis	-0.607
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	89960000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PROTEIN (RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT)
Molecular weight formula_weight	65009.2 kDa
EC 编号 ec_number	2.5.1.-
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	14982

MHGRLKVKTSEEQAEAKRLEREQKLKLYQSATQAVFQKRQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPHDVLCCVHVSREEACLSVCFSRPLTVGSRMGTLLLMVDEAPLSVEWRTPDGRNRPSHVWLCDLPAASLNDQLPQHTFRVIWTGSDSQKECVLLKDRPECWCRDSATDEQLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKFLLENSVLKMEYADVRVLHLAHKDLTVLCHLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDGVANLPRLQELLLCNNRLQQSAAIQPLVSCPRLVLLNLQGNSLCQEEGIQERLAEMLPSVSSILT

Entity 2 Entity 2 polymer

Description description	PROTEIN (RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT)
Molecular weight formula_weight	36892.2 kDa
EC 编号 ec_number	2.5.1.-
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MGTQQKDVTIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQIKPVSPVFCMPEEVLQRVNVQPELVS

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	829

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1dcea1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.6 — Protein prenylyltransferase
Family Family family	a.118.6.1 — Protein prenylyltransferase

Domain ID domain_id	d1dcea2
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.4 — Rab geranylgeranyltransferase alpha-subunit, insert domain
Family Family family	b.7.4.1 — Rab geranylgeranyltransferase alpha-subunit, insert domain

Domain ID domain_id	d1dcea3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamily	c.10.2 — L domain-like
Family Family family	c.10.2.2 — Rab geranylgeranyltransferase alpha-subunit, C-terminal domain

Domain ID domain_id	d1dceb_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.3 — Protein prenyltransferases

Domain ID domain_id	d1dcec1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.6 — Protein prenylyltransferase
Family Family family	a.118.6.1 — Protein prenylyltransferase

Domain ID domain_id	d1dcec2
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.4 — Rab geranylgeranyltransferase alpha-subunit, insert domain
Family Family family	b.7.4.1 — Rab geranylgeranyltransferase alpha-subunit, insert domain

Domain ID domain_id	d1dcec3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamily	c.10.2 — L domain-like
Family Family family	c.10.2.2 — Rab geranylgeranyltransferase alpha-subunit, C-terminal domain

Domain ID domain_id	d1dced_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.4 — Terpenoid cyclases/Protein prenyltransferases
Family Family family	a.102.4.3 — Protein prenyltransferases

CATH v4.4 (8 domains)

Domain ID domain_id	1dceA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	120 — Protein prenylyltransferase

Domain ID domain_id	1dceA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1130 — Rab geranylgeranyltransferase alpha-subunit, insert domain

Domain ID domain_id	1dceA03
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	1dceB00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1dceC01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	120 — Protein prenylyltransferase

Domain ID domain_id	1dceC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1130 — Rab geranylgeranyltransferase alpha-subunit, insert domain

Domain ID domain_id	1dceC03
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	1dceD00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	57.864 Å
Unit-cell length b length_b	77.439 Å
Unit-cell length c length_c	121.775 Å
Unit-cell angle α angle_alpha	74.60 °
Unit-cell angle β angle_beta	79.91 °
Unit-cell angle γ angle_gamma	67.89 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2147
R_free r_free	0.2634

fit	/app/data/saxs_computation/dc/1dce/1dce.fit
pddf	/app/data/pr_computation/dc/1dce/1dce.pr.out
profile	/app/data/saxs_computation/dc/1dce/1dce.dat

CRYSTAL STRUCTURE OF RAB GERANYLGERANYLTRANSFERASE FROM RAT BRAIN

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (RAB GERANYLGERANYLTRANSFERASE ALPHA SUBUNIT)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (RAB GERANYLGERANYLTRANSFERASE BETA SUBUNIT)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)