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- PDB-2cev: ARGINASE FROM BACILLUS CALDEVELOX, NATIVE STRUCTURE AT PH 8.5 -

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Basic information

Entry
Database: PDB / ID: 2cev
TitleARGINASE FROM BACILLUS CALDEVELOX, NATIVE STRUCTURE AT PH 8.5
ComponentsPROTEIN (ARGINASE)
KeywordsHYDROLASE / ENZYME / ARGININE HYDROLYSIS / NITROGEN METABOLISM / MANGANESE METALLOENZYME
Function / homology
Function and homology information


arginase / arginase activity / : / urea cycle / manganese ion binding / 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
GUANIDINE / : / Arginase
Similarity search - Component
Biological speciesBacillus caldovelox (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBewley, M.C. / Jeffrey, P.D. / Patchett, M.L. / Kanyo, Z.F. / Baker, E.N.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structures of Bacillus caldovelox arginase in complex with substrate and inhibitors reveal new insights into activation, inhibition and catalysis in the arginase superfamily.
Authors: Bewley, M.C. / Jeffrey, P.D. / Patchett, M.L. / Kanyo, Z.F. / Baker, E.N.
History
DepositionMar 10, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 16, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: 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_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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ARGINASE)
B: PROTEIN (ARGINASE)
C: PROTEIN (ARGINASE)
D: PROTEIN (ARGINASE)
E: PROTEIN (ARGINASE)
F: PROTEIN (ARGINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,87124
Polymers194,8576
Non-polymers1,01418
Water12,052669
1
A: PROTEIN (ARGINASE)
B: PROTEIN (ARGINASE)
C: PROTEIN (ARGINASE)
hetero molecules

A: PROTEIN (ARGINASE)
B: PROTEIN (ARGINASE)
C: PROTEIN (ARGINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,87124
Polymers194,8576
Non-polymers1,01418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area15190 Å2
ΔGint-101 kcal/mol
Surface area59060 Å2
MethodPISA, PQS
2
D: PROTEIN (ARGINASE)
E: PROTEIN (ARGINASE)
F: PROTEIN (ARGINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,93612
Polymers97,4293
Non-polymers5079
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15090 Å2
ΔGint-104 kcal/mol
Surface area58830 Å2
MethodPISA
3
D: PROTEIN (ARGINASE)
E: PROTEIN (ARGINASE)
F: PROTEIN (ARGINASE)
hetero molecules

D: PROTEIN (ARGINASE)
E: PROTEIN (ARGINASE)
F: PROTEIN (ARGINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,87124
Polymers194,8576
Non-polymers1,01418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)106.220, 275.580, 138.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein
PROTEIN (ARGINASE)


Mass: 32476.248 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus caldovelox (bacteria) / Strain: BACILLUS SPECIES DSM 411 / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P53608, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH5N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: HANGING DROP VAPOUR DIFFUSION, MIXING 2 UL PROTEIN WITH 2 UL RESERVOIR SOLUTION. PROTEIN SOLUTION 27 MG/ML PROTEIN, 10 MM MOPS,PH 7.5. RESERVOIR SOLUTION 27-30% MONOMETHYLPEG 5000, 10 MM ...Details: HANGING DROP VAPOUR DIFFUSION, MIXING 2 UL PROTEIN WITH 2 UL RESERVOIR SOLUTION. PROTEIN SOLUTION 27 MG/ML PROTEIN, 10 MM MOPS,PH 7.5. RESERVOIR SOLUTION 27-30% MONOMETHYLPEG 5000, 10 MM MNCL2, 10 MM GUANIDINE HYDROCHLORIDE, IN 0.1 M BISTRISPROPANE/HCL, PH 8.5., VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
127.3 mg/mlprotein1drop
210 mMMOPS1drop
327-30 %mPEG50001reservoir
410 mM1reservoirMnCl2
510 mMguanidine hydrochloride1reservoir
60.1 MBis-Tris propane/HCl1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 15, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 93307 / % possible obs: 87.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.4
Reflection shellResolution: 2.15→2.3 Å / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 3.1 / % possible all: 63.2
Reflection
*PLUS
Num. measured all: 436708
Reflection shell
*PLUS
% possible obs: 63.2 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LOW RESOLUTION STRUCTURE OF A DIFFERENT CRYSTAL FORM

Resolution: 2.15→6 Å / Isotropic thermal model: INDIVIDUAL ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 -5 %RANDOM
Rwork0.195 ---
all-87695 --
obs-87695 87.9 %-
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.15→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13608 0 36 669 14313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.42
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

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