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- PDB-1a7t: METALLO-BETA-LACTAMASE WITH MES -

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Basic information

Entry
Database: PDB / ID: 1a7t
TitleMETALLO-BETA-LACTAMASE WITH MES
ComponentsMETALLO-BETA-LACTAMASE
KeywordsHYDROLASE / HYDROLASE (BETA-LACTAMASE) / METALLO BETA-LACTAMASE / ZINC
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 / : / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / 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 speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.85 Å
AuthorsFitzgerald, P.M.D. / Wu, J.K. / Toney, J.H.
Citation
Journal: Biochemistry / Year: 1998
Title: Unanticipated inhibition of the metallo-beta-lactamase from Bacteroides fragilis by 4-morpholineethanesulfonic acid (MES): a crystallographic study at 1.85-A resolution.
Authors: Fitzgerald, P.M. / Wu, J.K. / Toney, J.H.
#1: Journal: Protein Expr.Purif. / Year: 1997
Title: High-Yield Expression, Purification, and Characterization of Active, Soluble Bacteroides Fragilis Metallo-Beta-Lactamase, Ccra
Authors: Toney, J.H. / Wu, J.K. / Overbye, K.M. / Thompson, C.M. / Pompliano, D.L.
History
DepositionMar 17, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)51,47310
Polymers50,7752
Non-polymers6988
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.270, 66.960, 69.480
Angle α, β, γ (deg.)90.00, 103.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein METALLO-BETA-LACTAMASE / CLASS B BETA-LACTAMASE


Mass: 25387.666 Da / Num. of mol.: 2 / Mutation: A171T, D208N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: TAL3636 / Gene: CCRA / Variant: CLINICAL ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P25910, 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 1.88 Å3/Da / Density % sol: 34.7 %
Crystal growpH: 6.1
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 100 MM POTASSIUM ACETATE, 100 MM MES, PH 6.1
Crystal grow
*PLUS
pH: 6.3 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme11
210 mMsodium cacodylate11
32 mMdithiothreitol11
43 mMsodium azide11
5100 mMMES12
6100 mMpotassium acetate12
718-21 %PEG400012

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 5, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. obs: 29508 / % possible obs: 91.3 % / Observed criterion σ(I): 1 / Redundancy: 2.06 % / Rmerge(I) obs: 0.032 / Rsym value: 0.032 / Net I/σ(I): 42.8
Reflection shellResolution: 1.85→1.97 Å / Redundancy: 1.47 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.074 / % possible all: 73.9
Reflection shell
*PLUS
% possible obs: 73.9 % / Num. unique obs: 3950

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Processing

Software
NameClassification
PHASESphasing
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.85→10 Å / σ(F): 1
Details: INITIAL CYCLES OF REFINEMENT WERE PERFORMED USING PROGRAM X-PLOR. 10% OF THE DATA (RANDOMLY SELECTED) WERE SET ASIDE FOR CALCULATION OF A FREE R-FACTOR. AT THE END OF THE X-PLOR PHASE OF THE ...Details: INITIAL CYCLES OF REFINEMENT WERE PERFORMED USING PROGRAM X-PLOR. 10% OF THE DATA (RANDOMLY SELECTED) WERE SET ASIDE FOR CALCULATION OF A FREE R-FACTOR. AT THE END OF THE X-PLOR PHASE OF THE REFINEMENT, THE WORKING R WAS 0.173 AND R-FREE WAS 0.242.
RfactorNum. reflection% reflection
Rwork0.151 --
obs-29267 91.3 %
Displacement parametersBiso mean: 15.8 Å2
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 30 337 4222
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0350.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.961
X-RAY DIFFRACTIONp_mcangle_it1.5341.5
X-RAY DIFFRACTIONp_scbond_it1.4541
X-RAY DIFFRACTIONp_scangle_it2.3991.5
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.1660.15
X-RAY DIFFRACTIONp_singtor_nbd0.2030.5
X-RAY DIFFRACTIONp_multtor_nbd0.2010.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1990.5
X-RAY DIFFRACTIONp_planar_tor2.93
X-RAY DIFFRACTIONp_staggered_tor15.520
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.93 Å / Total num. of bins used: 12 / Num. reflection obs: 2722 / Rfactor obs: 0.188

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