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- PDB-8oe1: Structure of P167S BlaC from Mycobacterium tuberculosis at pH 5 -

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Basic information

Entry
Database: PDB / ID: 8oe1
TitleStructure of P167S BlaC from Mycobacterium tuberculosis at pH 5
ComponentsBeta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


: / : / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSun, J. / Chikunova, A. / Ubbink, M.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council China
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Enhanced activity against a third-generation cephalosporin by destabilization of the active site of a class A beta-lactamase.
Authors: Sun, J. / Chikunova, A. / Boyle, A.L. / Voskamp, P. / Timmer, M. / Ubbink, M.
History
DepositionMar 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.3Oct 2, 2024Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline ..._diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,0788
Polymers56,5252
Non-polymers5536
Water3,801211
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3552
Polymers28,2631
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7236
Polymers28,2631
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.600, 54.178, 56.036
Angle α, β, γ (deg.)90.18, 111.10, 91.78
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-lactamase / Ambler class A beta-lactamase


Mass: 28262.686 Da / Num. of mol.: 2 / Mutation: P167S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, blaA, Rv2068c, MTCY49.07c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WKD3, beta-lactamase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M Na Cacod 5 pH (Buffer) 1.02 M Na3 Cit (Precipitant)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→54.15 Å / Num. obs: 33495 / % possible obs: 95.4 % / Redundancy: 1.6 % / CC1/2: 0.981 / Rpim(I) all: 0.034 / Net I/σ(I): 6.1
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2152 / CC1/2: 0.446 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→52.33 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.796 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 1637 4.9 %RANDOM
Rwork0.17201 ---
obs0.17405 31857 95.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.347 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0.01 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→52.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 36 211 4221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124089
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163856
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.6515570
X-RAY DIFFRACTIONr_angle_other_deg0.5051.5698843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0895530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.092538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62310611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024924
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02928
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_it1.6631.7832123
X-RAY DIFFRACTIONr_mcbond_other1.6621.7832123
X-RAY DIFFRACTIONr_mcangle_it2.5853.1932652
X-RAY DIFFRACTIONr_mcangle_other2.5853.1942653
X-RAY DIFFRACTIONr_scbond_it2.2242.0521966
X-RAY DIFFRACTIONr_scbond_other2.2232.0531967
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5053.6432919
X-RAY DIFFRACTIONr_long_range_B_refined4.87920.784726
X-RAY DIFFRACTIONr_long_range_B_other4.83620.384699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 118 -
Rwork0.264 2352 -
obs--93.95 %

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