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- PDB-5cev: ARGINASE FROM BACILLUS CALDEVELOX, L-LYSINE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 5cev
TitleARGINASE FROM BACILLUS CALDEVELOX, L-LYSINE COMPLEX
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 / LYSINE / : / Arginase
Similarity search - Component
Biological speciesBacillus caldovelox (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 16, 1999Deposition site: NDB / 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: Version format compliance
Revision 2.0Feb 16, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _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_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_asym.entity_id / _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.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.label_asym_id
Revision 3.0Sep 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / struct_site
Item: _atom_site.auth_asym_id / _pdbx_nonpoly_scheme.pdb_strand_id ..._atom_site.auth_asym_id / _pdbx_nonpoly_scheme.pdb_strand_id / _struct_site.details / _struct_site.pdbx_auth_asym_id

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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)196,75430
Polymers194,8576
Non-polymers1,89724
Water6,810378
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)196,75430
Polymers194,8576
Non-polymers1,89724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2
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)196,75430
Polymers194,8576
Non-polymers1,89724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)106.400, 277.000, 138.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
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
Details: EACH MOLECULE HAS AN L-LYSINE MOLECULE BOUND IN ITS ACTIVE SITE (THESE ARE LABELLED R 401 - R 406) AND A GUANIDINE ION AT AN EXTERNAL, INTER-SUBUNIT SITE (LABELLED R 407 - R 412).
Source: (gene. exp.) Bacillus caldovelox (bacteria) / Strain: BACILLUS SPECIES DSM 411 / Description: 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-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical
ChemComp-GAI / GUANIDINE


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


Mass: 18.015 Da / Num. of mol.: 378 / 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: MIXING 2 UL PROTEIN WITH 2 UL RESERVOIR SOLUTION PROTEIN SOLUTION 27 MG/ML PROTEIN, 10 MM MOPS, PH 7.5 RESERVOIR SOLUTION 28% MONOMETHYLPEG 2000, 5 MM MNCL2, 10 MM GUANIDINE HYDROCHLORIDE, ...Details: MIXING 2 UL PROTEIN WITH 2 UL RESERVOIR SOLUTION PROTEIN SOLUTION 27 MG/ML PROTEIN, 10 MM MOPS, PH 7.5 RESERVOIR SOLUTION 28% MONOMETHYLPEG 2000, 5 MM MNCL2, 10 MM GUANIDINE HYDROCHLORIDE, 10 MM L-LYSINE, IN 0.05 M BISTRISPROPANE/HCL, PH 8.5 , VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
128 %mmPEG20001reservoir
210 mMguanidine hydrochloride1reservoir
35 mM1reservoirMnCl2
450 mMBTP/HCl1reservoir
510 mML-lysine1reservoir

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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: Jan 1, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 68127 / % possible obs: 94.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 18
Reflection shellResolution: 2.5→2.7 Å / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 4.8 / % possible all: 72.7
Reflection
*PLUS
Num. measured all: 424670
Reflection shell
*PLUS
% possible obs: 72.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REFINED MODEL FOR THE PH 8.5 NATIVE STRUCTURE: 2CEV

2cev


Resolution: 2.5→8 Å / Isotropic thermal model: INDIVIDUAL ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 -5 %RANDOM
Rwork0.212 ---
obs-63576 94.5 %-
Refine analyzeLuzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13608 0 96 378 14082
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.47
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: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS

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