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- PDB-5oyo: Crystal structure of BlaC from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 5oyo
TitleCrystal structure of BlaC from Mycobacterium tuberculosis
ComponentsBeta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


penicillinase activity / cephalosporinase activity / 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTassoni, R. / Pannu, N.S.
CitationJournal: Biochemistry / Year: 2017
Title: Phosphate Promotes the Recovery of Mycobacterium tuberculosis beta-Lactamase from Clavulanic Acid Inhibition.
Authors: Elings, W. / Tassoni, R. / van der Schoot, S.A. / Luu, W. / Kynast, J.P. / Dai, L. / Blok, A.J. / Timmer, M. / Florea, B.I. / Pannu, N.S. / Ubbink, M.
History
DepositionSep 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,90613
Polymers58,9502
Non-polymers95611
Water2,432135
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9547
Polymers29,4751
Non-polymers4786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9536
Polymers29,4751
Non-polymers4775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.589, 41.417, 76.523
Angle α, β, γ (deg.)104.29, 90.07, 90.67
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 29 - 294 / Label seq-ID: 2 - 267

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Beta-lactamase


Mass: 29475.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, ERS027646_02769 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0T9EA39, UniProt: P9WKD3*PLUS, beta-lactamase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 5.0, 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96773 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96773 Å / Relative weight: 1
ReflectionResolution: 1.93→40.13 Å / Num. obs: 33346 / % possible obs: 94.2 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.074 / Net I/σ(I): 6.8
Reflection shellResolution: 1.93→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2851 / Rpim(I) all: 0.572 / % possible all: 81.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GDN

2gdn


Resolution: 2.1→40.13 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.897 / SU B: 6.823 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25043 1317 5 %RANDOM
Rwork0.20574 ---
obs0.20803 25143 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.828 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å20.57 Å20.04 Å2
2--2.92 Å20.37 Å2
3----1.12 Å2
Refinement stepCycle: 1 / Resolution: 2.1→40.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4030 0 59 135 4224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194174
X-RAY DIFFRACTIONr_bond_other_d0.0020.023889
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9735677
X-RAY DIFFRACTIONr_angle_other_deg1.01338964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7135538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29323.204181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0815623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4721538
X-RAY DIFFRACTIONr_chiral_restr0.0880.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214730
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02848
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_it1.492.0142153
X-RAY DIFFRACTIONr_mcbond_other1.4682.012145
X-RAY DIFFRACTIONr_mcangle_it2.2523.0082680
X-RAY DIFFRACTIONr_mcangle_other2.2523.0092681
X-RAY DIFFRACTIONr_scbond_it1.4952.162021
X-RAY DIFFRACTIONr_scbond_other1.4922.162021
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2263.1922996
X-RAY DIFFRACTIONr_long_range_B_refined3.63624.4264659
X-RAY DIFFRACTIONr_long_range_B_other3.63724.4324660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17380 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 88 -
Rwork0.297 1804 -
obs--93.85 %

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