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- PDB-1ttp: TRYPTOPHAN SYNTHASE (E.C.4.2.1.20) IN THE PRESENCE OF CESIUM, ROO... -

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Basic information

Entry
Database: PDB / ID: 1ttp
TitleTRYPTOPHAN SYNTHASE (E.C.4.2.1.20) IN THE PRESENCE OF CESIUM, ROOM TEMPERATURE
Components(TRYPTOPHAN SYNTHASE) x 2
KeywordsCARBON-OXYGEN LYASE
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
: / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsRhee, S. / Parris, K. / Ahmed, S. / Miles, E.W. / Davies, D.R.
Citation
Journal: Biochemistry / Year: 1996
Title: Exchange of K+ or Cs+ for Na+ induces local and long-range changes in the three-dimensional structure of the tryptophan synthase alpha2beta2 complex.
Authors: Rhee, S. / Parris, K.D. / Ahmed, S.A. / Miles, E.W. / Davies, D.R.
#1: Journal: Bio/Technology / Year: 1990
Title: The Tryptophan Synthase Multienzyme Complex: Exploring Structure-Function Relationships with X-Ray Crystallography and Mutagenesis
Authors: Hyde, C.C. / Miles, E.W.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Three-Dimensional Structure of the Tryptophan Synthase Alpha2Beta2 Multienzyme Complex from Salmonella Typhimurium
Authors: Hyde, C.C. / Ahmed, S.A. / Padlan, E.A. / Miles, E.W. / Davies, D.R.
#3: Journal: J.Biol.Chem. / Year: 1985
Title: Crystallization and Preliminary X-Ray Crystallographic Data of the Tryptophan Synthase Alpha2Beta2 Complex from Salmonella Typhimurium
Authors: Ahmed, S.A. / Miles, E.W. / Davies, D.R.
History
DepositionOct 11, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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)72,2015
Polymers71,6882
Non-polymers5133
Water25214
1
A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules

A: TRYPTOPHAN SYNTHASE
B: TRYPTOPHAN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,40110
Polymers143,3764
Non-polymers1,0266
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10530 Å2
ΔGint-243 kcal/mol
Surface area44160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)185.300, 61.300, 68.100
Angle α, β, γ (deg.)90.00, 94.80, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO A 28
2: SER A 247 - PRO A 248 OMEGA = 210.04 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO B 56 / 4: CIS PROLINE - PRO B 196

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Components

#1: Protein TRYPTOPHAN SYNTHASE


Mass: 28698.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: STRUCTURE IN THE PRESENCE OF CESIUM / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: TB2211 / Gene: TRPA/TRPB/TRPC / Plasmid: PSTH8 / Gene (production host): TRPA/TRPB/TRPC / Production host: Escherichia coli (E. coli) / References: UniProt: P00929, tryptophan synthase
#2: Protein TRYPTOPHAN SYNTHASE


Mass: 42988.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: STRUCTURE IN THE PRESENCE OF CESIUM / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: TB2211 / Gene: TRPA/TRPB/TRPC / Plasmid: PSTH8 / Gene (production host): TRPA/TRPB/TRPC / Production host: Escherichia coli (E. coli)
References: UniProt: P00933, UniProt: P0A2K1*PLUS, tryptophan synthase
#3: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#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.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.8 / Method: unknown / Details: pH is adjusted to 7.8 with NaOH
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMBicine11
21 mMNa-EDTA11
30.8-1.5 mMspermine11
412 %PEG800011

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 30, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 25385 / % possible obs: 74.2 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.099
Reflection
*PLUS
Num. measured all: 179673 / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 43.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.302 -6.7 %
Rwork0.217 --
obs0.217 22351 67.2 %
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4887 0 17 14 4918
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.86
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.58
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 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.194 / Rfactor Rfree: 0.306
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.19
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.58

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