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- PDB-1k7e: CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 1k7e
TitleCRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE 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: 2.3 Å
AuthorsWeyand, M. / Schlichting, I. / Marabotti, A. / Mozzarelli, A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structures of a new class of allosteric effectors complexed to tryptophan synthase.
Authors: Weyand, M. / Schlichting, I. / Marabotti, A. / Mozzarelli, A.
History
DepositionOct 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 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 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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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)71,9895
Polymers71,4862
Non-polymers5023
Water4,270237
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)143,97810
Polymers142,9734
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)182.651, 59.081, 67.300
Angle α, β, γ (deg.)90.00, 94.55, 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: 42787.688 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: P0A2K1, tryptophan synthase

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Non-polymers , 4 types, 240 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.: 237 / 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: 2.48 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.8 / Details: PEG 8000, 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 mMdithioerythritol1drop
50.020 mMpyridoxal phosphate1drop
69-12 %PEG80001reservoir
71.5 mMspermine1reservoir
81 mMEDTA1reservoir
950 mMsodium bicine1reservoirpH7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2000 / Details: PREMIRROR, BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 3.26 % / Rsym value: 0.058 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.183 / % possible all: 88.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 35 Å / Num. obs: 29178 / Observed criterion σ(I): -3 / Num. measured all: 95120 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 88.7 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 2.2

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Processing

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

1qop


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 -5.1 %RANDOM
Rwork0.167 ---
obs0.171 27663 91 %-
Displacement parametersBiso mean: 20.513 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20.15 Å2
2--2.54 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4943 0 33 237 5213
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0510.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.5531.5
X-RAY DIFFRACTIONp_mcangle_it3.7722
X-RAY DIFFRACTIONp_scbond_it6.4233
X-RAY DIFFRACTIONp_scangle_it8.8734.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.250.2
X-RAY DIFFRACTIONp_singtor_nbd0.2740.3
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1690.5
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: 2.3 Å / % reflection Rfree: 5 % / Rfactor obs: 0.171 / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3.45

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