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- PDB-4s2l: Crystal Structure of OXA-163 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 4s2l
TitleCrystal Structure of OXA-163 beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / globular / carbamylation
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / metal ion binding / plasma membrane
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
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsStojanoski, V. / Liya, H. / Palzkill, T.G. / Prasad, B. / Sankaran, B.
CitationJournal: Biochemistry / Year: 2015
Title: Structural Basis for Different Substrate Profiles of Two Closely Related Class D beta-Lactamases and Their Inhibition by Halogens.
Authors: Stojanoski, V. / Chow, D.C. / Fryszczyn, B. / Hu, L. / Nordmann, P. / Poirel, L. / Sankaran, B. / Prasad, B.V. / Palzkill, T.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,0695
Polymers55,0002
Non-polymers693
Water12,430690
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.870, 125.750, 49.710
Angle α, β, γ (deg.)90.00, 116.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 27500.084 Da / Num. of mol.: 2 / Fragment: residues 25-261
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 0.1M HEPES, 16% w/v PEG8000, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2014
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.72→38.17 Å / Num. all: 51864 / Num. obs: 51864 / % possible obs: 86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.72-1.810.5282.47532199.8
5.44-38.170.02523.71676199.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 1.72→38.168 Å / SU ML: 0.22 / σ(F): 1.08 / σ(I): 2.4 / Phase error: 22.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 4951 4.99 %ramdon
Rwork0.1936 ---
all0.224 51964 --
obs0.1955 9961 96.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→38.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 3 690 4575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093978
X-RAY DIFFRACTIONf_angle_d1.3235382
X-RAY DIFFRACTIONf_dihedral_angle_d14.8351444
X-RAY DIFFRACTIONf_chiral_restr0.069566
X-RAY DIFFRACTIONf_plane_restr0.008690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.73950.28231250.27013131X-RAY DIFFRACTION96
1.7395-1.760.29711630.27413112X-RAY DIFFRACTION96
1.76-1.78150.31971790.2743155X-RAY DIFFRACTION96
1.7815-1.8040.3291890.25233072X-RAY DIFFRACTION96
1.804-1.82780.30311410.24713190X-RAY DIFFRACTION96
1.8278-1.85280.30921630.24923137X-RAY DIFFRACTION96
1.8528-1.87930.3191590.28133096X-RAY DIFFRACTION96
1.8793-1.90730.35681830.363031X-RAY DIFFRACTION93
1.9073-1.93710.43151520.36183104X-RAY DIFFRACTION96
1.9371-1.96890.33161600.24443131X-RAY DIFFRACTION96
1.9689-2.00280.2282130.20383119X-RAY DIFFRACTION96
2.0028-2.03920.23241730.19213102X-RAY DIFFRACTION97
2.0392-2.07850.22661900.18613192X-RAY DIFFRACTION96
2.0785-2.12090.22651690.18843089X-RAY DIFFRACTION97
2.1209-2.1670.22581340.18573277X-RAY DIFFRACTION96
2.167-2.21740.31411360.21793036X-RAY DIFFRACTION95
2.2174-2.27290.35011800.29963098X-RAY DIFFRACTION95
2.2729-2.33430.28921550.23313074X-RAY DIFFRACTION94
2.3343-2.4030.2091790.18983150X-RAY DIFFRACTION97
2.403-2.48050.21411720.18243232X-RAY DIFFRACTION97
2.4805-2.56920.24121820.17643095X-RAY DIFFRACTION97
2.5692-2.6720.21281510.17863265X-RAY DIFFRACTION98
2.672-2.79360.21041410.17053177X-RAY DIFFRACTION97
2.7936-2.94080.19441400.17423226X-RAY DIFFRACTION97
2.9408-3.1250.21831700.17693150X-RAY DIFFRACTION98
3.125-3.36610.23051490.16523204X-RAY DIFFRACTION97
3.3661-3.70460.18731670.16313152X-RAY DIFFRACTION97
3.7046-4.24010.16821520.15623051X-RAY DIFFRACTION94
4.2401-5.33970.18981880.14543228X-RAY DIFFRACTION99
5.3397-38.17710.18331960.15663234X-RAY DIFFRACTION100

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