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- PDB-5har: OXA-163 beta-lactamase - S70G mutant -

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Basic information

Entry
Database: PDB / ID: 5har
TitleOXA-163 beta-lactamase - S70G mutant
ComponentsBeta-lactamase
KeywordsHYDROLASE / serine 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsStojanoski, V. / Adamski, C.J. / Hu, L. / Mehta, S.C. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32956 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI55449 United States
CitationJournal: Biochemistry / Year: 2016
Title: Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine beta-Lactamases by Relieving Steric Strain.
Authors: Stojanoski, V. / Adamski, C.J. / Hu, L. / Mehta, S.C. / Sankaran, B. / Zwart, P. / Prasad, B.V. / Palzkill, T.
History
DepositionDec 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)27,5653
Polymers27,4701
Non-polymers942
Water4,666259
1
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1296
Polymers54,9402
Non-polymers1894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2480 Å2
ΔGint-13 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.340, 87.980, 124.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-302-

CL

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Components

#1: Protein Beta-lactamase /


Mass: 27470.059 Da / Num. of mol.: 1 / Fragment: UNP residues 25-261 / Mutation: S70G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: blaOXA-163 / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: F6KZJ2, beta-lactamase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 44.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M potassium acetate and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2014
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.74→62.38 Å / Num. obs: 25438 / % possible obs: 99.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 13.8
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2L

4s2l


Resolution: 1.74→62.38 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.74 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 1218 4.79 %Random selection
Rwork0.186 ---
obs0.1877 25438 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→62.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 5 261 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181999
X-RAY DIFFRACTIONf_angle_d0.7422691
X-RAY DIFFRACTIONf_dihedral_angle_d13.3921160
X-RAY DIFFRACTIONf_chiral_restr0.052282
X-RAY DIFFRACTIONf_plane_restr0.004345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.77550.4131540.34692715X-RAY DIFFRACTION100
1.7755-1.81410.38961370.33612710X-RAY DIFFRACTION100
1.8141-1.85630.37461530.30882682X-RAY DIFFRACTION100
1.8563-1.90280.3261110.27662724X-RAY DIFFRACTION100
1.9028-1.95420.2611430.24822706X-RAY DIFFRACTION100
1.9542-2.01170.27161200.23872718X-RAY DIFFRACTION100
2.0117-2.07670.2521120.22952712X-RAY DIFFRACTION100
2.0767-2.15090.21661420.21152740X-RAY DIFFRACTION100
2.1509-2.2370.25851150.20332728X-RAY DIFFRACTION100
2.237-2.33880.23561360.18692711X-RAY DIFFRACTION100
2.3388-2.46210.19291680.17332662X-RAY DIFFRACTION100
2.4621-2.61640.18641430.17812695X-RAY DIFFRACTION100
2.6164-2.81840.20871170.17172692X-RAY DIFFRACTION100
2.8184-3.1020.21931130.17962746X-RAY DIFFRACTION100
3.102-3.55090.19641680.1532671X-RAY DIFFRACTION100
3.5509-4.47360.17751460.13592682X-RAY DIFFRACTION99
4.4736-62.42510.18411340.14512704X-RAY DIFFRACTION100
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)
11.21510.3457-0.22341.6214-0.1290.9109-0.1439-0.37330.35390.25120.2660.4465-0.3297-0.2908-0.09820.26680.14150.04830.57710.03080.2559-15.96740.864125.219
21.0798-0.25550.17630.8577-0.04771.1985-0.16-0.4636-0.00690.18040.25290.0854-0.0327-0.0533-0.05620.18620.0987-0.00150.24230.00840.1227-2.3633-4.121519.9707
31.79240.35950.50490.36850.30080.6838-0.20530.0914-0.3277-0.0980.0984-0.13420.1127-0.0805-0.03090.1995-0.0321-0.00440.1325-0.01690.17450.6981-19.25630.9117
42.3470.54920.46520.94840.10431.2969-0.111-0.3171-0.1790.04490.0844-0.2130.25960.0924-0.08520.22050.0915-0.02920.18880.00560.180611.245-16.981213.0701
51.6349-0.1972-0.06311.084-0.02251.4624-0.1129-0.40130.02550.14570.0745-0.16780.13330.06850.03920.15460.0493-0.02720.2201-0.03480.14686.4033-7.730715.8
61.3765-0.8509-0.11731.1319-0.21592.1645-0.0963-0.2231-0.03850.17030.35090.3058-0.015-0.4283-0.19630.15260.05110.01120.23030.08170.1954-9.8716-2.912113.2591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 142 )
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 194 )
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 261 )

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