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- PDB-1a5s: CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 1a5s
TitleCRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH 5-FLUOROINDOLE PROPANOL PHOSPHATE AND L-SER BOUND AS AMINO ACRYLATE TO THE BETA SITE
Components(TRYPTOPHAN SYNTHASE ...) x 2
KeywordsCOMPLEX (LYASE/INHIBITOR) / LYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE / COMPLEX (LYASE-INHIBITOR) / COMPLEX (LYASE-INHIBITOR) complex
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
5-FLUOROINDOLE PROPANOL PHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / SERINE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH PDB ENTRY 1WSY. / Resolution: 2.3 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 17, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)72,3366
Polymers71,6882
Non-polymers6484
Water2,090116
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)144,67212
Polymers143,3764
Non-polymers1,2978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)182.700, 60.800, 67.500
Angle α, β, γ (deg.)90.00, 94.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

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TRYPTOPHAN SYNTHASE ... , 2 types, 2 molecules AB

#1: Protein TRYPTOPHAN SYNTHASE (ALPHA CHAIN)


Mass: 28698.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P00929, tryptophan synthase
#2: Protein TRYPTOPHAN SYNTHASE (BETA CHAIN)


Mass: 42988.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli)
References: UniProt: P00933, UniProt: P0A2K1*PLUS, tryptophan synthase

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Non-polymers , 5 types, 120 molecules

#3: Chemical ChemComp-FIP / 5-FLUOROINDOLE PROPANOL PHOSPHATE


Mass: 273.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13FNO4P
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsRESIDUE 902 C SER IS NOT REALLY SERINE BUT AN AMINOACRYLATE COVALENTLY BOUND TO THE PYRIDOXAL PHOSPHATE (PLP).

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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: 2.61 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: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Nov 1, 1995 / Details: SYNCHROTRON
RadiationMonochromator: SYNCHROTRON / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 31198 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.4 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: 68449
Reflection shell
*PLUS
% possible obs: 89.8 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: ISOMORPHOUS WITH PDB ENTRY 1WSY.
Starting model: 1WSY

1wsy
PDB Unreleased entry


Resolution: 2.3→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3126 10 %RANDOM
Rwork0.177 ---
obs0.177 30327 93.8 %-
Displacement parametersBiso mean: 25.6 Å2
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 40 116 5032
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.3
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_it1.53.6
X-RAY DIFFRACTIONx_mcangle_it24.7
X-RAY DIFFRACTIONx_scbond_it25.5
X-RAY DIFFRACTIONx_scangle_it2.57.2
LS refinement shellResolution: 2.3→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3223 160 -
Rwork0.2596 1290 -
obs--89.8 %
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

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