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- PDB-6h27: Structure of S70C BlaC from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6h27
TitleStructure of S70C BlaC from Mycobacterium tuberculosis
ComponentsBlaC
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / extracellular region
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
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsTassoni, R. / Pannu, N.S. / Ubbink, M.
CitationJournal: Biochemistry / Year: 2019
Title: New Conformations of Acylation Adducts of Inhibitors of beta-Lactamase from Mycobacterium tuberculosis.
Authors: Tassoni, R. / Blok, A. / Pannu, N.S. / Ubbink, M.
History
DepositionJul 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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: BlaC
B: BlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2855
Polymers58,9822
Non-polymers3023
Water2,612145
1
A: BlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6733
Polymers29,4911
Non-polymers1822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6112
Polymers29,4911
Non-polymers1201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.600, 76.410, 79.320
Angle α, β, γ (deg.)90.00, 90.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 28 - 294 / Label seq-ID: 1 - 267

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

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Components

#1: Protein BlaC


Mass: 29491.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A5I7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NH4NO3 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.63→79.31 Å / Num. obs: 58936 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rpim(I) all: 0.05 / Net I/σ(I): 9.7
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 6.7 % / Num. unique obs: 2940 / CC1/2: 0.762 / Rpim(I) all: 0.377 / % possible all: 98.9

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Processing

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

2gdn


Resolution: 1.63→79.31 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.079 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27514 2922 5 %RANDOM
Rwork0.23407 ---
obs0.23601 56014 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.679 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20.43 Å2
2--0.29 Å20 Å2
3---1.35 Å2
Refinement stepCycle: 1 / Resolution: 1.63→79.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 0 20 145 4201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194155
X-RAY DIFFRACTIONr_bond_other_d0.0020.023871
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.9695660
X-RAY DIFFRACTIONr_angle_other_deg1.08538924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5445541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01423.204181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11315629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8811539
X-RAY DIFFRACTIONr_chiral_restr0.1160.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214713
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02850
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_it1.5011.6322152
X-RAY DIFFRACTIONr_mcbond_other1.5011.6322151
X-RAY DIFFRACTIONr_mcangle_it2.1222.4442688
X-RAY DIFFRACTIONr_mcangle_other2.1222.4452689
X-RAY DIFFRACTIONr_scbond_it1.8851.8112003
X-RAY DIFFRACTIONr_scbond_other1.8851.8112003
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.692.6552970
X-RAY DIFFRACTIONr_long_range_B_refined3.43519.6894595
X-RAY DIFFRACTIONr_long_range_B_other3.43519.6914596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17220 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.629→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 259 -
Rwork0.286 4068 -
obs--99.45 %

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