4i1o

Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3

Method: X-RAY DIFFRACTION D_max: 144.0 Å Quality: GOOD

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

Ras-related protein Rab-1B

Homo sapiens

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 3–174	Fragment：UNP residues 3-174	LepB × 1 （Q5ZSM7） MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.249
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 3–174	Fragment：UNP residues 3-174	LepB × 1 （Q5ZSM7） MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.249
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 3–174	Fragment：UNP residues 3-174	LepB × 1 （Q5ZSM7） MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.249
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 3–174	Fragment：UNP residues 3-174	LepB × 1 （Q5ZSM7） MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.249

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 4I1O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JZA Crystal structure of human Rab1b in complex with the GEF domain of DrrA/SidM from Legionella pneumophila Deposited 2009-09-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 3–174（172 aa） Fragment：UNP residues 3-174	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；292 K；0.1 M Sodium citrate, 35% v/v PEG 600, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.80 Å R-free 0.234
3NKV Crystal structure of Rab1b covalently modified with AMP at Y77 Deposited 2010-06-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–174（172 aa） Fragment：Rab1b-AMP	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 BA BARIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；298 K；15% (v/v) isopropanol, 15% (w/v) PEG4000, 0.1 M imidazole, 10 mM BaCl2, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.70 Å R-free 0.187
3NKV Crystal structure of Rab1b covalently modified with AMP at Y77 Deposited 2010-06-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 3–174（172 aa） Fragment：Rab1b-AMP	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 BA BARIUM ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；298 K；15% (v/v) isopropanol, 15% (w/v) PEG4000, 0.1 M imidazole, 10 mM BaCl2, pH 6.0, vapor diffusion, hanging drop, temperature 298K	Resolution 1.70 Å R-free 0.187
4HLQ Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of TBC1D20 from homo sapiens Deposited 2012-10-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–174（172 aa）	Not recorded	SO4 SULFATE ION × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；1.6M ammonium sulphate, 0.1M Hepes pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.274
4HLQ Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of TBC1D20 from homo sapiens Deposited 2012-10-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 3–174（172 aa）	Not recorded	SO4 SULFATE ION × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；1.6M ammonium sulphate, 0.1M Hepes pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.274
4HLQ Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of TBC1D20 from homo sapiens Deposited 2012-10-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 3–174（172 aa）	Not recorded	SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；1.6M ammonium sulphate, 0.1M Hepes pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.274
4HLQ Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of TBC1D20 from homo sapiens Deposited 2012-10-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 3–174（172 aa）	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；1.6M ammonium sulphate, 0.1M Hepes pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.274
4HLQ Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of TBC1D20 from homo sapiens Deposited 2012-10-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 3–174（172 aa）	Not recorded	SO4 SULFATE ION × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；1.6M ammonium sulphate, 0.1M Hepes pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.274
5O74 Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP Deposited 2017-06-08	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 B 3–174（172 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml	Resolution 2.50 Å R-free 0.266
5O74 Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP Deposited 2017-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 3–174（172 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml	Resolution 2.50 Å R-free 0.266
5O74 Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP Deposited 2017-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 3–174（172 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml	Resolution 2.50 Å R-free 0.266
5O74 Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP Deposited 2017-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 3–174（172 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml	Resolution 2.50 Å R-free 0.266
5O74 Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP Deposited 2017-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 3–174（172 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml	Resolution 2.50 Å R-free 0.266
5O74 Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP Deposited 2017-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 3–174（172 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；19% PEG 600, 100mM NaCitrate pH 5.5, protein concentration 22mg/ml	Resolution 2.50 Å R-free 0.266
5SZH Structure of human Rab1b in complex with the bMERB domain of Mical-cL Deposited 2016-08-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–201（201 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20-22% PEG3350 0.1M bis-Tris Propane 0.2M tri-Sodium Citrate	Resolution 2.30 Å R-free 0.207
5SZK Structure of human N-terminally engineered Rab1b in complex with the bMERB domain of Mical-cL Deposited 2016-08-14	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 B 1–201（201 aa）	Mutation：N2A, P3K, E4T	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M bis-tris pH 7.5, 0.2M sodium malonate and 20% (w/v) PEG3350	Resolution 2.80 Å R-free 0.261
6SKU Legionella effector AnkX in complex with human Rab1b Deposited 2019-08-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–174（172 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；3.5 M Sodium formate	Resolution 3.20 Å R-free 0.288
8ALK Structure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate Rab1 Deposited 2022-08-01	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 B 3–174（172 aa）	Mutation：S76T	CA CALCIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 OJU 2-[[[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxyethyl-[3-(2-chloranylethanoylamino)propyl]-dimethyl-azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；MES 0.1M pH 5, PEG6000 5%	Resolution 2.15 Å R-free 0.228

