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- PDB-6h28: Structure of S70A BlaC from Mycobacterium tuberculosis obtained f... -

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Basic information

Entry
Database: PDB / ID: 6h28
TitleStructure of S70A BlaC from Mycobacterium tuberculosis obtained from crystals produced in the absence of DTT
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
DI(HYDROXYETHYL)ETHER / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8587
Polymers58,9182
Non-polymers1,9405
Water3,369187
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0953
Polymers29,4591
Non-polymers1,6362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7634
Polymers29,4591
Non-polymers3043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.590, 41.700, 76.760
Angle α, β, γ (deg.)101.31, 90.02, 90.05
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: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 29 - 296 / Label seq-ID: 2 - 269

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

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Components

#1: Protein Beta-lactamase


Mass: 29459.061 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
#2: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.19→40.89 Å / Num. obs: 458598 / % possible obs: 83.8 % / Redundancy: 3.6 % / CC1/2: 0.991 / Rpim(I) all: 0.068 / Net I/σ(I): 7.4
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 12483 / CC1/2: 0.452 / Rpim(I) all: 0.461 / % possible all: 45.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GDN

2gdn


Resolution: 1.19→40.89 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.951 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22377 6608 5.1 %RANDOM
Rwork0.18762 ---
obs0.18949 121830 83.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.077 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-0.39 Å2
2--1.62 Å20.06 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.19→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 30 187 4293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0144220
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173773
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.6655752
X-RAY DIFFRACTIONr_angle_other_deg1.2431.6488821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59620.8225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77715633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6471539
X-RAY DIFFRACTIONr_chiral_restr0.1280.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024865
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02751
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_it1.8161.1852172
X-RAY DIFFRACTIONr_mcbond_other1.81.1852171
X-RAY DIFFRACTIONr_mcangle_it2.1781.7872714
X-RAY DIFFRACTIONr_mcangle_other2.1821.7882715
X-RAY DIFFRACTIONr_scbond_it2.9311.4892048
X-RAY DIFFRACTIONr_scbond_other2.9311.4892048
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2012.1383034
X-RAY DIFFRACTIONr_long_range_B_refined2.88914.8594674
X-RAY DIFFRACTIONr_long_range_B_other2.89214.8634675
X-RAY DIFFRACTIONr_rigid_bond_restr4.1837989
X-RAY DIFFRACTIONr_sphericity_free12.65130
X-RAY DIFFRACTIONr_sphericity_bonded9.56657961
Refine LS restraints NCS

Ens-ID: 1 / Number: 8741 / 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: 1.193→1.224 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 274 -
Rwork0.332 5189 -
obs--48.13 %

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