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- PDB-4g3h: Crystal structure of helicobacter pylori arginase -

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Basic information

Entry
Database: PDB / ID: 4g3h
TitleCrystal structure of helicobacter pylori arginase
ComponentsArginase (RocF)
KeywordsHYDROLASE / arginase / Rossmann Fold / Hydrolytic enzyme / manganous ion binding / Hydrolysis
Function / homology
Function and homology information


arginine catabolic process to ornithine / arginase / arginase activity / manganese ion binding / cytoplasm
Similarity search - Function
Ureohydrolase domain / Arginase / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, J. / Zhang, X. / Li, D. / Hu, Y. / Zou, Q. / Wang, D.
CitationJournal: To be Published
Title: Structure and function studies on Helicobacter pylori arginase
Authors: Zhang, J. / Zhang, X. / Li, D. / Hu, Y. / Zou, Q. / Wang, D.
History
DepositionJul 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Data collection
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginase (RocF)
B: Arginase (RocF)
C: Arginase (RocF)
D: Arginase (RocF)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,64712
Polymers152,2074
Non-polymers4408
Water12,160675
1
A: Arginase (RocF)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1623
Polymers38,0521
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arginase (RocF)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1623
Polymers38,0521
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Arginase (RocF)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1623
Polymers38,0521
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Arginase (RocF)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1623
Polymers38,0521
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.690, 102.240, 148.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Arginase (RocF)


Mass: 38051.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_1399 / Production host: Escherichia coli (E. coli) / References: UniProt: O25949
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 675 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% polyethylene glycol 3350, 100mM Bis-Tris pH 5.5, 1mM MnCl2, 15mM guanidine hydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→34.918 Å / Num. all: 73851 / Num. obs: 66320 / % possible obs: 89.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 %
Reflection shellHighest resolution: 2.2 Å / % possible all: 89.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.9 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.23 7448 RANDOM
Rwork0.218 --
obs0.23 66320 -
all-73768 -
Solvent computationBsol: 74.8104 Å2
Displacement parametersBiso max: 158.78 Å2 / Biso mean: 36.3794 Å2 / Biso min: 7.25 Å2
Baniso -1Baniso -2Baniso -3
1-19.407 Å20 Å20 Å2
2---10.012 Å20 Å2
3----9.395 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.035 Å0.03 Å
Luzzati d res low-34.9 Å
Luzzati sigma a0.5 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9756 0 8 675 10439
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.258
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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