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- PDB-3lvz: New refinement of the crystal structure of BJP-1, a subclass B3 m... -

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Basic information

Entry
Database: PDB / ID: 3lvz
TitleNew refinement of the crystal structure of BJP-1, a subclass B3 metallo-beta-lactamase of Bradyrhizobium japonicum
ComponentsBlr6230 protein
KeywordsHYDROLASE / class B3 metallo-beta-lactamase / beta-lactam hydrolysis
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / metal ion binding
Similarity search - Function
Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsDocquier, J.D. / Benvenuti, M. / Calderone, V. / Stoczko, M. / Rossolini, G.M. / Mangani, S.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2010
Title: High-resolution crystal structure of the subclass B3 metallo-beta-lactamase BJP-1: rational basis for substrate specificity and interaction with sulfonamides.
Authors: Docquier, J.D. / Benvenuti, M. / Calderone, V. / Stoczko, M. / Menciassi, N. / Rossolini, G.M. / Mangani, S.
History
DepositionFeb 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Blr6230 protein
B: Blr6230 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3588
Polymers63,9652
Non-polymers3926
Water8,683482
1
A: Blr6230 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1794
Polymers31,9831
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Blr6230 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1794
Polymers31,9831
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.501, 44.773, 76.966
Angle α, β, γ (deg.)78.92, 89.51, 61.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Blr6230 protein / subclass B3 metallo-beta-lactamase


Mass: 31982.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA 100 / Gene: blr6230, Bradyrhizobium / Plasmid: pET-9a / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: Q89GW5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30-35% PEG 4000, 0.5M sodium acetate, 5mM ZnCl2 pH 8.0-8.5, 0.1M TrisHCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2813 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2005 / Details: mirrors
RadiationMonochromator: Si(111) liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2813 Å / Relative weight: 1
ReflectionResolution: 1.4→38.58 Å / Num. all: 87611 / Num. obs: 87611 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.6 / Redundancy: 3.7 % / Biso Wilson estimate: 14.05 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.1
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 1.8 / Num. unique all: 10821 / % possible all: 77.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.4→32.24 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.065 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19348 8006 9.1 %RANDOM
Rwork0.16217 ---
obs0.16503 79602 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.088 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.068 Å0.065 Å
Refinement stepCycle: LAST / Resolution: 1.4→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4109 0 6 482 4597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224266
X-RAY DIFFRACTIONr_bond_other_d0.0010.022844
X-RAY DIFFRACTIONr_angle_refined_deg2.2041.9725804
X-RAY DIFFRACTIONr_angle_other_deg1.09337004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15224.824170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12415717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.991516
X-RAY DIFFRACTIONr_chiral_restr0.1310.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214789
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_mcbond_it1.2731.52735
X-RAY DIFFRACTIONr_mcbond_other0.4461.51118
X-RAY DIFFRACTIONr_mcangle_it2.04624393
X-RAY DIFFRACTIONr_scbond_it2.99331531
X-RAY DIFFRACTIONr_scangle_it4.6274.51401
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 434 -
Rwork0.341 4237 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6926-0.3266-0.18240.75880.28260.6242-0.012-0.08250.0039-0.01340.0357-0.0059-0.02780.0523-0.02370.00370.0012-0.00080.0126-0.0030.003-0.35591.43630.4558
20.92410.1871-0.12770.5225-0.13320.6076-0.0070.0815-0.00610.00570.03790.0214-0.0077-0.0278-0.0310.0045-0.0029-0.0030.01030.00270.00949.6977-14.6764-36.6101
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 294
2X-RAY DIFFRACTION2B22 - 294

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