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- PDB-9hpu: Crystal structure of OXA-57 -

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Basic information

Entry
Database: PDB / ID: 9hpu
TitleCrystal structure of OXA-57
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / Class-D Beta-lactamase
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / 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/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShaw, J.M. / Bragginton, E.C. / Hinchliffe, P. / Spencer, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure and dynamics of Burkholderia pseudomallei OXA-57, a distinctive low efficiency class D beta-lactamase with carbapenem-hydrolyzing activity
Authors: Bragginton, E.C. / Colenso, C.K. / Calvopina, K. / Hinchliffe, P. / Shaw, J.M. / Tooke, C.L. / Seng, R. / Chantratita, N. / Schofiled, C.J. / Spencer, J.
History
DepositionDec 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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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)27,0572
Polymers27,0341
Non-polymers231
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-7 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.788, 110.346, 64.796
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 27033.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: oxa-57 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6ZZZ2, beta-lactamase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Acetate 0.1 M Bis-Tris: HCl, pH 6.5 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→42.59 Å / Num. obs: 22269 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.998 / Net I/σ(I): 8.9
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1309 / CC1/2: 0.38

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Processing

Software
NameVersionClassification
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.01 Å / SU ML: 0.2162 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2143 1101 4.95 %
Rwork0.189 21136 -
obs0.1903 22237 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.41 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 1 134 1945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611854
X-RAY DIFFRACTIONf_angle_d0.83152515
X-RAY DIFFRACTIONf_chiral_restr0.0499270
X-RAY DIFFRACTIONf_plane_restr0.0061323
X-RAY DIFFRACTIONf_dihedral_angle_d20.3721662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.31681400.30182596X-RAY DIFFRACTION99.89
1.88-1.980.26491240.26272609X-RAY DIFFRACTION99.82
1.98-2.110.26321550.22232591X-RAY DIFFRACTION99.85
2.11-2.270.2331340.1992609X-RAY DIFFRACTION99.96
2.27-2.50.22561520.18332624X-RAY DIFFRACTION100
2.5-2.860.24311320.18292639X-RAY DIFFRACTION100
2.86-3.60.18871100.18312699X-RAY DIFFRACTION100
3.6-42.010.19021540.16992769X-RAY DIFFRACTION99.97
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)
11.485718268840.2073236299370.6454215020465.254868514031.367194929873.330455793190.01919932271120.03133361490360.176783669388-0.111429853918-0.1183080607970.0571967628534-0.0499593791099-0.0003459420805350.08156616256160.1191255396770.0249469689676-0.02872468333220.1953921035810.04271185339540.23864070315926.115462260521.97913766864.33093408812
24.43440131691.69915675296-0.1335626255344.179989497250.6700027444421.777745340470.006893504993040.491665399366-0.157387296096-0.733337788204-0.06386814487931.317491350670.293646916583-0.4664021177920.1427109006850.412998027270.0242907518602-0.1821092690070.382067573028-0.06379920350240.55689197475313.193490548710.8055037288-5.79254850401
31.194207239020.380848502840.6869921450517.540957609821.413397915631.626330239310.07727229420830.007081017867550.02654783784110.299736645443-0.114585792816-0.05092534371680.1430678860750.0186117581550.03344135240560.1812218753680.00729902236990.007228175393350.2078527972440.002940223972260.17564007880527.022697998511.28590355086.60661782648
43.6301370314-0.739841398691-0.7119311095965.908672966780.1395412091313.216471951310.05621397806890.197032384930.216312885516-0.290025729267-0.1243395893180.232379066281-0.224312476776-0.1904801332460.07226404175570.1984661339550.0112592134105-0.05401696484120.2256124425110.01222020602850.24300993541323.771313093224.51163802151.2166141605
55.97679894137-1.165225937190.3549390149843.921768592872.410623051834.26866685711-0.0691919701666-0.1847320005490.851861446642-0.102598873481-0.1635856881130.833260877881-0.126889806519-0.3638879485950.2169032786630.2975515012880.0716945538852-0.02484125189920.2681960395730.0216994979770.43744344565718.773124905232.75675084046.46308257535
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 22 through 76 )22 - 761 - 55
22chain 'A' and (resid 77 through 105 )77 - 10556 - 84
33chain 'A' and (resid 106 through 169 )106 - 16985 - 148
44chain 'A' and (resid 170 through 229 )170 - 229149 - 202
55chain 'A' and (resid 230 through 266 )230 - 266203 - 233

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