1d3v

CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, AN L-ARGININE ANALOG

Method: X-RAY DIFFRACTION D_max: 117.6 Å Quality: REASONABLE

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

PROTEIN (ARGINASE)

Rattus norvegicus

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–323	Not recorded	MN MANGANESE (II) ION × 6 ABH 2(S)-AMINO-6-BORONOHEXANOIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.1；pH 8.10	Resolution 1.70 Å R-free 0.179
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–323	Not recorded	MN MANGANESE (II) ION × 6 ABH 2(S)-AMINO-6-BORONOHEXANOIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.1；pH 8.10	Resolution 1.70 Å R-free 0.179

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 1D3V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HQ5 CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH S-(2-BORONOETHYL)-L-CYSTEINE, AN L-ARGININE ANALOGUE Deposited 2000-12-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa）	Not recorded	MN MANGANESE (II) ION × 6 S2C S-2-(BORONOETHYL)-L-CYSTEINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 1500, BICINE, manganese chloride, 2-(boronoethyl)-L-cysteine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.194
1HQ5 CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH S-(2-BORONOETHYL)-L-CYSTEINE, AN L-ARGININE ANALOGUE Deposited 2000-12-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 1–323（323 aa）	Not recorded	MN MANGANESE (II) ION × 6 S2C S-2-(BORONOETHYL)-L-CYSTEINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 1500, BICINE, manganese chloride, 2-(boronoethyl)-L-cysteine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.194
1HQF CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH N-HYDROXY-L-ARGININE Deposited 2000-12-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Not recorded	MN MANGANESE (II) ION × 6 HAR N-OMEGA-HYDROXY-L-ARGININE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, BICINE, manganese chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.289
1HQG CRYSTAL STRUCTURE OF THE H141C ARGINASE VARIANT COMPLEXED WITH PRODUCTS ORNITHINE AND UREA Deposited 2000-12-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Mutation：H141C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H141C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：H141C Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 6 ORN L-ornithine × 3 URE UREA × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, BICINE, manganese chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.232
1HQH CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH NOR-N-HYDROXY-L-ARGININE Deposited 2000-12-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Not recorded	MN MANGANESE (II) ION × 6 NNH NOR-N-OMEGA-HYDROXY-L-ARGININE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, BICINE, manganese chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.259
1HQX R308K ARGINASE VARIANT Deposited 2000-12-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Mutation：R308K Mutation：R308K Mutation：R308K	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, BICINE, manganese chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.296
1P8M Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. Deposited 2003-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–314（314 aa） Fragment：Arginase I Chain B 1–314（314 aa） Fragment：Arginase I Chain C 1–314（314 aa） Fragment：Arginase I	Mutation：D128E Mutation：D128E Mutation：D128E	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, Bicine, Manganese Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.84 Å R-free 0.298
1P8N Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. Deposited 2003-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Fragment：Arginase I Chain B 6–319（314 aa） Fragment：Arginase I Chain C 6–319（314 aa） Fragment：Arginase I	Mutation：D232A Mutation：D232A Mutation：D232A	MN MANGANESE (II) ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, Bicine, Manganese Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.305
1P8O Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. Deposited 2003-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Fragment：Arginase I Chain B 6–319（314 aa） Fragment：Arginase I Chain C 6–319（314 aa） Fragment：Arginase I	Mutation：D128N Mutation：D128N Mutation：D128N	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, Bicine, Manganese Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.96 Å R-free 0.297
1P8P Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. Deposited 2003-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Fragment：Arginase I Chain B 6–319（314 aa） Fragment：Arginase I Chain C 6–319（314 aa） Fragment：Arginase I	Mutation：H101N Mutation：H101N Mutation：H101N	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；PEG 8000, Bicine, Manganese Chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.263
1P8Q Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Cluster of Arginase I. Deposited 2003-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Fragment：Arginase I Chain B 6–319（314 aa） Fragment：Arginase I Chain C 6–319（314 aa） Fragment：Arginase I	Mutation：D234E Mutation：D234E Mutation：D234E	MN MANGANESE (II) ION × 6 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, Bicine, Manganese Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.95 Å R-free 0.287
1P8R Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. Deposited 2003-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–313（308 aa） Fragment：Arginase I	Mutation：H101E	CL CHLORIDE ION × 6 MN MANGANESE (II) ION × 6 S2C S-2-(BORONOETHYL)-L-CYSTEINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；HEPES-NaOH, isopropanol, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.201
