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- PDB-7l5v: Crystal Structure of the Class D Beta-lactamase OXA-935 from Pseu... -

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Basic information

Entry
Database: PDB / ID: 7l5v
TitleCrystal Structure of the Class D Beta-lactamase OXA-935 from Pseudomonas aeruginosa, Monoclinic Crystal Form
ComponentsBeta-lactamase
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: 1.3 Å
AuthorsMinasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Brunzelle, J.S. / 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
DepositionDec 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)55,4472
Polymers55,4472
Non-polymers00
Water12,232679
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-12 kcal/mol
Surface area21650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.074, 75.043, 82.746
Angle α, β, γ (deg.)90.000, 91.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase / OXA-935 Beta-lactamase


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: pMCSG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 Magic
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 679 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 6.0 mg/ml, 0.01M Tris pH 8.3; Screen - Classics II (G9): 0.2M Ammonium acetate, 0.1M Tris pH 8.5, 25% (w/v) PEG 3350

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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: 1.3→30 Å / Num. obs: 126515 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 10.6 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.033 / Rrim(I) all: 0.079 / Rsym value: 0.072 / Χ2: 1.001 / Net I/σ(I): 20.6
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5121 / CC1/2: 0.854 / CC star: 0.96 / Rpim(I) all: 0.247 / Rrim(I) all: 0.575 / Rsym value: 0.517 / Χ2: 1 / % possible all: 74

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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: 1.3→23.95 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.461 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1699 6069 4.8 %RANDOM
Rwork0.1492 ---
obs0.1502 119981 91.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.15 Å2 / Biso mean: 15.778 Å2 / Biso min: 4.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å2-1.17 Å2
2--0.09 Å20 Å2
3----0.43 Å2
Refinement stepCycle: final / Resolution: 1.3→23.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 0 0 725 4606
Biso mean---28.71 -
Num. residues----492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134195
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184012
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.6315698
X-RAY DIFFRACTIONr_angle_other_deg0.3271.589280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8255539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.73623.632201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.18915768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6821519
X-RAY DIFFRACTIONr_chiral_restr0.0620.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0560.024850
X-RAY DIFFRACTIONr_gen_planes_other0.0490.02968
X-RAY DIFFRACTIONr_rigid_bond_restr0.69438207
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 390 -
Rwork0.232 7667 -
all-8057 -
obs--79.37 %
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)
11.20170.23960.50441.0738-0.18870.77510.0480.1302-0.0278-0.0835-0.01360.05210.070.0426-0.03440.02850.00790.02380.0245-0.0170.07912.044-3.5171.037
24.3439-2.57592.33553.8349-1.43744.0289-0.2749-0.09550.21140.37940.1469-0.2518-0.3864-0.10570.12810.08590.0213-0.01030.008-0.0010.075111.95117.63616.184
30.6963-0.22320.441.07910.14760.875-0.02770.10220.0676-0.087-0.0366-0.0832-0.07480.11150.06430.026-0.00420.03430.04240.02480.094413.3655.7441.855
41.6146-1.30362.13762.6692-2.74184.0821-0.0299-0.16650.04420.03960.13250.20130.0324-0.2837-0.10260.0245-0.00650.02580.0315-0.00590.08811.3671.19810.662
51.7012-1.11280.80582.2467-1.01671.52490.003-0.096-0.09410.12040.06690.22060.0303-0.1189-0.06980.0224-0.00960.03710.0178-0.00760.0899-2.32-4.0028.828
60.5656-0.46270.11541.62630.51261.5619-0.0863-0.05830.09050.2645-0.0243-0.1015-0.01780.05440.11060.0843-0.0169-0.00720.0207-0.00850.068321.933-1.50239.316
71.5213-0.10140.92411.47-0.85392.23520.1092-0.0603-0.1137-0.1354-0.0383-0.00890.29320.0653-0.07090.11140.01010.01760.01130.01570.065220.076-20.8324.115
81.5121-0.29181.21641.68-1.09162.33570.12340.0677-0.03970.061-0.084-0.19640.17490.2089-0.03940.07730.0085-0.01890.0270.00380.088130.744-10.39335.732
90.8383-0.32470.43311.07610.00611.4899-0.0420.02450.06210.1119-0.0508-0.0634-0.01930.01590.09280.0365-0.00540.01740.00280.0060.049519.545-4.32927.556
101.4014-0.85370.5992.5459-0.87942.2833-0.0571-0.11380.00190.18560.02070.23820.0072-0.20080.03650.0842-0.01180.0250.0287-0.02540.06813.008-1.37738.489
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 83
2X-RAY DIFFRACTION2A84 - 108
3X-RAY DIFFRACTION3A109 - 192
4X-RAY DIFFRACTION4A193 - 216
5X-RAY DIFFRACTION5A217 - 266
6X-RAY DIFFRACTION6B20 - 83
7X-RAY DIFFRACTION7B84 - 133
8X-RAY DIFFRACTION8B134 - 172
9X-RAY DIFFRACTION9B173 - 216
10X-RAY DIFFRACTION10B217 - 265

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