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- PDB-6wjm: The crystal structure beta-lactamase from Desulfarculus baarsii D... -

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Basic information

Entry
Database: PDB / ID: 6wjm
TitleThe crystal structure beta-lactamase from Desulfarculus baarsii DSM 2075
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / structural genomic / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
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 enzyme family / Beta-lactamase, class-A / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
ALANINE / CITRIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesDesulfarculus baarsii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsChang, C. / Welk, L. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: The crystal structure beta-lactamase from Desulfarculus baarsii DSM 2075
Authors: Chang, C. / Welk, L. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2884
Polymers30,8141
Non-polymers4733
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.722, 73.460, 42.923
Angle α, β, γ (deg.)90.000, 110.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 30814.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14) (bacteria)
Strain: ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14 / Gene: Deba_2488 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E1QJV5, beta-lactamase
#2: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1M Sodium citrate, 20% 2-propanol, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 109222 / % possible obs: 88 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.027 / Rrim(I) all: 0.067 / Χ2: 0.924 / Net I/σ(I): 13.4 / Num. measured all: 589969
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1-1.023.40.25829770.9060.1490.31.74448.3
1.02-1.043.80.21138210.9450.1150.2421.40662.3
1.04-1.064.20.17651250.970.090.1991.11482.5
1.06-1.084.40.15755020.9770.0790.1771.11688.4
1.08-1.14.50.14455150.9780.0720.1621.09289.3
1.1-1.134.60.1355570.9840.0650.1461.05189.4
1.13-1.154.70.12353470.9840.060.1381.00987.2
1.15-1.195.10.11456560.9870.0550.1270.94491.2
1.19-1.225.10.10756480.9870.0520.120.91891.6
1.22-1.265.10.10556810.9870.050.1170.87791.6
1.26-1.35.10.154830.9870.0480.1120.80988.1
1.3-1.365.60.10557440.9890.0480.1160.79793.1
1.36-1.425.80.10858230.9880.0490.1190.77393.7
1.42-1.495.90.11358210.990.050.1240.76294.1
1.49-1.5960.10856370.9890.0480.1190.79690.2
1.59-1.716.60.09359610.9930.0390.1010.80196.2
1.71-1.886.60.07460050.9940.0310.0810.85196.5
1.88-2.156.20.05957910.9950.0260.0650.93593.4
2.15-2.716.70.04960920.9960.020.0530.92197.3
2.71-506.50.04460360.9960.0190.0480.93695.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SBC-Collectdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3w4q

3w4q


Resolution: 1→27.13 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1406 5126 5.02 %
Rwork0.1226 97070 -
obs0.1235 102196 82.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.75 Å2 / Biso mean: 21.6493 Å2 / Biso min: 11.39 Å2
Refinement stepCycle: final / Resolution: 1→27.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 44 355 2356
Biso mean--32.11 37.52 -
Num. residues----269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1-1.010.1281430.135171375618
1.01-1.020.1517590.12441136119529
1.02-1.040.14880.10661486157439
1.04-1.050.13531070.10222120222753
1.05-1.060.12351330.10242543267665
1.06-1.080.11481500.10192844299472
1.08-1.090.1271360.10053103323979
1.09-1.110.1271420.10093235337782
1.11-1.130.10781710.10123382355385
1.13-1.140.12471550.09813201335683
1.14-1.160.11171900.09723603379390
1.16-1.190.11741730.09563532370591
1.19-1.210.10952180.09323536375491
1.21-1.230.12512090.09493608381792
1.23-1.260.10551910.09863562375392
1.26-1.290.11371910.09183432362387
1.29-1.320.11871920.13573376592
1.32-1.360.11861920.10173655384793
1.36-1.40.13042010.10033689389094
1.4-1.440.13132000.10063693389394
1.44-1.490.13052160.09813650386694
1.49-1.550.11091820.09883575375791
1.55-1.620.12792110.10433613382493
1.62-1.710.14011940.11033828402296
1.71-1.820.16551970.12193811400897
1.82-1.960.13632040.12543793399797
1.96-2.150.14991660.12643643380992
2.15-2.470.14731940.13493850404497
2.47-3.110.14922290.1413856408598
3.11-27.130.14371920.12633805399795

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