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- PDB-5ctn: Structure of BPu1 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 5ctn
TitleStructure of BPu1 beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5R7 / CITRATE ANION / Beta-lactamase
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Class D beta-lactamases do exist in Gram-positive bacteria.
Authors: Toth, M. / Antunes, N.T. / Stewart, N.K. / Frase, H. / Bhattacharya, M. / Smith, C.A. / Vakulenko, S.B.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Oct 5, 2016Group: Non-polymer description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6625
Polymers54,6282
Non-polymers1,0343
Water7,548419
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9263
Polymers27,3141
Non-polymers6122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7372
Polymers27,3141
Non-polymers4231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.802, 80.002, 64.949
Angle α, β, γ (deg.)90.000, 92.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase /


Mass: 27314.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: BPUM_2340 / Production host: Escherichia coli (E. coli) / References: UniProt: A8FFI9, beta-lactamase
#2: Chemical ChemComp-5R7 / (2~{S},3~{R})-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid / Doripenem(open form, pyrroline tautomer form 3, SP3 connection to Thio as R isomer)


Mass: 422.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26N4O6S2
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2% Tacsimate, 0.1 M sodium citrate pH 5.6, 16% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→37.6 Å / Num. obs: 104369 / % possible obs: 97.6 % / Redundancy: 4 % / Net I/σ(I): 19.85
Reflection shellResolution: 1.35→1.4 Å / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 2.18 / % possible all: 94.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
MOLREPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→37.568 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1868 5194 4.98 %
Rwork0.1595 99128 -
obs0.1609 104322 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.68 Å2 / Biso mean: 26.2546 Å2 / Biso min: 11.65 Å2
Refinement stepCycle: final / Resolution: 1.35→37.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 67 431 4344
Biso mean--36.86 35.93 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064113
X-RAY DIFFRACTIONf_angle_d1.1155564
X-RAY DIFFRACTIONf_chiral_restr0.044581
X-RAY DIFFRACTIONf_plane_restr0.005700
X-RAY DIFFRACTIONf_dihedral_angle_d13.6851582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.36540.34131610.29853037319890
1.3654-1.38150.33621780.27833291346997
1.3815-1.39830.32231520.26413297344997
1.3983-1.4160.24611630.24933248341196
1.416-1.43460.27951750.23773184335995
1.4346-1.45430.25181650.21323332349798
1.4543-1.47510.27511650.19843340350599
1.4751-1.49710.24942090.18753298350799
1.4971-1.52050.20521740.17173301347599
1.5205-1.54540.20181840.17343333351798
1.5454-1.57210.19391740.16693304347898
1.5721-1.60060.20451910.16433309350098
1.6006-1.63140.17871860.15713260344697
1.6314-1.66470.19311530.15073324347797
1.6647-1.70090.19271580.1473219337796
1.7009-1.74050.1721710.14323322349398
1.7405-1.7840.20071600.1473355351598
1.784-1.83230.19341840.1493344352899
1.8323-1.88620.20021700.15313318348898
1.8862-1.9470.18431460.1543371351798
1.947-2.01660.20411720.14533343351599
2.0166-2.09740.19781370.15063342347997
2.0974-2.19280.17661780.15033200337895
2.1928-2.30840.16521920.15453364355699
2.3084-2.4530.19361680.16053371353999
2.453-2.64240.17891980.16253337353599
2.6424-2.90820.19511600.16623365352599
2.9082-3.32880.17841910.15993254344596
3.3288-4.1930.16531990.14513356355599
4.193-37.5830.16021800.14483409358998

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