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- PDB-3e6v: X-ray structure of human arginase I-D183N mutant: the complex with ABH -

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Basic information

Entry
Database: PDB / ID: 3e6v
TitleX-ray structure of human arginase I-D183N mutant: the complex with ABH
ComponentsArginase-1
KeywordsHYDROLASE / amino acid recognition / Mutant / amino group recognition / Alternative splicing / Arginine metabolism / Cytoplasm / Disease mutation / Manganese / Metal-binding / Phosphoprotein / Polymorphism / Urea cycle
Function / homology
Function and homology information


positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / Urea cycle / arginase / arginase activity / : / urea cycle / response to nematode / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan ...positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / Urea cycle / arginase / arginase activity / : / urea cycle / response to nematode / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation / L-arginine catabolic process / negative regulation of T cell proliferation / specific granule lumen / azurophil granule lumen / manganese ion binding / adaptive immune response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Arginase / Ureohydrolase domain / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2(S)-AMINO-6-BORONOHEXANOIC ACID / : / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsDi Costanzo, L. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2009
Title: Probing the specificity determinants of amino acid recognition by arginase.
Authors: Shishova, E.Y. / Di Costanzo, L. / Emig, F.A. / Ash, D.E. / Christianson, D.W.
History
DepositionAug 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginase-1
B: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1628
Polymers69,5582
Non-polymers6046
Water6,233346
1
A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24212
Polymers104,3373
Non-polymers9069
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7960 Å2
ΔGint-44 kcal/mol
Surface area32380 Å2
MethodPISA
2
B: Arginase-1
hetero molecules

B: Arginase-1
hetero molecules

B: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24212
Polymers104,3373
Non-polymers9069
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7930 Å2
ΔGint-49 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.036, 91.036, 69.773
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Arginase-1 / Type I arginase / Liver-type arginase


Mass: 34778.895 Da / Num. of mol.: 2 / Mutation: D183N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Plasmid: Pet11D / Production host: Escherichia coli (E. coli) / References: UniProt: P05089, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ABH / 2(S)-AMINO-6-BORONOHEXANOIC ACID


Mass: 191.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15BNO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.75 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.89 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
Details: Double bounce Si (111) monochromator with sagittal horizontal focussing, Rh-c oated Si mirror for vertical focussing.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 1.72→30 Å / Num. obs: 66499 / % possible obs: 97 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.5
Reflection shellResolution: 1.72→1.82 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / Num. unique all: 6672 / % possible all: 96.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZAV

1zav


Resolution: 1.72→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: THE DATA DIFFRACTION IS AFFECTED BY PERFECT TWINNING. TWIN FRACTION: 0.5; OPERATOR: -H, -K, L THE STRUCTURE FACTOR FILE CONTAINS THE UNTWINNED STRUCTURE FACTORS THAT THE DEPOSITORS USED FOR ...Details: THE DATA DIFFRACTION IS AFFECTED BY PERFECT TWINNING. TWIN FRACTION: 0.5; OPERATOR: -H, -K, L THE STRUCTURE FACTOR FILE CONTAINS THE UNTWINNED STRUCTURE FACTORS THAT THE DEPOSITORS USED FOR THE REFINEMENT PROCESS
RfactorNum. reflectionSelection details
Rfree0.232 2597 RANDOM
Rwork0.219 --
obs-58910 -
Refinement stepCycle: LAST / Resolution: 1.72→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 0 30 346 5154
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_deg22.9
LS refinement shellResolution: 1.72→1.82 Å / Rfactor Rfree: 0.324 / Rfactor Rwork: 0.287

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