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- PDB-2gmn: Crystal structure of BJP-1, a subclass B3 metallo-beta-lactamase ... -

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Basic information

Entry
Database: PDB / ID: 2gmn
TitleCrystal structure of BJP-1, a subclass B3 metallo-beta-lactamase of Bradyrhizobium japonicum
ComponentsMetallo-beta-lactamase
KeywordsHYDROLASE / metallo-beta-lactamase
Function / homology
Function and homology information


: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsCalderone, V. / Benvenuti, M. / Stoczko, M. / Docquier, J.D. / Rossolini, G.M. / Mangani, S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2006
Title: Postgenomic scan of metallo-beta-lactamase homologues in rhizobacteria: identification and characterization of BJP-1, a subclass B3 ortholog from Bradyrhizobium japonicum.
Authors: Stoczko, M. / Frere, J.M. / Rossolini, G.M. / Docquier, J.D.
History
DepositionApr 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase
B: Metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2678
Polymers59,8752
Non-polymers3926
Water12,845713
1
A: Metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1344
Polymers29,9371
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1344
Polymers29,9371
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.501, 44.773, 76.966
Angle α, β, γ (deg.)78.92, 89.51, 61.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Metallo-beta-lactamase


Mass: 29937.283 Da / Num. of mol.: 2 / Fragment: residues 21-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 110 / Production host: Escherichia coli (E. coli)
References: GenBank: 27381341, UniProt: Q89GW5*PLUS, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris, 0.4M Na acetate, 40% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.281302 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2005
RadiationMonochromator: Si(311) and Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.281302 Å / Relative weight: 1
ReflectionResolution: 1.4→38.576 Å / Num. obs: 87661 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.4→1.48 Å / % possible all: 77.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
CCP4(SCALA)data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→38.58 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.319 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21322 8006 9.1 %RANDOM
Rwork0.17633 ---
all0.1797 79603 --
obs0.1797 79603 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.071 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.05 Å2-0.09 Å2
2--0.27 Å20.05 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 6 713 4757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224124
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9735586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.415526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94625.119168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72515712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5951514
X-RAY DIFFRACTIONr_chiral_restr0.0730.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023082
X-RAY DIFFRACTIONr_nbd_refined0.1870.22006
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22862
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2578
X-RAY DIFFRACTIONr_metal_ion_refined0.0460.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.241
X-RAY DIFFRACTIONr_mcbond_it0.8231.52680
X-RAY DIFFRACTIONr_mcangle_it1.27424206
X-RAY DIFFRACTIONr_scbond_it1.8231611
X-RAY DIFFRACTIONr_scangle_it2.6814.51380
X-RAY DIFFRACTIONr_rigid_bond_restr1.07334291
X-RAY DIFFRACTIONr_sphericity_free2.9723719
X-RAY DIFFRACTIONr_sphericity_bonded2.91234038
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 434 -
Rwork0.275 4238 -
obs--100 %

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