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- PDB-6h2c: Structure of BlaC from Mycobacterium tuberculosis bound to the tr... -

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Basic information

Entry
Database: PDB / ID: 6h2c
TitleStructure of BlaC from Mycobacterium tuberculosis bound to the trans-enamine adduct derived from clavulanic acid.
ComponentsBeta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
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 / CARBON DIOXIDE / (2E)-3-[(4-hydroxy-2-oxobutyl)amino]prop-2-enal / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)62,69612
Polymers58,9502
Non-polymers3,74610
Water2,018112
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9016
Polymers29,4751
Non-polymers4265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7956
Polymers29,4751
Non-polymers3,3205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.650, 41.980, 76.917
Angle α, β, γ (deg.)78.40, 89.95, 89.75
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: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 28 - 295 / Label seq-ID: 1 - 268

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

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Components

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Protein , 1 types, 2 molecules AB

#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: A0A655AHQ9*PLUS, beta-lactamase

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Non-polymers , 6 types, 122 molecules

#2: Chemical ChemComp-ISS / (2E)-3-[(4-hydroxy-2-oxobutyl)amino]prop-2-enal


Mass: 157.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#6: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate, pH 5.0 25% w/v PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 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: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.93→41.12 Å / Num. obs: 34426 / % possible obs: 94.4 % / Redundancy: 2.3 % / CC1/2: 0.974 / Rpim(I) all: 0.124 / Net I/σ(I): 4.4
Reflection shellResolution: 1.93→2 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3078 / CC1/2: 0.709 / Rpim(I) all: 0.342 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GDN

2gdn


Resolution: 1.93→41.12 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.874 / SU B: 7.015 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.192 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26694 1723 5 %RANDOM
Rwork0.22859 ---
obs0.23054 32697 94.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.358 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20.26 Å2-0.35 Å2
2--2.73 Å20.37 Å2
3----1.5 Å2
Refinement stepCycle: 1 / Resolution: 1.93→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 72 112 4202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194170
X-RAY DIFFRACTIONr_bond_other_d0.0020.023899
X-RAY DIFFRACTIONr_angle_refined_deg1.661.9785665
X-RAY DIFFRACTIONr_angle_other_deg1.01438980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39923.182176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55515620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1521538
X-RAY DIFFRACTIONr_chiral_restr0.0870.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214720
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02858
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_it0.8921.4322150
X-RAY DIFFRACTIONr_mcbond_other0.891.4292145
X-RAY DIFFRACTIONr_mcangle_it1.4432.1372680
X-RAY DIFFRACTIONr_mcangle_other1.4422.1382681
X-RAY DIFFRACTIONr_scbond_it1.0261.5532020
X-RAY DIFFRACTIONr_scbond_other1.0261.5532018
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6022.2782983
X-RAY DIFFRACTIONr_long_range_B_refined2.90317.2674570
X-RAY DIFFRACTIONr_long_range_B_other2.90217.2744571
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17326 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.932→1.982 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 111 -
Rwork0.329 2148 -
obs--82.48 %

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