8 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAB1B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–175； UniProt 3–174 Author chain C； PDBConstruct 4–175； UniProt 3–174 Author chain E； PDBConstruct 4–175； UniProt 3–174 Author chain G； PDBConstruct 4–175； UniProt 3–174

LepB

Legionella pneumophila subsp. pneumophila

UniProt Q5ZSM7

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 D； UniProt 317–618	Fragment：GAP domain (UNP residues 317-618) Mutation：K457A, E458A, K460A	Ras-related protein Rab-1B × 1 （Q9H0U4） MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.249
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 317–618	Fragment：GAP domain (UNP residues 317-618) Mutation：K457A, E458A, K460A	Ras-related protein Rab-1B × 1 （Q9H0U4） MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.249
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 317–618	Fragment：GAP domain (UNP residues 317-618) Mutation：K457A, E458A, K460A	Ras-related protein Rab-1B × 1 （Q9H0U4） MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.249
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 317–618	Fragment：GAP domain (UNP residues 317-618) Mutation：K457A, E458A, K460A	Ras-related protein Rab-1B × 1 （Q9H0U4） MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1 M sodium cacodylate, pH 6.4, 0.2 M magnesium chloride, 17% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.249

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4I1O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4I1M Crystal structure of the Legionella pneumophila GAP domain of LepB Deposited 2012-11-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 317–618（302 aa） Fragment：GAP domain (UNP residues 317-618)	Mutation：K457A, E458A, K460A	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bicine, pH 7.5, 0.75 M lithium chloride, 6% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.238
4I1M Crystal structure of the Legionella pneumophila GAP domain of LepB Deposited 2012-11-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 317–618（302 aa） Fragment：GAP domain (UNP residues 317-618)	Mutation：K457A, E458A, K460A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bicine, pH 7.5, 0.75 M lithium chloride, 6% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.238
4I1M Crystal structure of the Legionella pneumophila GAP domain of LepB Deposited 2012-11-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 317–618（302 aa） Fragment：GAP domain (UNP residues 317-618)	Mutation：K457A, E458A, K460A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bicine, pH 7.5, 0.75 M lithium chloride, 6% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.238
4IRU Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3 Deposited 2013-01-15	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 326–623（298 aa） Fragment：LepB GAP domain, catalytic core	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 4 GOL GLYCEROL × 7 K POTASSIUM ION × 5 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.288
4IRU Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3 Deposited 2013-01-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 326–623（298 aa） Fragment：LepB GAP domain, catalytic core	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 8 GOL GLYCEROL × 1 K POTASSIUM ION × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.288
4IRU Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3 Deposited 2013-01-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 326–623（298 aa） Fragment：LepB GAP domain, catalytic core	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.288

2 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5ZSM7_LEGPH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–302； UniProt 317–618 Author chain D； PDBConstruct 1–302； UniProt 317–618 Author chain F； PDBConstruct 1–302； UniProt 317–618 Author chain H； PDBConstruct 1–302； UniProt 317–618

