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- PDB-1a5b: CRYO-CRYSTALLOGRAPHY OF A TRUE SUBSTRATE, INDOLE-3-GLYCEROL PHOSP... -

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Basic information

Entry
Database: PDB / ID: 1a5b
TitleCRYO-CRYSTALLOGRAPHY OF A TRUE SUBSTRATE, INDOLE-3-GLYCEROL PHOSPHATE, BOUND TO A MUTANT (ALPHA D60N) TRYPTOPHAN SYNTHASE ALPHA2BETA2 COMPLEX REVEALS THE CORRECT ORIENTATION OF ACTIVE SITE ALPHA GLU 49
Components(TRYPTOPHAN SYNTHASE ...) x 2
KeywordsLYASE / CARBON-OXYGEN LYASE / MUTATION AT POSITION 60 (ASP --> ASN) IN THE A-SUBUNIT / TRUE SUBSTRATE INDOLE-3-GLYCEROL PHOSPHATE IN THE A-SUBUNIT
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
INDOLE-3-GLYCEROL PHOSPHATE / : / PYRIDOXAL-5'-PHOSPHATE / Tryptophan synthase alpha chain / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / ISOMORPHOUS / Resolution: 2 Å
AuthorsRhee, S. / Miles, E.W. / Davies, D.R.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Cryo-crystallography of a true substrate, indole-3-glycerol phosphate, bound to a mutant (alphaD60N) tryptophan synthase alpha2beta2 complex reveals the correct orientation of active site alphaGlu49.
Authors: Rhee, S. / Miles, E.W. / Davies, D.R.
History
DepositionFeb 12, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_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_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)72,2445
Polymers71,6712
Non-polymers5733
Water6,071337
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)144,48910
Polymers143,3424
Non-polymers1,1476
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)182.600, 59.700, 67.400
Angle α, β, γ (deg.)90.00, 94.60, 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: 28697.812 Da / Num. of mol.: 1 / Mutation: D60N
Source method: isolated from a genetically manipulated source
Details: LIGAND INDOLE-3-GLYCEROL PHOSPHATE BOUND TO THE A-SUBUNIT
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Cell line (production host): CB149 / Gene (production host): TRPA/TRPB / Production host: Escherichia coli (E. coli) / References: UniProt: P00929, tryptophan synthase
#2: Protein TRYPTOPHAN SYNTHASE (BETA CHAIN)


Mass: 42973.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LIGAND INDOLE-3-GLYCEROL PHOSPHATE BOUND TO THE A-SUBUNIT
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Cell line (production host): CB149 / Gene (production host): TRPA/TRPB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase

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Non-polymers , 4 types, 340 molecules

#3: Chemical ChemComp-IGP / INDOLE-3-GLYCEROL PHOSPHATE


Mass: 287.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14NO6P
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#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.: 337 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.8
Details: 50MM NABICINE (PH 7.8), 1MM NA-EDTA, 0.8-1.5MM SPERMINE, 12% PEG8000
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMN,N-bis(2-hydroxyethyl)glycine11
21 mMNa-EDTA11
30.8-1.5 mMspermine11
412 %PEG800011
511NaOH

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 45501 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.057 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.463 / % possible all: 77.8
Reflection
*PLUS
Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 79.4 % / Rmerge(I) obs: 0.424

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: ISOMORPHOUS / Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.283 -8.3 %X-PLOR SCRIPT
Rwork0.22 ---
obs0.22 39737 82.2 %-
Displacement parametersBiso mean: 26.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4831 0 35 337 5203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.86
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
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
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.332 -5.3 %
Rwork0.291 2777 -
obs--51.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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