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- PDB-5evl: Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase fr... -

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Basic information

Entry
Database: PDB / ID: 5evl
TitleCrystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Chromobacterium violaceum
ComponentsBeta-lactamase
KeywordsHYDROLASE / alpha-beta fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsKim, Y. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of Beta-Lactamase/D-Alanine Carboxypeptidase from Chromobacterium violaceum
Authors: Kim, Y. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Joachimiak, A.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9726
Polymers40,5561
Non-polymers4165
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.604, 59.262, 59.267
Angle α, β, γ (deg.)90.00, 98.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 40555.953 Da / Num. of mol.: 1 / Fragment: UNP residues 26-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: ampC, CV_1310 / Plasmid: pMCSG68 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q7NYG4, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 2.0 M Ammonium Sulfate, 0.1 M Citric Acid:NaOH, pH 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. all: 48204 / Num. obs: 48204 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.11 Å2 / Rsym value: 0.082 / Net I/σ(I): 18.3
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.68 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2104)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→35.909 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1815 2380 4.94 %random
Rwork0.1438 ---
obs0.1457 48177 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.5 Å2
Refinement stepCycle: LAST / Resolution: 1.52→35.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 22 156 2892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063014
X-RAY DIFFRACTIONf_angle_d0.8184113
X-RAY DIFFRACTIONf_dihedral_angle_d18.4171814
X-RAY DIFFRACTIONf_chiral_restr0.048431
X-RAY DIFFRACTIONf_plane_restr0.006552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.54890.28971070.21292602X-RAY DIFFRACTION96
1.5489-1.58260.23241540.17932674X-RAY DIFFRACTION100
1.5826-1.61940.23791520.15992659X-RAY DIFFRACTION100
1.6194-1.65990.20421430.14212702X-RAY DIFFRACTION100
1.6599-1.70480.20381440.12922680X-RAY DIFFRACTION100
1.7048-1.7550.20441340.12752705X-RAY DIFFRACTION100
1.755-1.81160.19791370.12172692X-RAY DIFFRACTION100
1.8116-1.87640.17261330.12122693X-RAY DIFFRACTION100
1.8764-1.95150.17411430.11632702X-RAY DIFFRACTION100
1.9515-2.04030.16911500.10952714X-RAY DIFFRACTION100
2.0403-2.14780.17671240.11522683X-RAY DIFFRACTION100
2.1478-2.28240.16461530.11262720X-RAY DIFFRACTION100
2.2824-2.45860.16691530.12862672X-RAY DIFFRACTION100
2.4586-2.70590.18731330.14062734X-RAY DIFFRACTION100
2.7059-3.09730.2041320.15582717X-RAY DIFFRACTION100
3.0973-3.90150.18251500.14852703X-RAY DIFFRACTION100
3.9015-35.91940.1651380.16982745X-RAY DIFFRACTION98

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