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- PDB-2kzh: Three-dimensional structure of a truncated phosphoribosylanthrani... -

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Basic information

Entry
Database: PDB / ID: 2kzh
TitleThree-dimensional structure of a truncated phosphoribosylanthranilate isomerase (residues 255-384) from Escherichia coli
ComponentsTryptophan biosynthesis protein trpCFTryptophan
KeywordsISOMERASE / TIM-BARREL / TRYPTOPHAN BIOSYNTHESIS / PROTEIN EVOLUTION / SUBDOMAIN
Function / homology
Function and homology information


phosphoribosylanthranilate isomerase / indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process
Similarity search - Function
N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain / N-(5'phosphoribosyl)anthranilate (PRA) isomerase / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
Tryptophan biosynthesis protein TrpCF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsSetiyaputra, S. / Mackay, J.P. / Patrick, W.M.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: The Structure of a Truncated Phosphoribosylanthranilate Isomerase Suggests a Unified Model for Evolution of the (beta alpha)8 Barrel Fold
Authors: Setiyaputra, S. / Mackay, J.P. / Patrick, W.M.
#1: Journal: Febs J. / Year: 2005
Title: In vitro selection and characterization of a stable subdomain of phosphoribosylanthranilate isomerase.
Authors: Patrick, W.M. / Blackburn, J.M.
History
DepositionJun 17, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan biosynthesis protein trpCF


Theoretical massNumber of molelcules
Total (without water)15,1371
Polymers15,1371
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Tryptophan biosynthesis protein trpCF / Tryptophan / N-(5'-phospho-ribosyl)anthranilate isomerase / PRAI / trPRAI


Mass: 15137.026 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: trpC, b1262, JW1254 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P00909, phosphoribosylanthranilate isomerase
Sequence detailsRESIDUES 132-134 ARE ACTUALLY RESIDUES FROM A LINKER THAT CONNECTS THE MOLECULE TO THE HEXAHISTIDINE TAG

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1242D 1H-13C HSQC
1333D CBCA(CO)NH
1433D HN(CA)CB
1533D HNCO
1632D 1H-1H NOESY
1733D HBHA(CO)NH
1833D H(CCO)NH
1933D C(CO)NH
11043D (H)CCH-TOCSY
11143D (H)CCH-COSY
11233D 1H-15N NOESY
11343D 1H-13C NOESY
11443D 1H-13C NOESY aromatic
11512D 1H-1H NOESY
11633D HNHA
11723D 1H-15N TOCSY
11833D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM trPRAI-1, 20 mM HEPES-2, 100 mM sodium chloride-3, 1 mM DTT-4, 0.1 mM DSS-5, 95% H2O/5% D2O95% H2O/5% D2O
20.6-1.0 mM [U-99% 15N] trPRAI-6, 20 mM HEPES-7, 100 mM sodium chloride-8, 1 mM DTT-9, 0.1 mM DSS-10, 95% H2O/5% D2O95% H2O/5% D2O
30.6-0.8 mM [U-98% 13C; U-98% 15N] trPRAI-11, 20 mM HEPES-12, 100 mM sodium chloride-13, 1 mM DTT-14, 0.1 mM DSS-15, 95% H2O/5% D2O95% H2O/5% D2O
40.7 mM [U-98% 13C; U-98% 15N] trPRAI-16, 20 mM HEPES-17, 100 mM sodium chloride-18, 1 mM DTT-19, 0.1 mM DSS-20, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.8 mMtrPRAI-11
20 mMHEPES-21
100 mMsodium chloride-31
1 mMDTT-41
0.1 mMDSS-51
mMtrPRAI-6[U-99% 15N]0.6-1.02
20 mMHEPES-72
100 mMsodium chloride-82
1 mMDTT-92
0.1 mMDSS-102
mMtrPRAI-11[U-98% 13C; U-98% 15N]0.6-0.83
20 mMHEPES-123
100 mMsodium chloride-133
1 mMDTT-143
0.1 mMDSS-153
0.7 mMtrPRAI-16[U-98% 13C; U-98% 15N]4
20 mMHEPES-174
100 mMsodium chloride-184
1 mMDTT-194
0.1 mMDSS-204
Sample conditionsIonic strength: 0.1 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichautomated noe peak assignments
CYANA3Guntert, Mumenthaler and Wuthrichnoe peaks calibration
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
Sparky3.113Goddardpeak picking
Sparky3.113Goddardchemical shift assignment
TALOSTALOS+Cornilescu, Delaglio and Baxprediction of protein backbone torsion angles from nmr chemical shifts
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readwater refinement
ProcheckNMR3.5.3Laskowski and MacArthurdata analysis
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Cartesian molecular dynamics
NMR constraintsNOE constraints total: 2238 / NOE intraresidue total count: 887 / NOE medium range total count: 481 / NOE sequential total count: 487 / Hydrogen bond constraints total count: 60 / Protein other angle constraints total count: 74 / Protein phi angle constraints total count: 102 / Protein psi angle constraints total count: 102
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.013 Å / Distance rms dev error: 0.0007 Å

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