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- PDB-2bc2: METALLO BETA-LACTAMASE II FROM BACILLUS CEREUS 569/H/9 AT PH 6.0,... -

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Basic information

Entry
Database: PDB / ID: 2bc2
TitleMETALLO BETA-LACTAMASE II FROM BACILLUS CEREUS 569/H/9 AT PH 6.0, TRIGONAL CRYSTAL FORM
ComponentsMETALLO BETA-LACTAMASE II
KeywordsHYDROLASE / BETA-LACTAMASE / ANTIBIOTIC / METALLOENZYME
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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 / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / 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 / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / 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 / DIFFERENCE FOURIER / 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 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 30, 2024Group: Structure summary / Category: 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
B: METALLO BETA-LACTAMASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6669
Polymers50,0552
Non-polymers6117
Water11,385632
1
A: METALLO BETA-LACTAMASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3815
Polymers25,0281
Non-polymers3544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: METALLO BETA-LACTAMASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2854
Polymers25,0281
Non-polymers2583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: METALLO BETA-LACTAMASE II
hetero molecules

B: METALLO BETA-LACTAMASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5708
Polymers50,0552
Non-polymers5156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area3000 Å2
ΔGint-179 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.320, 67.320, 177.900
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: (0.092376, 0.291462, 0.952112), (0.311053, -0.916794, 0.250471), (0.945893, 0.27302, -0.17535)
Vector: 19.37, 16.635, -27.931)

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Components

#1: Protein METALLO BETA-LACTAMASE II


Mass: 25027.531 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 2.33 Å3/Da / Density % sol: 39 %
Crystal growpH: 6 / Details: pH 6.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: other
Details: This particular structure is not described in this paper.

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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: 1.7→50 Å / Num. obs: 52908 / % possible obs: 97.7 % / Observed criterion σ(I): 4 / Redundancy: 3.1 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.06 / Net I/σ(I): 11
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.309 / % possible all: 86

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
CCP4data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 1.7→8 Å / Rfactor Rfree error: 0.0036 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Details: NO NCS RESTRAINTS WERE USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4905 5 %THIN SHELLS
Rwork0.2 ---
obs0.2 94013 95.66 %-
Displacement parametersBiso mean: 23.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.214 Å0.21 Å
Luzzati d res low-8 Å
Luzzati sigma a0.235 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 12 521 3879
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.498
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.368
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5341.5
X-RAY DIFFRACTIONx_mcangle_it2.3032
X-RAY DIFFRACTIONx_scbond_it3.0562
X-RAY DIFFRACTIONx_scangle_it4.6812.5
LS refinement shellResolution: 1.7→1.72 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.387 327 10.03 %
Rwork0.352 2275 -
obs--79.79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PAR2.PROTOP2.PRO
X-RAY DIFFRACTION2PARW.STELLATOPW.STELLA
X-RAY DIFFRACTION3TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.276
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.368

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