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- PDB-1c29: CRYSTAL STRUCTURE OF THE COMPLEX OF BACTERIAL TRYPTOPHAN SYNTHASE... -

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Basic information

Entry
Database: PDB / ID: 1c29
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF BACTERIAL TRYPTOPHAN SYNTHASE WITH THE TRANSITION STATE ANALOGUE INHIBITOR 4-(2-HYDROXYPHENYLTHIO)-1-BUTENYLPHOSPHONIC ACID
Components(TRYPTOPHAN SYNTHASE) x 2
KeywordsLYASE/LYASE INHIBITOR / 8-FOLD ALPHA-BETA BARREL / ENZYME-INHIBITOR COMPLEX / LYASE-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 / 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
4-(2-HYDROXYPHENYLTHIO)-1-BUTENYLPHOSPHONIC ACID / 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
AuthorsSachpatzidis, A. / Dealwis, C. / Lubetsky, J.B. / Liang, P.H. / Anderson, K.S. / Lolis, E.
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
DepositionJul 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2000Provider: 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_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_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_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_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
B: TRYPTOPHAN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2185
Polymers71,6882
Non-polymers5303
Water2,918162
1
A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules

A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,43610
Polymers143,3764
Non-polymers1,0616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)182.290, 58.870, 67.400
Angle α, β, γ (deg.)90.00, 94.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein TRYPTOPHAN SYNTHASE


Mass: 28698.797 Da / Num. of mol.: 1 / Fragment: ALPHA CHAIN
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


Mass: 42988.996 Da / Num. of mol.: 1 / Fragment: BETA CHAIN
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, 165 molecules

#3: Chemical ChemComp-HE1 / 4-(2-HYDROXYPHENYLTHIO)-1-BUTENYLPHOSPHONIC ACID


Mass: 260.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13O4PS
Details: INHIBITOR OF THE ALPHA-REACTION OF TRYPTOPHAN SYNTHASE NONCOVALENTLY BOUND AT THE ALPHA SUBUNIT ACTIVE SITE
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Details: METAL COFACTOR BOUND AT THE BETA SUBUNIT ACTIVE SITE
#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: NATURAL COFACTOR OF TRYPTOPHAN SYNTHASE BOUND AS A SCHIFF BASE WITH BETA LYS- 87 AT THE BETA SUBUNIT ACTIVE SITE
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
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 / Details: pH was adjusted with NaOH
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: May 27, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→42.2 Å / Num. all: 30087 / Num. obs: 29830 / % possible obs: 92.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 11.63 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.9
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.174 / % possible all: 93
Reflection
*PLUS
Num. measured all: 245222
Reflection shell
*PLUS
% possible obs: 93 %

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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
Rfree0.275 2928 -RANDOM
Rwork0.208 ---
all0.218 29830 --
obs0.214 29401 91 %-
Refine analyzeLuzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 32 162 5120
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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