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- PDB-5hx9: Crystal structure of Beta-lactamase from Burkholderia vietnamiensis -

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Basic information

Entry
Database: PDB / ID: 5hx9
TitleCrystal structure of Beta-lactamase from Burkholderia vietnamiensis
ComponentsBeta-lactamase
KeywordsHYDROLASE / SSGCID / beta-lactamase / Burkholderia vietnamiensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia vietnamiensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Beta-lactamase from Burkholderia vietnamiensis
Authors: Conrady, D.G. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)29,6024
Polymers29,4161
Non-polymers1863
Water6,125340
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.500, 63.310, 99.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 29416.162 Da / Num. of mol.: 1 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria)
Strain: G4 / LMG 22486 / Gene: Bcep1808_5125 / Plasmid: BuviA.00104.b.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JP73, beta-lactamase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus Screen E8: 0.12 M Ethylene Glycols (equimolar mix of di- tri- tetra- and penta-ethylene glycol) 0.1M Buffer System 2 pH 7.5 (Na Hepes and MOPS acid), 50% Precipitant mix 4 (25% MPD, ...Details: Morpheus Screen E8: 0.12 M Ethylene Glycols (equimolar mix of di- tri- tetra- and penta-ethylene glycol) 0.1M Buffer System 2 pH 7.5 (Na Hepes and MOPS acid), 50% Precipitant mix 4 (25% MPD, 25% PEG1000, 25% PEG3350); BuamA.00078.a.B1.PS02512 at 52.5 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→39.04 Å / Num. obs: 24922 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 17.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.056 / Χ2: 0.96 / Net I/σ(I): 30.59 / Num. measured all: 240692
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.850.5243.5610403181118090.8960.57699.9
1.85-1.90.4144.5210565177117680.9410.45399.8
1.9-1.950.3046.1910592169716960.9570.33299.9
1.95-2.010.2447.8410861167116690.9720.26599.9
2.01-2.080.1910.3211004163316320.9820.20699.9
2.08-2.150.14714.6611971157715770.9890.158100
2.15-2.230.12319.1213420150815080.9950.131100
2.23-2.320.11321.0613468145614560.9960.12100
2.32-2.430.09823.7113891142314230.9970.104100
2.43-2.550.07930.4313939134913480.9980.08399.9
2.55-2.680.07232.8914272128112810.9980.076100
2.68-2.850.06438.5415476121412140.9990.067100
2.85-3.040.05644.9516471116011600.9990.058100
3.04-3.290.04356.27154661085108510.044100
3.29-3.60.03273.251405999699610.033100
3.6-4.020.02983.911271890590510.03100
4.02-4.650.02588.071128281181110.026100
4.65-5.690.02780.1962469769710.028100
5.69-8.050.02972.25741855755710.031100
8.050.02295.61379233233010.02399.4

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Processing

Software
NameVersionClassification
PHENIXdev_2299refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W4Q

3w4q


Resolution: 1.8→39.04 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.195 2147 8.62 %
Rwork0.1532 22774 -
obs0.1567 24921 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.09 Å2 / Biso mean: 21.2123 Å2 / Biso min: 7.76 Å2
Refinement stepCycle: final / Resolution: 1.8→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 12 344 2234
Biso mean--34.42 31.11 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091991
X-RAY DIFFRACTIONf_angle_d0.9272725
X-RAY DIFFRACTIONf_chiral_restr0.062326
X-RAY DIFFRACTIONf_plane_restr0.007361
X-RAY DIFFRACTIONf_dihedral_angle_d17.2281224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.84190.26271320.215414871619
1.8419-1.8880.25251530.197314911644
1.888-1.9390.21191450.170914571602
1.939-1.99610.2481490.159814971646
1.9961-2.06050.23061210.169115161637
2.0605-2.13410.23431400.161214851625
2.1341-2.21960.20221500.151215091659
2.2196-2.32060.19411390.147315081647
2.3206-2.44290.1651370.149115431680
2.4429-2.59590.1891540.140614811635
2.5959-2.79630.18811420.148815101652
2.7963-3.07760.16461270.156815431670
3.0776-3.52270.17791760.147415121688
3.5227-4.43720.18561480.13315651713
4.4372-39.04870.19181340.156916701804
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)
10.58440.18980.12242.98770.62933.8734-0.08560.7106-0.0306-0.65940.11110.11220.02620.0871-0.00140.22240.0401-0.02090.407-0.0040.1719.8654-2.8314-40.0251
22.43812.5513-1.40462.8065-1.43340.8169-0.0650.22660.3141-0.01050.150.2046-0.0501-0.1198-0.06410.11520.019-0.0080.17080.05180.154817.92843.4177-28.8267
31.4565-0.47310.30522.07290.07631.96380.0601-0.14220.01130.3080.1069-0.0277-0.0951-0.1442-0.12810.1440.00740.00090.08570.02420.112620.5824-7.6749-2.1312
42.03940.39310.41470.97-0.08042.83910.15950.0046-0.46690.1798-0.0847-0.09890.3141-0.1192-0.0590.20990.0125-0.04570.1093-0.00260.19819.6199-22.7117-4.1227
51.46750.43280.41541.2192-0.41361.4820.0420.13280.08650.0615-0.00270.075-0.0625-0.095-0.02610.10470.0280.01510.08240.00890.114.4422-5.8358-13.5014
64.971-0.12250.43626.54940.57045.32580.10380.01790.36050.3338-0.1436-0.3797-0.38170.31420.02350.1597-0.0542-0.02560.13570.03840.162629.0231.1994-9.1768
76.88370.75162.22365.30092.38081.59730.10810.0732-0.56690.16260.0698-0.42220.36160.9085-0.12260.16240.0814-0.00090.4089-0.01990.181633.1835-8.7698-27.0646
83.40351.8663-0.23463.4308-0.46590.9161-0.05820.2738-0.0647-0.15570.0204-0.10470.03940.21870.04190.09740.02890.00180.1880.00870.091323.1928-7.5874-26.0878
96.20935.8426-0.68825.8121-1.06692.4648-0.1590.2363-0.2854-0.44630.023-0.5798-0.020.16680.04930.16470.05790.04060.28360.01870.147428.0902-4.8255-33.9701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 51 )A27 - 51
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 68 )A52 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 98 )A69 - 98
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 118 )A99 - 118
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 194 )A119 - 194
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 212 )A195 - 212
7X-RAY DIFFRACTION7chain 'A' and (resid 213 through 229 )A213 - 229
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 273 )A230 - 273
9X-RAY DIFFRACTION9chain 'A' and (resid 274 through 289 )A274 - 289

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