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- PDB-1k8z: CRYSTAL STRUCTURE OF THE TRYPTOPHAN SYNTHASE BETA-SER178PRO MUTAN... -

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Basic information

Entry
Database: PDB / ID: 1k8z
TitleCRYSTAL STRUCTURE OF THE TRYPTOPHAN SYNTHASE BETA-SER178PRO MUTANT COMPLEXED WITH N-[1H-INDOL-3-YL-ACETYL]GLYCINE ACID
Components(TRYPTOPHAN SYNTHASE ...) x 2
KeywordsLYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-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
N-[1H-INDOL-3-YL-ACETYL]GLYCINE ACID / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWeyand, M. / Schlichting, I. / Marabotti, A. / Mozzarelli, A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of the beta Ser178--> Pro mutant of tryptophan synthase. A "knock-out" allosteric enzyme.
Authors: Weyand, M. / Schlichting, I. / Herde, P. / Marabotti, A. / Mozzarelli, A.
History
DepositionOct 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)71,9995
Polymers71,4972
Non-polymers5023
Water6,792377
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)143,99810
Polymers142,9934
Non-polymers1,0056
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)184.420, 61.035, 67.534
Angle α, β, γ (deg.)90.00, 94.69, 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) / Gene: TRPA/TRPB / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase
#2: Protein TRYPTOPHAN SYNTHASE BETA CHAIN


Mass: 42797.723 Da / Num. of mol.: 1 / Mutation: S178P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: TRPA/TRPB / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 4 types, 380 molecules

#3: Chemical ChemComp-IAG / N-[1H-INDOL-3-YL-ACETYL]GLYCINE ACID


Mass: 232.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2O3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growpH: 7.8 / Details: pH 7.80
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 mMsodium bicine1droppH7.8
310 mMsodium-EDTA1drop
41 mMdithiothreitol1drop
50.020 mMpyridoxal 5-phosphate1drop
69-12 %PEG80001reservoir
71.5 mMspermine1reservoir
81 mMEDTA1reservoir
950 mMBicine1reservoirpH7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→43.4 Å / Num. obs: 79408 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 2.597 % / Rsym value: 0.063 / Net I/σ(I): 9.29
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.354 % / Mean I/σ(I) obs: 2.11 / Rsym value: 0.334 / % possible all: 96.1
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 79508 / Num. measured all: 206209 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 96.1 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.11

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Processing

Software
NameClassification
CNSrefinement
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QOP

1qop


Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26491 4063 5.1 %RANDOM
Rwork0.20947 ---
obs0.21228 75314 96.4 %-
Displacement parametersBiso mean: 25.914 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4925 0 33 377 5335
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0860.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1670.5
X-RAY DIFFRACTIONp_mcbond_it3.8561.5
X-RAY DIFFRACTIONp_mcangle_it4.7662
X-RAY DIFFRACTIONp_scbond_it6.4893
X-RAY DIFFRACTIONp_scangle_it9.0084.5
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.480.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1720.5
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.7 Å / % reflection Rfree: 5 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg6.358

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