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- PDB-1v5x: Crystal structure of Phosphoribosyl anthranilate isomerase from T... -

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Basic information

Entry
Database: PDB / ID: 1v5x
TitleCrystal structure of Phosphoribosyl anthranilate isomerase from Thermus Thermophilus
ComponentsPhosphoribosylanthranilate isomerase
KeywordsISOMERASE / alpha-beta barrel / TrpF / phosphoribosyl anthranilate isomerase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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
N-(5'-phosphoribosyl)anthranilate isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTaka, J. / Kunishima, N. / Yutani, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biochem.(Tokyo) / Year: 2005
Title: Stabilization due to dimer formation of phosphoribosyl anthranilate isomerase from Thermus thermophilus HB8: X-ray Analysis and DSC experiments.
Authors: Taka, J. / Ogasahara, K. / Jeyakanthan, J. / Kunishima, N. / Kuroishi, C. / Sugahara, M. / Yokoyama, S. / Yutani, K.
History
DepositionNov 26, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Phosphoribosylanthranilate isomerase
B: Phosphoribosylanthranilate isomerase


Theoretical massNumber of molelcules
Total (without water)43,9552
Polymers43,9552
Non-polymers00
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-9 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.205, 144.205, 144.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
DetailsThe biological assembly is a dimer generated in the asymmetric unit.

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Components

#1: Protein Phosphoribosylanthranilate isomerase / / PRA isomerase


Mass: 21977.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: UniProt: P83825, phosphoribosylanthranilate isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.92 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.1
Details: Isopropanol, Sodium Acetate, pH 5.1, microbatch, temperature 293K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
129.63 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
30.2 M1dropNaCl
427.5 %iso-propanol1reservoir
50.1 Msodium acetate1reservoirpH5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 3, 2003 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. all: 35156 / Num. obs: 35156 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 29.43 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.076 / Net I/σ(I): 9.92
Reflection shellResolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 3 / Num. unique all: 3404 / Rsym value: 0.698 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 307402 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NSJ

1nsj


Resolution: 2→35 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1749 -RANDOM
Rwork0.262 ---
all0.264 35100 --
obs0.264 35100 99.8 %-
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 0 301 3357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.361 199 -
Rwork0.35 --
obs-4273 99.4 %
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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