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- PDB-2o2j: Mycobacterium tuberculosis tryptophan synthase beta chain dimer (... -

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Basic information

Entry
Database: PDB / ID: 2o2j
TitleMycobacterium tuberculosis tryptophan synthase beta chain dimer (apoform)
ComponentsTryptophan synthase beta chain
KeywordsLYASE / Amino-acid biosynthesis / Tryptophan biosynthesis / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / cytoplasm
Similarity search - Function
Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tryptophan synthase beta chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsBurenkov, G.P. / Kachalova, G.S. / Bartunik, H.D. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: To be Published
Title: Structure Tryptophan SYNTHASE beta chain dimer from MYCOBACTERIUM Tuberculosis
Authors: Kachalova, G.S. / Burenkov, G.P. / I Strizhov, N. / I Svergun, D. / Bartunik, H.D.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan synthase beta chain
B: Tryptophan synthase beta chain


Theoretical massNumber of molelcules
Total (without water)89,3882
Polymers89,3882
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.823, 114.966, 159.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Tryptophan synthase beta chain


Mass: 44694.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: trpB / Plasmid: p6d, pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: P66984, UniProt: P9WFX9*PLUS, tryptophan synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 42.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, 2.0 M Ammonium Formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 26, 2004 / Details: Au-coated planar; toroidal mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.56→30 Å / Num. all: 23336 / Num. obs: 22608 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 13.5
Reflection shellResolution: 2.56→2.63 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2 / Num. unique all: 1622 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O2E

2o2e


Resolution: 2.56→10 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.876 / SU B: 12.016 / SU ML: 0.266 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.638 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30376 1224 5.1 %RANDOM
Rwork0.20958 ---
obs0.21441 22608 96.9 %-
all-23335 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.799 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.56→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 0 20 4758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0390.0224812
X-RAY DIFFRACTIONr_angle_refined_deg3.1121.9536511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0415627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.15723.116215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.83615775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0471546
X-RAY DIFFRACTIONr_chiral_restr0.1930.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023676
X-RAY DIFFRACTIONr_nbd_refined0.30.22362
X-RAY DIFFRACTIONr_nbtor_refined0.3450.23240
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3250.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3050.27
X-RAY DIFFRACTIONr_mcbond_it1.8381.53258
X-RAY DIFFRACTIONr_mcangle_it2.91324924
X-RAY DIFFRACTIONr_scbond_it4.43331839
X-RAY DIFFRACTIONr_scangle_it6.3144.51587
LS refinement shellResolution: 2.56→2.626 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 101 -
Rwork0.304 1514 -
obs--93.35 %

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