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- PDB-1ujp: Crystal Structure of Tryptophan Synthase A-Subunit From Thermus t... -

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Basic information

Entry
Database: PDB / ID: 1ujp
TitleCrystal Structure of Tryptophan Synthase A-Subunit From Thermus thermophilus HB8
ComponentsTryptophan synthase alpha chain
KeywordsLYASE / Tryptophan Synthase / Tryptophan / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / cytosol
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
CITRIC ACID / Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsAsada, Y. / Yokoyama, S. / Kuramitsu, S. / Miyano, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biochem.(Tokyo) / Year: 2005
Title: Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry.
Authors: Asada, Y. / Sawano, M. / Ogasahara, K. / Nakamura, J. / Ota, M. / Kuroishi, C. / Sugahara, M. / Yutani, K. / Kunishima, N.
History
DepositionAug 8, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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)29,1702
Polymers28,9781
Non-polymers1921
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.400, 76.868, 42.774
Angle α, β, γ (deg.)90.00, 115.08, 90.00
Int Tables number4
Space group name H-MP1211

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: P16608, tryptophan synthase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.07 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.6
Details: Ammonium Acetate, tri-Sodium Citrate dihydrate, PEG 4000, Glycerol anhydrous, pH 5.6, MICROBATCH, temperature 291K
Crystal grow
*PLUS
Temperature: 291 K / pH: 8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
128.27 mg/mlprotein11
220 mMTris-HCl11pH8.0
30.2 M11NaCl
40.17 Mammonium acetate12
585 mMcitrate-NaOH12pH5.6
625.5 %(w/v)PEG400012
715 %(v/v)glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 5, 2003 / Details: mirrors
RadiationMonochromator: Bending Magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.34→30 Å / Num. all: 55454 / Num. obs: 55454 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.042 / Net I/σ(I): 14.1
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 3.6 / Num. unique all: 5551 / Rsym value: 0.304 / % possible all: 100
Reflection
*PLUS
Num. measured all: 201760
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GEQ

1geq


Resolution: 1.34→27.3 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2621 -RANDOM
Rwork0.203 ---
all0.204 55414 --
obs0.204 55414 99.3 %-
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å21.4 Å2
2--2.32 Å20 Å2
3----0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.34→27.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 13 303 2149
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 1.34→1.4 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.271 332 -
Rwork0.255 --
obs-6554 99.4 %
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Lowest resolution: 1.39 Å

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