1P8R Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. Deposited 2003-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 6–313（308 aa） Fragment：Arginase I	Mutation：H101E	CL CHLORIDE ION × 6 MN MANGANESE (II) ION × 6 S2C S-2-(BORONOETHYL)-L-CYSTEINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；HEPES-NaOH, isopropanol, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.201
1P8S Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. Deposited 2003-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Fragment：Arginase I Chain B 6–319（314 aa） Fragment：Arginase I Chain C 6–319（314 aa） Fragment：Arginase I	Mutation：D232C Mutation：D232C Mutation：D232C	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, Bicine, Manganese Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.20 Å R-free 0.315
1R1O Amino Acid Sulfonamides as Transition-State Analogue Inhibitors of Arginase Deposited 2003-09-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Not recorded	MN MANGANESE (II) ION × 6 SDC S-[2-(AMINOSULFONYL)ETHYL]-D-CYSTEINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, bicine, manganese chloride, SDC, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.290
1RLA THREE-DIMENSIONAL STRUCTURE OF RAT LIVER ARGINASE, THE BINUCLEAR MANGANESE METALLOENZYME OF THE UREA CYCLE Deposited 1996-08-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Not recorded	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.229
1T4P Arginase-dehydro-ABH complex Deposited 2004-04-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Chain B 6–319（314 aa） Chain C 6–319（314 aa）	Not recorded	MN MANGANESE (II) ION × 6 2BH [(1E,5S)-5-AMINO-5-CARBOXYPENT-1-ENYL](TRIHYDROXY)BORATE(1-) × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；278 K；bicine, PEG8000, MnCl2, dehydro-ABH, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.60 Å R-free 0.292
1T4R arginase-descarboxy-nor-NOHA complex Deposited 2004-04-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Chain B 6–319（314 aa） Chain C 6–319（314 aa）	Not recorded	MN MANGANESE (II) ION × 6 AHI 3-{[(E)-AMINO(HYDROXYIMINO)METHYL]AMINO}PROPAN-1-AMINIUM × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；bicine, PEG8000, MnCl2, descarboxy-nor-NOHA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.291
1T4S arginase-L-valine complex Deposited 2004-04-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Chain B 6–319（314 aa） Chain C 6–319（314 aa）	Not recorded	MN MANGANESE (II) ION × 6 VAL VALINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；bicine, PEG8000, L-valine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.292
1T4T arginase-dinor-NOHA complex Deposited 2004-04-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Chain B 6–319（314 aa） Chain C 6–319（314 aa）	Not recorded	MN MANGANESE (II) ION × 6 DIR 3-{[(E)-AMINO(HYDROXYIMINO)METHYL]AMINO}ALANINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；bicine, PEG8000, dinor-NOHA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.281
1T5F arginase I-AOH complex Deposited 2004-05-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Chain B 6–319（314 aa） Chain C 6–319（314 aa）	Not recorded	MN MANGANESE (II) ION × 6 DHH (S)-2-AMINO-7,7-DIHYDROXYHEPTANOIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；bicine, PEG8000, AOH, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.241
1T5G Arginase-F2-L-Arginine complex Deposited 2004-05-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Chain B 6–319（314 aa） Chain C 6–319（314 aa）	Not recorded	F FLUORIDE ION × 6 MN MANGANESE (II) ION × 6 ARG ARGININE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；bicine, PEG8000, L-arginine, NaF, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.254
1TA1 H141C mutant of rat liver arginase I Deposited 2004-05-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Chain B 6–319（314 aa） Chain C 6–319（314 aa）	Mutation：H141C Mutation：H141C Mutation：H141C	MN MANGANESE (II) ION × 6 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；bicine, PEG8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.248
1TBH H141D mutant of rat liver arginase I Deposited 2004-05-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Chain B 6–319（314 aa） Chain C 6–319（314 aa）	Mutation：H141D Mutation：H141D Mutation：H141D	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；bicine, PEG8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.296
1TBJ H141A mutant of rat liver arginase I Deposited 2004-05-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Chain B 6–319（314 aa） Chain C 6–319（314 aa）	Mutation：H141A Mutation：H141A Mutation：H141A	MN MANGANESE (II) ION × 6 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；bicine, PEG8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.299
1TBL H141N mutant of rat liver arginase I Deposited 2004-05-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Chain B 6–319（314 aa） Chain C 6–319（314 aa）	Mutation：H141N Mutation：H141N Mutation：H141N	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；bicine, PEG8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.306
1ZPE Arginase I covalently modified with butylamine at Q19C Deposited 2005-05-16	Different construct Different mutation/modification 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 6–319（314 aa）	Mutation：C119A, C168A, C303A, H141A, Q19(BBC) Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；277 K；Bicine, PEG 8000, MnCl2, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.233
1ZPE Arginase I covalently modified with butylamine at Q19C Deposited 2005-05-16	Different construct Different mutation/modification 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 6–319（314 aa）	Mutation：C119A, C168A, C303A, H141A, Q19(BBC) Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；277 K；Bicine, PEG 8000, MnCl2, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.233
