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- PDB-7n1m: Crystal Structure of the Class D Beta-lactamase OXA-935 from Pseu... -

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Basic information

Entry
Database: PDB / ID: 7n1m
TitleCrystal Structure of the Class D Beta-lactamase OXA-935 from Pseudomonas aeruginosa, Orthorhombic Crystal Form
ComponentsBeta-lactamase OXA-935
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Class D beta-Lactamase / OXA-935
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsMinasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Brunzelle, J.B. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Antimicrob.Agents Chemother. / Year: 2022
Title: Functional and Structural Characterization of OXA-935, a Novel OXA-10-Family beta-Lactamase from Pseudomonas aeruginosa.
Authors: Pincus, N.B. / Rosas-Lemus, M. / Gatesy, S.W.M. / Bertucci, H.K. / Brunzelle, J.S. / Minasov, G. / Shuvalova, L.A. / Lebrun-Corbin, M. / Satchell, K.J.F. / Ozer, E.A. / Hauser, A.R. / Bachta, K.E.R.
History
DepositionMay 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase OXA-935
B: Beta-lactamase OXA-935
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,56024
Polymers55,4472
Non-polymers2,11322
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-284 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.675, 91.377, 125.788
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 OXA-935


Mass: 27723.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaOXA-935 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 Magic
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.47 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 6.0 mg/ml, 0.01M Tris pH 8.3; Screen - AmSO4 (A9): 0.2M Ammonium iodide, 2.2M Ammonium sulfate; Cryo: 2M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 5, 2020 / Details: Be
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 40444 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 33.4 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.046 / Rrim(I) all: 0.154 / Rsym value: 0.147 / Χ2: 1.013 / Net I/σ(I): 19.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.754 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 2011 / CC1/2: 0.538 / Rpim(I) all: 0.544 / Rsym value: 1.754 / Χ2: 1.003 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1e3u

1e3u


Resolution: 1.96→29.77 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.166 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 1983 4.9 %RANDOM
Rwork0.1867 ---
obs0.1889 38401 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.71 Å2 / Biso mean: 44.352 Å2 / Biso min: 20.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å20 Å2-0 Å2
2--0.38 Å2-0 Å2
3----3.36 Å2
Refinement stepCycle: final / Resolution: 1.96→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 115 170 4059
Biso mean--79.39 45.28 -
Num. residues----477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133971
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183703
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.635384
X-RAY DIFFRACTIONr_angle_other_deg1.251.588551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.935479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.69523.979191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.40115702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4581516
X-RAY DIFFRACTIONr_chiral_restr0.0740.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
LS refinement shellResolution: 1.96→2.006 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.302 135 -
Rwork0.296 2681 -
obs--95.68 %
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)
15.9528-1.2056-1.27161.61370.0971.19080.00810.287-0.5035-0.1767-0.14120.1418-0.0786-0.06170.13320.1828-0.028-0.02490.1193-0.02680.07564.8931-6.5124-14.0722
20.8771-0.05840.38432.46060.65123.595-0.06350.16380.1393-0.5272-0.01380.1297-0.0655-0.02150.07730.1766-0.04230.00170.07810.010.06528.26745.5539-4.7516
31.9395-0.87-0.62571.94651.18324.74710.0253-0.11670.1487-0.0801-0.0651-0.0091-0.6331-0.26820.03980.10250.0416-0.01180.0311-0.01230.08256.390517.768711.3908
41.39320.0998-0.091.9414-0.93973.3888-0.07620.02460.0976-0.3117-0.0209-0.1555-0.01040.12890.09710.0724-0.01620.03260.02790.00210.054613.09977.48481.4397
54.1105-2.11971.34473.9683-1.3553.10.10440.1067-0.1245-0.56240.0410.39810.4178-0.2913-0.14540.1801-0.0875-0.05210.07110.00220.04580.6445-0.4288-2.5359
61.57742.65781.073111.91451.45861.7633-0.0588-0.2578-0.05390.5226-0.0280.6906-0.0544-0.27730.08680.1674-0.02910.08860.15770.01970.11323.2666-9.059439.7318
70.7989-0.57030.2952.4944-1.38823.42390.06620.0549-0.0714-0.1238-0.3048-0.44360.44810.57220.23850.06710.06470.02410.11350.02590.184522.2331-11.619621.6499
86.1856-0.0703-1.74692.3838-0.54154.4254-0.0326-0.1285-0.15230.3032-0.1975-0.51210.16670.69080.23010.07230.0079-0.10950.15540.05850.238427.12-7.818332.2609
91.8890.02070.14813.0737-0.81062.9761-0.11060.10090.06240.0484-0.074-0.4053-0.0440.17890.18450.0082-0.005-0.00670.04590.0180.119816.5488-3.485822.7873
101.5814-1.11550.73734.3109-1.78713.40.0298-0.0515-0.18130.13680.11890.160.2668-0.259-0.14870.0516-0.03850.00590.08170.00320.07917.2546-10.831129.1107
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 33
2X-RAY DIFFRACTION2A34 - 83
3X-RAY DIFFRACTION3A84 - 137
4X-RAY DIFFRACTION4A138 - 207
5X-RAY DIFFRACTION5A208 - 265
6X-RAY DIFFRACTION6B19 - 39
7X-RAY DIFFRACTION7B40 - 131
8X-RAY DIFFRACTION8B132 - 167
9X-RAY DIFFRACTION9B168 - 214
10X-RAY DIFFRACTION10B215 - 265

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