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- PDB-6n14: Phosphoserine BlaC, Class A serine beta-lactamase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 6n14
TitlePhosphoserine BlaC, Class A serine beta-lactamase from Mycobacterium tuberculosis
ComponentsBeta-lactamase
KeywordsHYDROLASE / phosphoserine / beta-lactamase / Mycobacterium tuberculosis / inhibitor
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
PHOSPHATE ION / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52169460473 Å
AuthorsMoural, T.W. / White, D.S. / Choy, C.J. / Kang, C. / Berkman, C.E.
CitationJournal: Int J Mol Sci / Year: 2019
Title: Crystal Structure of Phosphoserine BlaC fromMycobacterium tuberculosisInactivated by Bis(Benzoyl) Phosphate.
Authors: Moural, T.W. / White, D.S. / Choy, C.J. / Kang, C. / Berkman, C.E.
History
DepositionNov 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8903
Polymers32,7001
Non-polymers1902
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.840, 68.037, 75.454
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 32699.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, ERS027646_02769 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0T9EA39, UniProt: P9WKD3*PLUS, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
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: 1.96 Å3/Da / Density % sol: 37.12 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M HEPES pH 7.4, 2.25 M ammonium phosphate monobasic, protein concertation 15 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2017
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 40045 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.04 / Rrim(I) all: 0.107 / Rsym value: 0.099 / Net I/σ(I): 17.586
Reflection shellResolution: 1.52→1.56 Å / Mean I/σ(I) obs: 1.92 / CC1/2: 0.623 / Rpim(I) all: 0.403 / Rrim(I) all: 0.914 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gdn

2gdn


Resolution: 1.52169460473→28.0973861897 Å / SU ML: 0.117484022888 / Cross valid method: THROUGHOUT / σ(F): 1.34370318253 / Phase error: 15.6852788604
RfactorNum. reflection% reflection
Rfree0.169388858906 1999 4.9998749406 %
Rwork0.154653334812 --
obs0.155398583746 39981 99.7330872081 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.7185917212 Å2
Refinement stepCycle: LAST / Resolution: 1.52169460473→28.0973861897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 10 329 2328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003305566561042036
X-RAY DIFFRACTIONf_angle_d0.7450864803042782
X-RAY DIFFRACTIONf_chiral_restr0.0461959306333319
X-RAY DIFFRACTIONf_plane_restr0.00426064510041366
X-RAY DIFFRACTIONf_dihedral_angle_d16.18678229971211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5217-1.55970.2631280396491380.2384471505612622X-RAY DIFFRACTION96.6048302415
1.5597-1.60190.24478397271380.2161304634732631X-RAY DIFFRACTION99.7837837838
1.6019-1.6490.2122025988081430.1866800607512692X-RAY DIFFRACTION100
1.649-1.70230.1909590242511410.1744978649082685X-RAY DIFFRACTION99.9646268129
1.7023-1.76310.2044516692991410.1660707080172687X-RAY DIFFRACTION100
1.7631-1.83370.1727068220221430.1578188549012701X-RAY DIFFRACTION100
1.8337-1.91710.1794502539851420.1548417092442706X-RAY DIFFRACTION100
1.9171-2.01820.1616933302831420.1388591293192687X-RAY DIFFRACTION100
2.0182-2.14460.1673158752451410.1323248944342700X-RAY DIFFRACTION100
2.1446-2.31010.150265026371430.1314193291532712X-RAY DIFFRACTION100
2.3101-2.54240.1348416018121440.1350774149912740X-RAY DIFFRACTION100
2.5424-2.910.1737952949871460.1452646473352751X-RAY DIFFRACTION100
2.91-3.6650.1671207718691440.1438840923322760X-RAY DIFFRACTION99.9655765921
3.665-28.10220.1555704975221530.1686391371752908X-RAY DIFFRACTION99.934704538

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