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1zpe

Arginase I covalently modified with butylamine at Q19C

Method: X-RAY DIFFRACTION Dmax: 95.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Arginase 1

Rattus norvegicus

UniProt P07824

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 6–319 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 6–319 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 6–319 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
4 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 6–319 Chain B； UniProt 6–319 Chain C； UniProt 6–319 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

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 1ZPE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D3V CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, AN L-ARGININE ANALOG Deposited 1999-10-01 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）
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
1D3V CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, AN L-ARGININE ANALOG Deposited 1999-10-01 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 1–323（323 aa）
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
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 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）
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification 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 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 mutation/modification 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
1ZPG Arginase I covalently modified with propylamine at Q19C Deposited 2005-05-16 Different mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 39 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 1–314； UniProt 6–319 Author chain B； PDBConstruct 1–314； UniProt 6–319 Author chain C； PDBConstruct 1–314； UniProt 6–319

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

SAXS profile for 1zpe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1zpe
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1zpe
Deposition date deposition_date2005-05-16
Structure title titleArginase I covalently modified with butylamine at Q19C
Keywords keywordschemically modified enzyme, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.82 Å
Radius of gyration Rg (electron density) rg_electron29.98 Å
Forward intensity I(0) i0155027000.00
Molecular weight molecular_weight102000.0 kDa
Excluded volume excluded_volume128940 ų
Envelope volume envelope_volume151970 ų
Hydration-shell volume shell_volume41402 ų
Envelope diameter envelope_diameter95.1 Å
Shell Rg shell_rg37.91 Å
Envelope Rg envelope_rg29.96 Å
Shape Rg shape_rg30.01 Å
Total Rg total_rg30.58 Å
Total atoms total_atoms7179
Residues n_residues939
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax95.6 Å
Rg (real space) rg_real30.70 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real1.5500e+08
I(0) uncertainty (real space) i0_real_error2.2140e+06
Rg (reciprocal space) rg_reciprocal30.76 Å
I(0) (reciprocal space) i0_reciprocal155000000.0000
Solution quality estimate total_estimate0.9092
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.7 Å
Skewness Skewness skewness0.172
Kurtosis Kurtosis kurtosis-0.656
Angular range angular_range— – 0.2550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha70230000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.962
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1zpea1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.1 — Arginase-like amidino hydrolases
Domain ID domain_idd1zpeb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.1 — Arginase-like amidino hydrolases
Domain ID domain_idd1zpec_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.1 — Arginase-like amidino hydrolases

CATH v4.4 (3 domains)

Domain ID domain_id1zpeA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily10 — Ureohydrolase domain
Domain ID domain_id1zpeB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily10 — Ureohydrolase domain
Domain ID domain_id1zpeC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily10 — Ureohydrolase domain
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8. Citations (1)

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9. Files and Curves (10)