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- PDB-4s2m: Crystal Structure of OXA-163 complexed with iodide in the active site -

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Basic information

Entry
Database: PDB / ID: 4s2m
TitleCrystal Structure of OXA-163 complexed with iodide in the active site
ComponentsBeta-lactamase
KeywordsHYDROLASE / globular
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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
IODIDE ION / Beta-lactamase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsStojanoski, V. / Hu, L. / Palzkill, T.G. / Prasad, 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 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Sep 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,36624
Polymers109,8284
Non-polymers2,53820
Water1,24369
1
A: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,43714
Polymers54,9142
Non-polymers1,52312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,92910
Polymers54,9142
Non-polymers1,0158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.630, 68.410, 70.223
Angle α, β, γ (deg.)62.20, 68.00, 71.58
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 25 - 261 / Label seq-ID: 1 - 233

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Beta-lactamase


Mass: 27457.082 Da / Num. of mol.: 4 / 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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 298 K
Details: 0.1M Sodium Iodine 15% w/v PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.87→59.801 Å / Num. obs: 22060 / % possible obs: 75 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.87→2.99 Å / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HBR

3hbr


Resolution: 2.87→59.801 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.886 / SU B: 37.789 / SU ML: 0.378 / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1134 5.1 %RANDOM
Rwork0.201 ---
obs0.204 20926 95 %-
all-22060 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å2-0.73 Å2-0 Å2
2--0.14 Å20.58 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.87→59.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7653 0 20 69 7742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197849
X-RAY DIFFRACTIONr_bond_other_d0.0060.027413
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.90810613
X-RAY DIFFRACTIONr_angle_other_deg1.258316961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21924.51408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.655151380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1631544
X-RAY DIFFRACTIONr_chiral_restr0.0770.21117
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028949
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021991
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5263.6943732
X-RAY DIFFRACTIONr_mcbond_other2.5253.6943731
X-RAY DIFFRACTIONr_mcangle_it4.1445.5344651
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4573.8954117
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A147510.09
12B147510.09
21A149000.09
22C149000.09
31A145130.11
32D145130.11
41B149440.09
42C149440.09
51B144660.1
52D144660.1
61C145420.1
62D145420.1
LS refinement shellResolution: 2.87→2.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 73 -
Rwork0.322 1461 -
obs--88.72 %
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)
11.78960.37330.36260.2929-0.39253.04450.0654-0.14410.10680.0332-0.00820.0235-0.1093-0.1431-0.05730.1012-0.0490.00790.0474-0.03370.12810.4767-0.1064-0.4038
21.6765-0.71390.27291.2451-0.13132.03150.04960.1332-0.0371-0.08950.01040.03050.26340.4544-0.060.06130.02160.01480.1692-0.06540.054140.918718.283512.1959
31.2621-0.97250.59951.9674-0.54173.24210.0471-0.0735-0.09950.01560.02440.3275-0.1964-0.2109-0.07150.0535-0.02230.01390.0446-0.00990.228714.740836.498614.2986
40.65270.0875-0.52361.1043-0.06472.72560.0166-0.013-0.03590.023-0.0625-0.14880.15080.80610.04590.03250.0197-0.01030.3728-0.02140.102527.3179-4.5442-17.3713
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 261
2X-RAY DIFFRACTION2B25 - 261
3X-RAY DIFFRACTION3C25 - 261
4X-RAY DIFFRACTION4D25 - 261

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