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- PDB-1wxj: Crystal Structure Of Tryptophan Synthase A-Subunit with Indole-3-... -

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Basic information

Entry
Database: PDB / ID: 1wxj
TitleCrystal Structure Of Tryptophan Synthase A-Subunit with Indole-3-propanol phosphate From Thermus Thermophilus Hb8
Componentstryptophan synthase alpha chain
KeywordsLYASE / structural genomics / Thermus thermophilus HB8 / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
INDOLE-3-PROPANOL PHOSPHATE / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAsada, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure Of Tryptophan Synthase A-Subunit with Indole-3-propanol phosphate From Thermus Thermophilus Hb8
Authors: Asada, Y. / Kunishima, N.
History
DepositionJan 24, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tryptophan synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6176
Polymers28,9781
Non-polymers6395
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.631, 76.395, 42.721
Angle α, β, γ (deg.)90.00, 115.99, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is monomer

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Components

#1: Protein tryptophan synthase alpha chain / Tryptophan Synthase A-Subunit


Mass: 28977.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16608, tryptophan synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IPL / INDOLE-3-PROPANOL PHOSPHATE


Mass: 255.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14NO4P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.5
Details: INDOLE-3-PROPANOL PHOSPHATE, Tris-HCl, Ammonium Sulfate, pH 8.5, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 23, 2004 / Details: mirrors
RadiationMonochromator: Bending Magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 26921 / Num. obs: 26921 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.927 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.038 / Net I/σ(I): 15.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 4.01 / Num. unique all: 2664 / Rsym value: 0.253 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UJP

1ujp


Resolution: 1.7→27.08 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1345 -RANDOM
Rwork0.189 ---
all0.19 26898 --
obs0.19 26898 99.6 %-
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å24.52 Å2
2---1.23 Å20 Å2
3---3.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.7→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 37 278 2119
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.275 152 -
Rwork0.246 --
obs--94.2 %

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