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	4i1o
Deposition date deposition_date	2012-11-21
Structure title title	Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3
Keywords keywords	;GAP, RabGAP, hydrolase activator, Rab1b, lpg2490, GTPase-activating proteins, hydrolysis, Rab1 hydrolase, GTP hydrolase, PROTEIN TRANSPORT-HYDROLASE complex ;; PROTEIN TRANSPORT/HYDROLASE
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	45.31 Å
Radius of gyration Rg (electron density) rg_electron	44.96 Å
Forward intensity I(0) i0	565427000.00
Molecular weight molecular_weight	200590.0 kDa
Excluded volume excluded_volume	252410 Å³
Envelope volume envelope_volume	358180 Å³
Hydration-shell volume shell_volume	66026 Å³
Envelope diameter envelope_diameter	149.9 Å
Shell Rg shell_rg	50.93 Å
Envelope Rg envelope_rg	43.42 Å
Shape Rg shape_rg	44.94 Å
Total Rg total_rg	45.30 Å
Total atoms total_atoms	14224
Residues n_residues	1831
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	144.0 Å
Rg (real space) rg_real	45.13 Å
Rg uncertainty (real space) rg_real_error	1.19 Å
I(0) (real space) i0_real	5.6540e+08
I(0) uncertainty (real space) i0_real_error	1.0630e+07
Rg (reciprocal space) rg_reciprocal	45.31 Å
I(0) (reciprocal space) i0_reciprocal	565500000.0000
Solution quality estimate total_estimate	0.8929
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	65.8 Å
Skewness Skewness skewness	0.097
Kurtosis Kurtosis kurtosis	-0.562
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	46380000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.837

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Ras-related protein Rab-1B
Molecular weight formula_weight	20482.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	14370

GHMPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMGLEVLFQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	LepB
Molecular weight formula_weight	34131.9 kDa
Mutation mutation	K457A, E458A, K460A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

EELYQSILELKPLTLLMTSSTSFSETINQWADILKTTDMEKFSFDSNPINLLELVKQFNLYVDELAITCEANNVWAKERIDSTPNLFALYDNSGGEAIHGHAFVPYYKESIVLRRLFTVDPNTFNLSRFAAFEGPCQLYCAAHADSAWVKIQTLLTLGNGIINTLKIIKQAQAFGIDEAVTENLKALKEQFIAFQLAEADIKESLKAPSFAEPLPNKESEFFYPIDEKALAKMNGYQLATICLEELNSPKPSPLIERILSNKKFWKRINSAFESGVFKGRTDDPAGKIAKIREWHQLLQISG

来源 Source

来源生物 organism	Legionella pneumophila subsp. pneumophila
NCBI Class编号 ncbi_taxonomy_id	272624
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

▼

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4i1oa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d4i1oa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4i1oc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d4i1oc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4i1oe1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d4i1oe2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4i1og1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d4i1og2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (12 domains)

Domain ID domain_id	4i1oA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4i1oB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1700 —

Domain ID domain_id	4i1oB02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	830 —

Domain ID domain_id	4i1oC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4i1oD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1700 —

Domain ID domain_id	4i1oD02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	830 —

Domain ID domain_id	4i1oE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4i1oF01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1700 —

Domain ID domain_id	4i1oF02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	830 —

Domain ID domain_id	4i1oG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4i1oH01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1700 —

Domain ID domain_id	4i1oH02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	830 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	124.410 Å
Unit-cell length b length_b	124.410 Å
Unit-cell length c length_c	147.470 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.701 Å
Low-resolution limit resolution_low	49.157 Å
R factor r_factor	0.2191
R_work r_work	0.2174
R_free r_free	0.2486

fit	/app/data/saxs_computation/i1/4i1o/4i1o.fit
pddf	/app/data/pr_computation/i1/4i1o/4i1o.pr.out
profile	/app/data/saxs_computation/i1/4i1o/4i1o.dat

Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b bound to GDP and BeF3

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

Ras-related protein Rab-1B

State in the Current Structure

Other States of the Same Protein in the Database

LepB

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)