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- PDB-2o2e: Mycobacterium tuberculosis tryptophan synthase beta subunit dimer... -

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Basic information

Entry
Database: PDB / ID: 2o2e
TitleMycobacterium tuberculosis tryptophan synthase beta subunit 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 / 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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate 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: 2.2 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 subunit 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: Derived calculations / 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
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-19 kcal/mol
Surface area25800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.984, 56.461, 120.545
Angle α, β, γ (deg.)90.00, 117.00, 90.00
Int Tables number5
Space group name H-MC121

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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 / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.1M MES, 0.1 K/Na Tartrate, pH 6.4, 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: Jan 20, 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: 2.19→99 Å / Num. all: 39269 / Num. obs: 38769 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 13.5
Reflection shellResolution: 2.19→2.22 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 1.76 / % possible all: 81.9

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wsy

2wsy


Resolution: 2.2→19.92 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.889 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28072 1926 5 %RANDOM
Rwork0.21073 ---
obs0.21434 36537 99.61 %-
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: 47.771 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.19 Å2
2--0.22 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 0 34 4772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0410.0224814
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9331.9536515
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4635627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78423.18217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.49715775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7561546
X-RAY DIFFRACTIONr_chiral_restr0.2340.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023684
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.22273
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.23230
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2196
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4180.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9431.53288
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.91224924
X-RAY DIFFRACTIONr_scbond_it4.63431845
X-RAY DIFFRACTIONr_scangle_it6.5514.51591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 146 -
Rwork0.253 2663 -
obs--99.65 %

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