1ZPE Arginase I covalently modified with butylamine at Q19C Deposited 2005-05-16	Different construct Different mutation/modification 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 6–319（314 aa）	Mutation：C119A, C168A, C303A, H141A, Q19(BBC) Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；277 K；Bicine, PEG 8000, MnCl2, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.233
1ZPE Arginase I covalently modified with butylamine at Q19C Deposited 2005-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Chain B 6–319（314 aa） Chain C 6–319（314 aa）	Mutation：C119A, C168A, C303A, H141A, Q19(BBC) Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C119A, C168A, C303A, H141A, Q19(BBC) Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C119A, C168A, C303A, H141A, Q19(BBC) Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；277 K；Bicine, PEG 8000, MnCl2, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.233
1ZPG Arginase I covalently modified with propylamine at Q19C Deposited 2005-05-16	Different construct Different mutation/modification 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 6–319（314 aa）	Mutation：C119A, C168A, C303A, H141A, Q19C Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；277 K；Bicine, PEG 8000, MnCl2, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.220
1ZPG Arginase I covalently modified with propylamine at Q19C Deposited 2005-05-16	Different construct Different mutation/modification 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 6–319（314 aa）	Mutation：C119A, C168A, C303A, H141A, Q19C Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；277 K；Bicine, PEG 8000, MnCl2, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.220
1ZPG Arginase I covalently modified with propylamine at Q19C Deposited 2005-05-16	Different construct Different mutation/modification 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 6–319（314 aa）	Mutation：C119A, C168A, C303A, H141A, Q19C Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；277 K；Bicine, PEG 8000, MnCl2, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.220
1ZPG Arginase I covalently modified with propylamine at Q19C Deposited 2005-05-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 6–319（314 aa） Chain B 6–319（314 aa） Chain C 6–319（314 aa）	Mutation：C119A, C168A, C303A, H141A, Q19C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C119A, C168A, C303A, H141A, Q19C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C119A, C168A, C303A, H141A, Q19C Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；277 K；Bicine, PEG 8000, MnCl2, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.220
2RLA ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES THERMOSTABILITY AND CATALYTIC FUNCTION Deposited 1997-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Not recorded	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；12 - 18% PEG 8000, 50 MM BICINE PH = 8.5, 0.05% AZIDE, 1 MM MNCL2 SOAKED FOR 1 WEEK WITH 20 MM EDTA + DPA	Resolution 3.00 Å R-free 0.299
3E8Q X-ray structure of rat arginase I-T135A: the unliganded complex Deposited 2008-08-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Mutation：T135A Mutation：T135A Mutation：T135A	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；drops containing 3 microL of protein solution [5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM BEC, 2 mM MnCl2] and 3 microL of precipitant solution [0.1 M CHES (pH 9.5), 20% PEG 3350, 0.2 M NaCl] were equilibrated over a 1 mL reservoir of precipitant solution, VAPOR DIFFUSION, HANGING DROP	Resolution 2.90 Å R-free 0.296
3E8Z X-ray structure of rat arginase I-N130A mutant: the unliganded complex Deposited 2008-08-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Mutation：N130A Mutation：N130A Mutation：N130A	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；drops containing 3 microL of protein solution [5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM BEC, 2 mM MnCl2] and 3 microL of precipitant solution [0.1 M CHES (pH 9.5), 20% PEG 3350, 0.2 M NaCl] were equilibrated over a 1 mL reservoir of precipitant solution., VAPOR DIFFUSION, HANGING DROP	Resolution 2.00 Å R-free 0.280
3E9B X-ray structure of rat arginase I-T135A mutant: the complex with BEC Deposited 2008-08-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Mutation：T135A Mutation：T135A Mutation：T135A	MN MANGANESE (II) ION × 6 S2C S-2-(BORONOETHYL)-L-CYSTEINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；drops containing 3 microL of protein solution [5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM BEC, 2 mM MnCl2] and 3 microL of precipitant solution [0.1 M CHES (pH 9.5), 20% PEG 8000] were equilibrated over a 1 mL reservoir of precipitant solution. , VAPOR DIFFUSION, HANGING DROP	Resolution 2.15 Å R-free 0.274
3RLA ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES THERMOSTABILITY AND CATALYTIC FUNCTION Deposited 1997-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Mutation：H101N Mutation：H101N Mutation：H101N	MN MANGANESE (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；12 - 18% PEG 8000, 50 MM BICINE PH = 8.5, 0.05% AZIDE, 1 MM MNCL2	Resolution 2.54 Å R-free 0.282
4RLA ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES THERMOSTABILITY AND CATALYTIC FUNCTION Deposited 1997-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Mutation：H101N Mutation：H101N Mutation：H101N	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；12 - 18% PEG 8000, 50 MM BICINE PH = 8.5, 0.05% AZIDE, 1 MM MNCL2 SOAKED FOR 1 WEEK IN 15MM EDTA + DPA	Resolution 2.94 Å R-free 0.246
5RLA ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES THERMOSTABILITY AND CATALYTIC FUNCTION Deposited 1997-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–323（323 aa） Chain B 1–323（323 aa） Chain C 1–323（323 aa）	Mutation：H101N Mutation：H101N Mutation：H101N	MN MANGANESE (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；12 - 18% PEG 8000, 50 MM BICINE PH = 8.5, 0.05% AZIDE, 1 MM MNCL2 SOAKED FOR 1 WEEK IN 15MM EDTA + DPA	Resolution 2.74 Å R-free 0.270

