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- PDB-1kfb: CRYSTAL STRUCTURE OF ALPHAT183V MUTANT OF TRYPTOPHAN SYNTHASE FRO... -

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Basic information

Entry
Database: PDB / ID: 1kfb
TitleCRYSTAL STRUCTURE OF ALPHAT183V MUTANT OF TRYPTOPHAN SYNTHASE FROM SALMONELLA TYPHIMURIUM WITH Indole Glycerol Phosphate
Components
  • TRYPTOPHAN SYNTHASE ALPHA CHAIN
  • TRYPTOPHAN SYNTHASE BETA CHAIN
KeywordsLYASE / HELIX
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol
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
INDOLE-3-GLYCEROL PHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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
DepositionNov 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: TRYPTOPHAN SYNTHASE ALPHA CHAIN
B: TRYPTOPHAN SYNTHASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0194
Polymers71,4852
Non-polymers5342
Water9,458525
1
A: TRYPTOPHAN SYNTHASE ALPHA CHAIN
B: TRYPTOPHAN SYNTHASE BETA CHAIN
hetero molecules

A: TRYPTOPHAN SYNTHASE ALPHA CHAIN
B: TRYPTOPHAN SYNTHASE BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0388
Polymers142,9694
Non-polymers1,0694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)181.937, 60.255, 67.119
Angle α, β, γ (deg.)90.00, 94.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-659-

HOH

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Components

#1: Protein TRYPTOPHAN SYNTHASE ALPHA CHAIN


Mass: 28696.824 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
#2: Protein TRYPTOPHAN SYNTHASE BETA CHAIN


Mass: 42787.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1
#3: Chemical ChemComp-IGP / INDOLE-3-GLYCEROL PHOSPHATE


Mass: 287.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14NO6P
#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.: 525 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
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→91.3 Å / Num. all: 57355 / Num. obs: 57355 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 9.9 Å2
Reflection shellResolution: 1.9→2 Å / % possible all: 79.6
Reflection
*PLUS
Num. obs: 54830 / Num. measured all: 153263 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 79.6 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementResolution: 1.9→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2221550.76 / Data cutoff high rms absF: 2221550.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2784 5.1 %RANDOM
Rwork0.164 ---
obs0.164 54815 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.4153 Å2 / ksol: 0.412936 e/Å3
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.48 Å20 Å2-0.94 Å2
2--5.48 Å20 Å2
3----2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4856 0 34 525 5415
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it2.682
X-RAY DIFFRACTIONc_scangle_it3.782.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 439 5.5 %
Rwork0.227 7548 -
obs--84.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMTRPS_LIG.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4TRPS_LIG.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å

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