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- PDB-5nj2: Crystal structure of BlaC from Mycobacterium tuberculosis bound t... -

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Basic information

Entry
Database: PDB / ID: 5nj2
TitleCrystal structure of BlaC from Mycobacterium tuberculosis bound to phosphate
ComponentsBeta-lactamase
KeywordsHYDROLASE
Function / homology
Function and homology information


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 / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL / Chem-ETE / PHOSPHATE ION / 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: 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
DepositionMar 27, 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)59,94611
Polymers58,9502
Non-polymers9969
Water5,188288
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7475
Polymers29,4751
Non-polymers2724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1996
Polymers29,4751
Non-polymers7245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.591, 41.683, 76.841
Angle α, β, γ (deg.)101.28, 90.11, 90.43
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: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 30 - 293 / Label seq-ID: 3 - 265

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 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0T9EA39, UniProt: P9WKD3*PLUS, beta-lactamase

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Non-polymers , 5 types, 297 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#5: Chemical ChemComp-AE4 / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate buffer, pH 5.0, 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 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: 1.19→75.36 Å / Num. obs: 96841 / % possible obs: 62.7 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.041 / Net I/σ(I): 11.3
Reflection shellResolution: 1.19→1.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 689 / CC1/2: 0.523 / Rpim(I) all: 0.467

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Processing

SoftwareName: REFMAC / Version: 7.0.033 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GDN

2gdn


Resolution: 1.19→75.36 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.829 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18953 4773 4.9 %RANDOM
Rwork0.16683 ---
obs0.16797 92053 62.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.803 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20.32 Å20.03 Å2
2--0.71 Å2-0.01 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.19→75.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 60 288 4393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194206
X-RAY DIFFRACTIONr_bond_other_d0.0020.023899
X-RAY DIFFRACTIONr_angle_refined_deg2.1851.9675726
X-RAY DIFFRACTIONr_angle_other_deg1.12438985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49822.989184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44515623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6681539
X-RAY DIFFRACTIONr_chiral_restr0.1530.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02863
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_it1.3151.0622156
X-RAY DIFFRACTIONr_mcbond_other1.2991.0592151
X-RAY DIFFRACTIONr_mcangle_it1.9331.592685
X-RAY DIFFRACTIONr_mcangle_other1.9351.592686
X-RAY DIFFRACTIONr_scbond_it2.2341.3072050
X-RAY DIFFRACTIONr_scbond_other2.2341.3082051
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1371.883038
X-RAY DIFFRACTIONr_long_range_B_refined3.83313.284665
X-RAY DIFFRACTIONr_long_range_B_other3.83313.2854666
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17232 / 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: 1.19→1.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 15 -
Rwork0.325 383 -
obs--3.48 %

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