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- PDB-4gku: Crystal structure of beta lactamase in PET-15B -

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Basic information

Entry
Database: PDB / ID: 4gku
TitleCrystal structure of beta lactamase in PET-15B
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / beta lactamase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.915 Å
AuthorsZhang, Y. / Cao, C.
CitationJournal: To be published
Title: Crystal structure of beta lactamase in PET-15B
Authors: Zhang, Y. / Cao, C.
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9421
Polymers28,9421
Non-polymers00
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.009, 72.817, 74.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase TEM / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2


Mass: 28941.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M magnesium chloride, 0.1M BIS-Tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.2605 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2605 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 37743 / Num. obs: 37743 / % possible obs: 98.1 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 100.8 / Redundancy: 13.1 %
Reflection shellResolution: 1.91→1.98 Å / % possible all: 89.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.915→34.917 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 17.83 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 3600 9.79 %RANDOM
Rwork0.1631 ---
obs0.1664 36758 96.33 %-
all-37743 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9168 Å2-0 Å2-0 Å2
2---1.1581 Å20 Å2
3----1.7588 Å2
Refinement stepCycle: LAST / Resolution: 1.915→34.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 0 315 2341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072061
X-RAY DIFFRACTIONf_angle_d1.0162790
X-RAY DIFFRACTIONf_dihedral_angle_d13.739775
X-RAY DIFFRACTIONf_chiral_restr0.069321
X-RAY DIFFRACTIONf_plane_restr0.004363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9147-1.98310.29142950.2222301787
1.9831-2.06250.20173690.1696323695
2.0625-2.15640.20363510.1521333296
2.1564-2.270.16463730.1414333697
2.27-2.41220.20843480.1549329197
2.4122-2.59840.19043930.1608334897
2.5984-2.85980.19883700.1578334698
2.8598-3.27330.21573620.1728339598
3.2733-4.1230.17373700.15383429100
4.123-34.92270.19753690.17133428100

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