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- PDB-1jcm: TRPC STABILITY MUTANT CONTAINING AN ENGINEERED DISULPHIDE BRIDGE ... -

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Basic information

Entry
Database: PDB / ID: 1jcm
TitleTRPC STABILITY MUTANT CONTAINING AN ENGINEERED DISULPHIDE BRIDGE AND IN COMPLEX WITH A CDRP-RELATED SUBSTRATE
ComponentsINDOLE-3-GLYCEROL-PHOSPHATE SYNTHASE
KeywordsLYASE / beta-alpha-barrel / disulphide bridge / stability mutant
Function / homology
Function and homology information


phosphoribosylanthranilate isomerase / indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / L-tryptophan biosynthetic process
Similarity search - Function
N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain / N-(5'phosphoribosyl)anthranilate (PRA) isomerase / Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel ...N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain / N-(5'phosphoribosyl)anthranilate (PRA) isomerase / Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-137 / PHOSPHATE ION / : / Tryptophan biosynthesis protein TrpCF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIvens, A. / Mayans, O. / Szadkowski, H. / Wilmanns, M. / Kirschner, K.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Stabilization of a (betaalpha)8-barrel protein by an engineered disulfide bridge.
Authors: Ivens, A. / Mayans, O. / Szadkowski, H. / Jurgens, C. / Wilmanns, M. / Kirschner, K.
History
DepositionJun 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_special_symmetry / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: INDOLE-3-GLYCEROL-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8378
Polymers28,9161
Non-polymers9217
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: INDOLE-3-GLYCEROL-PHOSPHATE SYNTHASE
hetero molecules

P: INDOLE-3-GLYCEROL-PHOSPHATE SYNTHASE
hetero molecules

P: INDOLE-3-GLYCEROL-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,51124
Polymers86,7483
Non-polymers2,76321
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area10590 Å2
ΔGint-123 kcal/mol
Surface area28080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.638, 81.638, 156.745
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Cell settinghexagonal
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11P-705-

PO4

21P-705-

PO4

31P-702-

PO4

41P-703-

PO4

51P-703-

PO4

61P-704-

PO4

71P-704-

PO4

81P-708-

HOH

91P-800-

HOH

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Components

#1: Protein INDOLE-3-GLYCEROL-PHOSPHATE SYNTHASE / E.C.4.1.1.48 / IGPS / TRYPTOPHAN BIOSYNTHESIS PROTEIN TRPCF


Mass: 28916.039 Da / Num. of mol.: 1
Fragment: N-TERMINAL DOMAIN (1-259 AA) OF THE BIFUNCTIONAL ENZYME ANTHRANILATE ISOMERASE, IGPS:PRAI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21A(+)-ECTRPC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 775124, UniProt: P00909*PLUS, indole-3-glycerol-phosphate synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-137 / 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE


Mass: 351.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18NO9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50 mM potassium phosphate pH 5.0, 1.2 M ammonium sulphate, 5 mM EDTA, pH 5.0, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Temperature: 8 ℃ / Details: Wilmanns, M., (1990) Protein Eng., 3, 173. / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.05 Mpotassium phosphate1droppH7.5
20.005 MEDTA1drop
30.002 M1,4-dithioerythritol1drop
40.02 %(w/v)1dropNaN3
510-15 mg/mlprotein1drop
60.05 Mpotassium phosphate1reservoirpH5.0
71.2 Mammonium sulfate1reservoir
80.005 MEDTA1reservoir
90.002 M1,4-dithioerythritol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.911 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 17306 / Redundancy: 8.8 % / Biso Wilson estimate: 52.7 Å2 / Rsym value: 0.041 / Net I/σ(I): 24.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 935 / Rsym value: 0.25
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 93.7 % / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 78 % / Rmerge(I) obs: 0.25

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.319 1099 6.5 %random
Rwork0.241 ---
obs-16944 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7 Å2-6.4 Å20 Å2
2---2.7 Å20 Å2
3---5.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 53 135 2221
LS refinement shellResolution: 2.1→2.2 Å /
RfactorNum. reflection
Rfree0.49 93
Rwork0.44 -
obs-1407
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.44

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