33 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARGI1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–323； UniProt 1–323 Author chain B； PDBConstruct 1–323； UniProt 1–323

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	1d3v
Deposition date deposition_date	1999-10-01
Structure title title	CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, AN L-ARGININE ANALOG
Keywords keywords	BINUCLEAR MANGANESE CLUSTER, BORONIC ACID INHIBITOR, PERFECTLY TWINNED CRYSTAL, HYDROLASE; 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	38.28 Å
Radius of gyration Rg (electron density) rg_electron	38.23 Å
Forward intensity I(0) i0	64683300.00
Molecular weight molecular_weight	67112.0 kDa
Excluded volume excluded_volume	84709 Å³
Envelope volume envelope_volume	112000 Å³
Hydration-shell volume shell_volume	23820 Å³
Envelope diameter envelope_diameter	117.2 Å
Shell Rg shell_rg	45.68 Å
Envelope Rg envelope_rg	37.09 Å
Shape Rg shape_rg	38.23 Å
Total Rg total_rg	38.65 Å
Total atoms total_atoms	4718
Residues n_residues	616
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	117.6 Å
Rg (real space) rg_real	38.69 Å
Rg uncertainty (real space) rg_real_error	1.26 Å
I(0) (real space) i0_real	6.4680e+07
I(0) uncertainty (real space) i0_real_error	1.2040e+06
Rg (reciprocal space) rg_reciprocal	38.45 Å
I(0) (reciprocal space) i0_reciprocal	64670000.0000
Solution quality estimate total_estimate	0.5955
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.222
Kurtosis Kurtosis kurtosis	-1.274
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	56510000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.041; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.248; Smooth: 0.367

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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 (ARGINASE)
Molecular weight formula_weight	35019.1 kDa
EC 编号 ec_number	3.5.3.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5015

MSSKPKPIEIIGAPFSKGQPRGGVEKGPAALRKAGLVEKLKETEYNVRDHGDLAFVDVPNDSPFQIVKNPRSVGKANEQLAAVVAETQKNGTISVVLGGDHSMAIGSISGHARVHPDLCVIWVDAHTDINTPLTTSSGNLHGQPVAFLLKELKGKFPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYIIKTLGIKYFSMTEVDKLGIGKVMEETFSYLLGRKKRPIHLSFDVDGLDPVFTPATGTPVVGGLSYREGLYITEEIYKTGLLSGLDIMEVNPTLGKTPEEVTRTVNTAVALTLSCFGTKREGNHKPETDYLKPPK

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	2(S)-AMINO-6-BORONOHEXANOIC ACID
Molecular weight formula_weight	192.0 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	297

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d3va_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.42 — Arginase/deacetylase
Superfamily Superfamily superfamily	c.42.1 — Arginase/deacetylase
Family Family family	c.42.1.1 — Arginase-like amidino hydrolases

Domain ID domain_id	d1d3vb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.42 — Arginase/deacetylase
Superfamily Superfamily superfamily	c.42.1 — Arginase/deacetylase
Family Family family	c.42.1.1 — Arginase-like amidino hydrolases

CATH v4.4 (2 domains)

Domain ID domain_id	1d3vA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	10 — Ureohydrolase domain

Domain ID domain_id	1d3vB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	10 — Ureohydrolase domain

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8. Citations (1)

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Unit-cell length a length_a	91.300 Å
Unit-cell length b length_b	91.300 Å
Unit-cell length c length_c	69.900 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	6

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1570
R_work r_work	0.1570
R_free r_free	0.1790

fit	/app/data/saxs_computation/d3/1d3v/1d3v.fit
pddf	/app/data/pr_computation/d3/1d3v/1d3v.pr.out
profile	/app/data/saxs_computation/d3/1d3v/1d3v.dat