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- PDB-1bc2: ZN-DEPENDENT METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS -

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Basic information

Entry
Database: PDB / ID: 1bc2
TitleZN-DEPENDENT METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS
ComponentsMETALLO-BETA-LACTAMASE II
KeywordsHYDROLASE / METALLO BETA-LACTAMASE / PENICILLINASE / ANTIBIOTIC RESISTANCE
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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...: / 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 / MIR / Resolution: 1.9 Å
AuthorsFabiane, S.M. / Sutton, B.J.
CitationJournal: 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
DepositionApr 11, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / software / 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.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 / _software.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METALLO-BETA-LACTAMASE II
B: METALLO-BETA-LACTAMASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4458
Polymers49,9912
Non-polymers4546
Water7,206400
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.630, 67.630, 178.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.088469, 0.316692, 0.944394), (0.305181, -0.911133, 0.27695), (0.948176, 0.26371, -0.177256)
Vector: 19.51032, 15.86954, -28.04501)

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Components

#1: Protein METALLO-BETA-LACTAMASE II


Mass: 24995.533 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: STARTING MATERIAL HAS SEVERAL RAGGED N-TERMINI / 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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 41 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5
Details: HANGING DROP METHOD. PROTEIN WAS DISSOLVED IN 10MM TRIS PH7, 1MM ZINC SULPHATE. WELL SOLUTION CONTAINED 100MM TRIS-HCL PH4.5, 75% AMMONIUM SULPHATE. 6UL DROPS WERE MADE WITH 3UL PROTEIN ...Details: HANGING DROP METHOD. PROTEIN WAS DISSOLVED IN 10MM TRIS PH7, 1MM ZINC SULPHATE. WELL SOLUTION CONTAINED 100MM TRIS-HCL PH4.5, 75% AMMONIUM SULPHATE. 6UL DROPS WERE MADE WITH 3UL PROTEIN SOLUTION 50% DILUTED (WATER) WELL SOLUTION., vapor diffusion - hanging drop
PH range: 4.5-7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18-20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mg/mlprotein1drop
20.500 mM1dropZnSO4
310 mMTris-HCl1drop
40.125 %(w/v)sodium azide1drop
510 mMTris-HCl1reservoir
60.125 %(w/v)sodium azide1reservoir
770-75 %(v/v)satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 135 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→60 Å / Num. obs: 37917 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 28.04 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.07
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 6.4 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
SOLOMONphasing
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
TRUNCATEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: GAUSSIAN / Cross valid method: THROUGHOUT / σ(F): 0
Details: LYS 227 IS INVOLVED IN UNUSUAL NON-CRYSTALLOGRAPHIC SYMMETRY INTERACTIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2260 6 %SHELLS
Rwork0.208 ---
obs0.208 36523 97.1 %-
Displacement parametersBiso mean: 31.33 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-8 Å
Luzzati sigma a0.27 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 14 400 3760
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_deg1.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.09
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.238
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.641.5
X-RAY DIFFRACTIONx_mcangle_it3.042
X-RAY DIFFRACTIONx_scbond_it2.612
X-RAY DIFFRACTIONx_scangle_it4.812.5
LS refinement shellResolution: 1.9→1.93 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 113 6.07 %
Rwork0.359 1616 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PAR2.PROTOP2.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.093
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.238

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