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- PDB-1lbm: CRYSTAL STRUCTURE OF PHOSPHORIBOSYL ANTHRANILATE ISOMERASE (PRAI)... -

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Basic information

Entry
Database: PDB / ID: 1lbm
TitleCRYSTAL STRUCTURE OF PHOSPHORIBOSYL ANTHRANILATE ISOMERASE (PRAI) IN COMPLEX WITH REDUCED 1-(O-CARBOXYPHENYLAMINO)-1-DEOXYRIBULOSE 5-PHOSPHATE (RCDRP)
ComponentsPHOSPHORIBOSYL ANTHRANILATE ISOMERASE
KeywordsISOMERASE / BETA BARREL / ligand complex / product analogue complex / tryptophan biosynthesis
Function / homology
Function and homology information


phosphoribosylanthranilate isomerase / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process
Similarity search - Function
N-(5'-phosphoribosyl)anthranilate isomerase family / 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
Chem-137 / N-(5'-phosphoribosyl)anthranilate isomerase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsHennig, M. / Sterner, R. / Kirschner, K.
Citation
Journal: Biochemistry / Year: 2002
Title: Two (betaalpha)(8)-barrel enzymes of histidine and tryptophan biosynthesis have similar reaction mechanisms and common strategies for protecting their labile substrates
Authors: Henn-Sax, M. / Thoma, R. / Schmidt, S. / Hennig, M. / Kirschner, K. / Sterner, R.
#1: Journal: Biochemistry / Year: 1997
Title: Crystal structure at 2.0 A resolution of phosphoribosyl anthranilate isomerase from the hyperthermophile Thermotoga maritima: Possible determinants of protein stability
History
DepositionApr 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: PHOSPHORIBOSYL ANTHRANILATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4222
Polymers23,0711
Non-polymers3511
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PHOSPHORIBOSYL ANTHRANILATE ISOMERASE
hetero molecules

A: PHOSPHORIBOSYL ANTHRANILATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8444
Polymers46,1412
Non-polymers7022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area4180 Å2
ΔGint-19 kcal/mol
Surface area15800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.835, 68.834, 187.163
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein PHOSPHORIBOSYL ANTHRANILATE ISOMERASE


Mass: 23070.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q56320, phosphoribosylanthranilate isomerase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM potassium phosphate , 2.1 M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
119 mg/mlprotein1drop
20.1 MMES1reservoirpH7.0
31.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 25, 1995
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 6978 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.099
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 28569

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
XDSdata reduction
X-PLORmodel building
X-PLOR3.1refinement
SCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1nsj

1nsj


Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 348 5 %random
Rwork0.17 ---
all-6978 --
obs-6978 --
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 23 69 1640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.8
Refinement
*PLUS
Highest resolution: 2.8 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

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