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- PDB-6h2a: Structure of S70A BlaC from Mycobacterium tuberculosis obtained f... -

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Basic information

Entry
Database: PDB / ID: 6h2a
TitleStructure of S70A BlaC from Mycobacterium tuberculosis obtained from crystals produced in the presence of DTT
Components
  • Beta-lactamase
  • Possible protein degradation product
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / PHOSPHATE ION / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
C: Beta-lactamase
H: Possible protein degradation product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,61920
Polymers88,7384
Non-polymers1,88216
Water95553
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3178
Polymers29,4591
Non-polymers8587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1427
Polymers29,4591
Non-polymers6836
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8004
Polymers29,4591
Non-polymers3413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: Possible protein degradation product


  • defined by author
  • 360 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)3601
Polymers3601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.864, 108.864, 260.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA29 - 2932 - 266
21ALAALABB29 - 2932 - 266
12LEULEUAA29 - 2942 - 267
22LEULEUCC29 - 2942 - 267
13HISHISBB29 - 2962 - 269
23HISHISCC29 - 2962 - 269

NCS ensembles :
ID
1
2
3

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCH

#1: Protein Beta-lactamase


Mass: 29459.061 Da / Num. of mol.: 3
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
#2: Protein/peptide Possible protein degradation product


Mass: 360.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 69 molecules

#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 4.35 Å3/Da / Density % sol: 71.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl, pH 7.0 1.7 M NH4H2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.54→49.73 Å / Num. obs: 714649 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rpim(I) all: 0.034 / Net I/σ(I): 18.9
Reflection shellResolution: 2.54→2.63 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 71706 / CC1/2: 0.701 / Rpim(I) all: 0.49 / % possible all: 99.9

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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: 2.54→49.73 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.371 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.231 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25634 2628 5 %RANDOM
Rwork0.228 ---
obs0.22945 49780 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.052 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20 Å2
2--2.1 Å20 Å2
3----4.19 Å2
Refinement stepCycle: 1 / Resolution: 2.54→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5885 0 108 53 6046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196090
X-RAY DIFFRACTIONr_bond_other_d0.0020.025669
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.9828289
X-RAY DIFFRACTIONr_angle_other_deg1.082313057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54323.127259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97915895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0061556
X-RAY DIFFRACTIONr_chiral_restr0.1010.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216839
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021237
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_it5.1616.1943147
X-RAY DIFFRACTIONr_mcbond_other5.1456.1933146
X-RAY DIFFRACTIONr_mcangle_it6.9669.2763922
X-RAY DIFFRACTIONr_mcangle_other6.9659.2783923
X-RAY DIFFRACTIONr_scbond_it6.0036.6442943
X-RAY DIFFRACTIONr_scbond_other6.0026.6442943
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2349.7814368
X-RAY DIFFRACTIONr_long_range_B_refined9.70773.0296433
X-RAY DIFFRACTIONr_long_range_B_other9.70673.0286433
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)
11A168320.06
12B168320.06
21A151240.07
22C151240.07
31B151240.08
32C151240.08
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 198 -
Rwork0.337 3628 -
obs--99.9 %

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