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- PDB-4wui: Crystal structure of TrpF from Jonesia denitrificans -

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Basic information

Entry
Database: PDB / ID: 4wui
TitleCrystal structure of TrpF from Jonesia denitrificans
ComponentsN-(5'-phosphoribosyl)anthranilate isomerase
KeywordsISOMERASE / TIM-BARREL / TRYPTOPHAN SYNTHESIS / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


phosphoribosylanthranilate isomerase / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process
Similarity search - Function
N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain / N-(5'phosphoribosyl)anthranilate (PRA) isomerase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / N-(5'-phosphoribosyl)anthranilate isomerase
Similarity search - Component
Biological speciesJonesia denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.09 Å
AuthorsMichalska, K. / Verduzco-Castro, E.A. / Endres, M. / Barona-Gomez, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: Biochem. J. / Year: 2016
Title: Co-occurrence of analogous enzymes determines evolution of a novel ( beta alpha )8-isomerase sub-family after non-conserved mutations in flexible loop.
Authors: Verduzco-Castro, E.A. / Michalska, K. / Endres, M. / Juarez-Vazquez, A.L. / Noda-Garcia, L. / Chang, C. / Henry, C.S. / Babnigg, G. / Joachimiak, A. / Barona-Gomez, F.
History
DepositionOct 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Refinement description
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-(5'-phosphoribosyl)anthranilate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0074
Polymers21,4311
Non-polymers5763
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.423, 64.289, 66.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N-(5'-phosphoribosyl)anthranilate isomerase / PRAI


Mass: 21431.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jonesia denitrificans (bacteria) / Strain: ATCC 14870 / DSM 20603 / CIP 55134 / Gene: trpF, Jden_0894 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD
References: UniProt: C7R2I5, phosphoribosylanthranilate isomerase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis/Tris propane:NaOH, pH 7, 2 M (NH4)2HCITRATE, no extra cryo

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.09→25 Å / Num. obs: 88243 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 32.6
Reflection shellResolution: 1.09→1.11 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.4 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000phasing
HKL-3000data scaling
SBC-Collectdata collection
SHARPphasing
ARPmodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.09→24.712 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 11.89 / Stereochemistry target values: ML
Details: Hydrogen atoms were added in riding positions. The mFo-DFc difference map shows a strong peak near His82, which is possibly a disordered citrate molecule.
RfactorNum. reflection% reflection
Rfree0.1376 1782 2.02 %
Rwork0.1279 --
obs0.1281 88155 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.09→24.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 39 260 1795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111676
X-RAY DIFFRACTIONf_angle_d1.5142326
X-RAY DIFFRACTIONf_dihedral_angle_d16.783586
X-RAY DIFFRACTIONf_chiral_restr0.092269
X-RAY DIFFRACTIONf_plane_restr0.01314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.13990.21962180.211810215X-RAY DIFFRACTION95
1.1399-1.20.15052170.145310708X-RAY DIFFRACTION100
1.2-1.27520.13532240.122310769X-RAY DIFFRACTION100
1.2752-1.37360.13612220.111810787X-RAY DIFFRACTION100
1.3736-1.51190.10842180.096210819X-RAY DIFFRACTION100
1.5119-1.73060.12082330.094210847X-RAY DIFFRACTION100
1.7306-2.18020.12732190.111310957X-RAY DIFFRACTION100
2.1802-24.71780.14462310.144611271X-RAY DIFFRACTION100

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