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- PDB-1c9d: CRYSTAL STRUCTURE OF THE COMPLEX OF BACTERIAL TRYPTOPHAN SYNTHASE... -

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Basic information

Entry
Database: PDB / ID: 1c9d
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF BACTERIAL TRYPTOPHAN SYNTHASE WITH THE TRANSITION STATE ANALOGUE INHIBITOR 4-(2-HYDROXY-4-FLUOROPHENYLTHIO)-BUTYLPHOSPHONIC ACID
Components(TRYPTOPHAN SYNTHASE ...) x 2
KeywordsLYASE / 8-FOLD ALPHA-BETA BARREL / ENZYME-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
Chem-HF1 / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsLolis, E. / Sachpatzidis, A.
Citation
Journal: Biochemistry / Year: 1999
Title: Crystallographic studies of phosphonate-based alpha-reaction transition-state analogues complexed to tryptophan synthase.
Authors: Sachpatzidis, A. / Dealwis, C. / Lubetsky, J.B. / Liang, P.H. / Anderson, K.S. / Lolis, E.
#1: Journal: J.Biol.Chem. / Year: 1988
Title: Three-Dimensional Structure of the Tryptophan Synthase Alpha 2 Beta 2 Multienzyme Complex from Salmonella typhimurium
Authors: Hyde, C.C. / Ahmed, S.A. / Padlan, E.A. / Miles, E.W. / Davies, D.R.
#2: Journal: 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
DepositionAug 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_src_syn / pdbx_struct_conn_angle / 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 / _entity.details / _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.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

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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)72,2365
Polymers71,6882
Non-polymers5483
Water3,387188
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)144,47210
Polymers143,3764
Non-polymers1,0976
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)184.220, 60.520, 67.790
Angle α, β, γ (deg.)90.00, 94.43, 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) / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / 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) / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 4 types, 191 molecules

#3: Chemical ChemComp-HF1 / 4-(2-HYDROXY-4-FLUOROPHENYLTHIO)-BUTYLPHOSPHONIC ACID


Mass: 278.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12FO4PS / Details: METAL COFACTOR BOUND AT THE BETA SUBUNIT
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
Details: INHIBITOR OF THE ALPHA-REACTION OF TRYPTOPHAN SYNTHASE
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O / Details: SOLVENT

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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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 12% PEG 4000, 0.75MM SPERMINE, 50MM SODIUM BICINE, 1MM EDTA, 5MM DTT, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
21 mMinhibitor1drop
350 mMBicine1reservoir
41 mMNaEDTA1reservoir
50.8-1.5 mMspermine1reservoir
612 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→45.9 Å / Num. all: 31780 / Num. obs: 31780 / % possible obs: 94.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 11.03 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.26
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.191 / % possible all: 81.2
Reflection
*PLUS
% possible obs: 95.2 % / Num. measured all: 95281
Reflection shell
*PLUS
% possible obs: 79.6 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
X-PLORphasing
RefinementResolution: 2.3→30 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
Details: RESTRAINED LEAST SQUARES REFINEMENT. CONJUGATE GRADIENT MINIMIZATION AND SIMULATED ANNEALING PROTOCOLS IMPLEMENTED IN XPLOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3161 -RANDOM
Rwork0.211 ---
all0.215 31780 --
obs0.215 31553 93.9 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 33 188 5147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.71
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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