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- PDB-3bc2: METALLO BETA-LACTAMASE II FROM BACILLUS CEREUS 569/H/9 AT PH 6.0,... -

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Basic information

Entry
Database: PDB / ID: 3bc2
TitleMETALLO BETA-LACTAMASE II FROM BACILLUS CEREUS 569/H/9 AT PH 6.0, MONOCLINIC CRYSTAL FORM
ComponentsMETALLO BETA-LACTAMASE II
KeywordsHYDROLASE / BETA-LACTAMASE / ANTIBIOTIC / METALLOENZYME
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase ...: / Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / 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
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFabiane, S.M. / Sutton, B.J.
Citation
#1: Journal: Biochemistry / Year: 1998
Title: Crystal Structure of the Zinc-Dependent Beta-Lactamase from Bacillus Cereus at 1.9 A Resolution: Binuclear Active Site with Features of a Mononuclear Enzyme
Authors: Fabiane, S.M. / Sohi, M.K. / Wan, T. / Payne, D.J. / Bateson, J.H. / Mitchell, T. / Sutton, B.J.
History
DepositionSep 9, 1997Processing site: BNL
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METALLO BETA-LACTAMASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0932
Polymers25,0281
Non-polymers651
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.440, 61.600, 69.830
Angle α, β, γ (deg.)90.00, 93.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein METALLO BETA-LACTAMASE II


Mass: 25027.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus cereus (bacteria) / Strain: 569/H/9 / References: UniProt: P04190, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUES 1 - 4 WERE NOT PRESENT IN CRYSTALLISATION MATERIAL, AS DETERMINED BY MASS SPECTROSCOPY.
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: 2.29 Å3/Da / Density % sol: 39 %
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Aug 1, 1996 / Details: MIRROR
RadiationMonochromator: PAIR OF SINGLE FLAT CRYSTALS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→40.3 Å / Num. obs: 30934 / % possible obs: 96.4 % / Observed criterion σ(I): 5 / Redundancy: 2.4 % / Biso Wilson estimate: 17.9 Å2 / Rsym value: 0.073 / Net I/σ(I): 5.14
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.282 / % possible all: 94.5

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY FOR 1BC2

1bc2


Resolution: 1.7→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
Details: DISORDERED REGIONS WERE NOT MODELLED. THEY ARE RESIDUES 5, 6, AND 32 - 38 IN BOTH NCS-RELATED MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1274 5 %RANDOM
Rwork0.227 ---
obs0.227 25508 73.724 %-
Displacement parametersBiso mean: 25.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.271 Å0.25 Å
Luzzati d res low-8 Å
Luzzati sigma a0.254 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 1 221 1879
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.394
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.33
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.288
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.3941.5
X-RAY DIFFRACTIONx_mcangle_it3.5262
X-RAY DIFFRACTIONx_scbond_it3.5062
X-RAY DIFFRACTIONx_scangle_it4.9942.5
LS refinement shellResolution: 1.9→1.92 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.258 32 2.8 %
Rwork0.304 598 -
obs--55 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PAR2.PROTOP2.PRO
X-RAY DIFFRACTION2PARW.STELLATOPW.STELLA
X-RAY DIFFRACTION3TOPH19.PEP

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