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- PDB-1k8x: Crystal Structure Of AlphaT183V Mutant Of Tryptophan Synthase Fro... -

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Basic information

Entry
Database: PDB / ID: 1k8x
TitleCrystal Structure Of AlphaT183V Mutant Of Tryptophan Synthase From Salmonella Typhimurium
Components
  • TRYPTOPHAN SYNTHASE, ALPHA PROTEIN
  • TRYPTOPHAN SYNTHASE, BETA PROTEIN
KeywordsLYASE / HELIX
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan metabolic process / L-tryptophan biosynthetic process / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / 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, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / 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 / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKulik, V. / Weyand, M. / Siedel, R. / Niks, D. / Arac, D. / Dunn, M.F. / Schlichting, I.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: On the Role of AlphaThr183 in the Allosteric Regulation and Catalytic Mechanism of Tryptophan Synthase
Authors: Kulik, V. / Weyand, M. / Siedel, R. / Niks, D. / Arac, D. / Dunn, M.F. / Schlichting, I.
History
DepositionOct 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: 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 27, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / software / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPTOPHAN SYNTHASE, ALPHA PROTEIN
B: TRYPTOPHAN SYNTHASE, BETA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8884
Polymers71,6182
Non-polymers2702
Water7,422412
1
A: TRYPTOPHAN SYNTHASE, ALPHA PROTEIN
B: TRYPTOPHAN SYNTHASE, BETA PROTEIN
hetero molecules

A: TRYPTOPHAN SYNTHASE, ALPHA PROTEIN
B: TRYPTOPHAN SYNTHASE, BETA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,7768
Polymers143,2354
Non-polymers5404
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)182.220, 59.990, 67.070
Angle α, β, γ (deg.)90.00, 94.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRYPTOPHAN SYNTHASE, ALPHA PROTEIN


Mass: 28698.797 Da / Num. of mol.: 1 / Mutation: T183V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P00929, tryptophan synthase
#2: Protein TRYPTOPHAN SYNTHASE, BETA PROTEIN


Mass: 42918.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 8000, EDTA, spermine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 mMNa+-bicine1droppH7.8
310 mMNa+-EDTA1drop
41 mMdithioerythritol1drop
520000 nMPLP1drop
650 mMNa+-bicine1reservoirpH7.8
75 mMdithioerythritol1reservoir
85 mMNa+-EDTA1reservoir
90.1 mMPLP1reservoir
102 mMspermine1reservoir
118-12 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.9→20.9 Å / Num. all: 56455 / Num. obs: 51264 / % possible obs: 90.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.9→2 Å / Num. unique all: 7522 / % possible all: 94
Reflection
*PLUS
Num. obs: 50864 / Num. measured all: 112612 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 92.1 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QOP

1qop


Resolution: 1.9→19.62 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.232 2614 RANDOM
Rwork0.192 --
all-51264 -
obs-51264 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.18 Å20 Å2-1.53 Å2
2--6.45 Å20 Å2
3----4.26 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4834 0 16 412 5262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.311 454 -
Rwork0.258 --
obs-8304 93.7 %
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 19.6 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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