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- PDB-2wsy: CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 2wsy
TitleCRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE
Components(TRYPTOPHAN SYNTHASE) x 2
KeywordsLYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / 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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate 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 / ISOMORPHOUS WITH PDB ENTRY 1WSY. / Resolution: 3.05 Å
AuthorsSchneider, T.R. / Gerhardt, E. / Lee, M. / Liang, P.-H. / Anderson, K.S. / Schlichting, I.
CitationJournal: Biochemistry / Year: 1998
Title: Loop closure and intersubunit communication in tryptophan synthase.
Authors: Schneider, T.R. / Gerhardt, E. / Lee, M. / Liang, P.H. / Anderson, K.S. / Schlichting, I.
History
DepositionFeb 18, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / 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_database_status.process_site / _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_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
B: TRYPTOPHAN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8274
Polymers71,5572
Non-polymers2702
Water0
1
A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules

A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,6538
Polymers143,1134
Non-polymers5404
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)185.100, 61.200, 67.600
Angle α, β, γ (deg.)90.00, 94.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRYPTOPHAN SYNTHASE /


Mass: 28698.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / Cell line: CB149 / Plasmid: PSTB7 / References: UniProt: P00929, tryptophan synthase
#2: Protein TRYPTOPHAN SYNTHASE /


Mass: 42857.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / Cell line: CB149 / Plasmid: PSTB7 / 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 / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P

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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: 2.67 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of enzyme and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme1drop
250 mMbicine1drop
30.02 Mpyridoxal phosphate1drop
450 mMbicine1reservoir
51-2 mMspermine1reservoir
610 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.86
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: SYNCHROTRON
RadiationMonochromator: SYNCHROTRON / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 3.05→10 Å / Num. obs: 13162 / % possible obs: 90.9 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 20.2
Reflection shellHighest resolution: 3.05 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.2 / % possible all: 89.8
Reflection
*PLUS
Num. measured all: 28423
Reflection shell
*PLUS
% possible obs: 89.8 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH PDB ENTRY 1WSY.
Starting model: 1WSY

1wsy
PDB Unreleased entry


Resolution: 3.05→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: TIGHTLY RESTRAINED, SEE P / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1355 10 %RANDOM
Rwork0.197 ---
obs0.197 12850 90.9 %-
Displacement parametersBiso mean: 20.4 Å2
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 3.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 0 16 0 4648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.003
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.05→3.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3842 67 -
Rwork0.3005 517 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM.IPP.NEWTOP.IPP.NEW
X-RAY DIFFRACTION3PARAM.PLP.NEWTOP.PLP.NEW
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.3005

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