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- PDB-9hpw: Crystal structure of meropenem bound to OXA-57 -

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Basic information

Entry
Database: PDB / ID: 9hpw
TitleCrystal structure of meropenem bound to OXA-57
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / Class-D Beta-lactamase complex with a carbapenem
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
Chem-MER / Beta-lactamase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsBragginton, 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)27,4192
Polymers27,0341
Non-polymers3851
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-0 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.931, 109.865, 66.357
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-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Monosaccharides (0.2 M D-Glucose, 0.2 M D-Mannose, 0.2 M D-Galactose, 0.2 M L-Fucose, 0.2 M D-Xylose, 0.2 M N-Acetyl-D-Glucosamine), 0.1 M Tris; BICINE pH 8.5, 37.5 % (v/v) ...Details: 0.12 M Monosaccharides (0.2 M D-Glucose, 0.2 M D-Mannose, 0.2 M D-Galactose, 0.2 M L-Fucose, 0.2 M D-Xylose, 0.2 M N-Acetyl-D-Glucosamine), 0.1 M Tris; BICINE pH 8.5, 37.5 % (v/v) Precipitant mix (25 % (v/v) MPD, 25 % (w/v) PEG 1000, 35 % (w/v) PEG 3350) 1hr soak in 10mM meropenem.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.912 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 2.42→56.53 Å / Num. obs: 9482 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.997 / Net I/σ(I): 11.7
Reflection shellResolution: 2.42→2.51 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 976 / CC1/2: 0.667

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→56.53 Å / SU ML: 0.3923 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.8898
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2601 482 5.11 %
Rwork0.1971 8950 -
obs0.2004 9432 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.34 Å2
Refinement stepCycle: LAST / Resolution: 2.42→56.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 26 12 1838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731869
X-RAY DIFFRACTIONf_angle_d0.88332537
X-RAY DIFFRACTIONf_chiral_restr0.0457276
X-RAY DIFFRACTIONf_plane_restr0.0052324
X-RAY DIFFRACTIONf_dihedral_angle_d21.7708665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.770.35741710.27532903X-RAY DIFFRACTION98.53
2.77-3.490.30971490.23642960X-RAY DIFFRACTION99.27
3.49-56.530.22721620.17183087X-RAY DIFFRACTION99.36
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)
17.797400040951.151092326260.4169519058295.093815863470.05449031619946.623437467510.372806480105-0.09365553929760.9235247181930.0953013992672-0.4057053452470.791172597263-0.939555407431-0.381894524409-0.05118945369780.69187591620.1774170106490.0005676801794840.50635092106-0.1288351277240.58814834504417.311874318128.24726464657.6081024987
24.318138369610.1997110937350.08586346056868.738695955152.525564590715.198903865050.1776435503-0.09296920616780.6041620758270.176061195201-0.248030461593-0.215391339793-0.395763909925-0.134957290480.06574065309260.5682277563070.1153561566270.009396050499680.3273138644870.0408450613670.52875388904825.757610961124.19283512199.15252211594
39.85040195093-0.779720777891-2.67913600973.471273540520.5375727513652.163936731-0.0647649007210.437982850481-0.881200970051-1.01642361429-0.1802829268040.5350157816391.58950521376-0.4372961501660.2898265920761.407978444020.0749137263096-0.2055708592680.686478577801-0.01507804654210.63493715548818.0638144458.35464072653-8.68220185005
44.682782035951.42078802902-1.076035683188.137687735111.12586062435.464722756490.2519762827470.5623652895540.384147843434-0.885396179168-0.1040482498471.51577514576-0.765831319756-1.4597876556-0.112033845650.7850381408530.241286805399-0.240040916760.874457440468-0.06464736885350.87680496983213.198132988514.5173915262-6.2049467579
53.047173222990.692539989518-0.1822101693018.972883840142.30848448693.414101582540.1368165039920.09743470234550.0431437926101-0.436019792498-0.257073217463-0.0375998606722-0.0556209531863-0.01228164866290.05851945149580.4181851365110.0850684276156-0.01038658587390.4119737561360.02567631366570.3734285261426.900206268915.26027403193.46405455565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 197 through 266 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 88 )
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 105 )
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 196 )

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