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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 / homologyBeta-lactamase, class-B, conserved site / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Beta-lactamases class B signature 1. / Beta-lactamases class B signature 2. / antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic ...Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Beta-lactamases class B signature 1. / Beta-lactamases class B signature 2. / antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / zinc ion binding / Metallo-beta-lactamase type 2
Function and homology information
Specimen sourceBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / 1.85 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 17, 1998 / Release: Jun 17, 1998
RevisionDateData content typeGroupProviderType
1.0Jun 17, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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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
Polyers50,7752
Non-polymers6988
Water6,071337
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
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-MP 1 21 1

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Components

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


Mass: 25387.666 Da / Num. of mol.: 2 / Mutation: A171T, D208N / Source: (gene. exp.) Bacteroides fragilis (bacteria) / Genus: Bacteroides / Strain: TAL3636 / Gene: CCRA / Variant: CLINICAL ISOLATE / Genus (production host): Escherichia / 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 / Formula: Zn / Zinc
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 195.237 Da / Num. of mol.: 2 / Formula: C6H13NO4S / MES (buffer) / Comment: pH buffer *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Formula: H2O / Water

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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 / Density percent 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
IDConcCommon 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 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Collection date: Feb 5, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.85 Å / D resolution low: 1 Å / Number obs: 29508 / Observed criterion sigma I: 1 / Rmerge I obs: 0.032 / Rsym value: 0.032 / NetI over sigmaI: 42.8 / Redundancy: 2.06 % / Percent possible obs: 91.3
Reflection shellRmerge I obs: 0.074 / Highest resolution: 1.85 Å / Lowest resolution: 1.97 Å / MeanI over sigI obs: 6.7 / Rsym value: 0.074 / Redundancy: 1.47 % / Percent possible all: 73.9
Reflection shell
*PLUS
Number unique obs: 3950 / Percent possible obs: 73.9

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Processing

Software
NameClassification
PHASESphasing
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling
RefineMethod to determine structure: MIR
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.
Sigma F: 1
Displacement parametersB iso mean: 15.8 Å2
Least-squares processR factor R work: 0.151 / Highest resolution: 1.85 Å / Lowest resolution: 1 Å / Number reflection obs: 29267 / Percent reflection obs: 91.3
Refine hist #LASTHighest resolution: 1.85 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 3855 / Nucleic acid: 0 / Ligand: 30 / Solvent: 337 / Total: 4222
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.020
X-RAY DIFFRACTIONp_angle_d0.0350.030
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.040
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9601.0
X-RAY DIFFRACTIONp_mcangle_it1.5341.5
X-RAY DIFFRACTIONp_scbond_it1.4541.0
X-RAY DIFFRACTIONp_scangle_it2.3991.5
X-RAY DIFFRACTIONp_plane_restr0.0170.020
X-RAY DIFFRACTIONp_chiral_restr0.1660.150
X-RAY DIFFRACTIONp_singtor_nbd0.2030.500
X-RAY DIFFRACTIONp_multtor_nbd0.2010.500
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1990.500
X-RAY DIFFRACTIONp_planar_tor2.93.0
X-RAY DIFFRACTIONp_staggered_tor15.520.0
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.020.0
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.151
Refine LS shell
*PLUS
Highest resolution: 1.85 Å / Total number of bins used: 12 / Lowest resolution: 1.93 Å / Number reflection obs: 2722 / R factor obs: 0.188

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