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- PDB-1nsj: CRYSTAL STRUCTURE OF PHOSPHORIBOSYL ANTHRANILATE ISOMERASE FROM T... -

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Basic information

Entry
Database: PDB / ID: 1nsj
TitleCRYSTAL STRUCTURE OF PHOSPHORIBOSYL ANTHRANILATE ISOMERASE FROM THERMOTOGA MARITIMA
ComponentsPHOSPHORIBOSYL ANTHRANILATE ISOMERASE
KeywordsISOMERASE / PHOSPHORIBOSYL ANTHRANILATE ISOMERASE / THERMOSTABILITY
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
PHOSPHATE ION / N-(5'-phosphoribosyl)anthranilate isomerase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsHennig, M. / Jansonius, J.N.J.
Citation
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.
Authors: Hennig, M. / Sterner, R. / Kirschner, K. / Jansonius, J.N.
#1: Journal: Protein Sci. / Year: 1996
Title: Phosphoribosyl Anthranilate Isomerase from Thermotoga Maritima is an Extremely Stable and Active Homodimer
Authors: Sterner, R. / Kleemann, G.R. / Szadkowski, H. / Lustig, A. / Hennig, M. / Kirschner, K.
History
DepositionSep 13, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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)23,1662
Polymers23,0711
Non-polymers951
Water1,910106
1
A: PHOSPHORIBOSYL ANTHRANILATE ISOMERASE
hetero molecules

A: PHOSPHORIBOSYL ANTHRANILATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3314
Polymers46,1412
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)68.400, 68.400, 185.400
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 / PRAI


Mass: 23070.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TRPF / Plasmid: PQE-60 / Gene (production host): TRPF / Production host: Escherichia coli (E. coli)
References: UniProt: Q56320, phosphoribosylanthranilate isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.71 Å3/Da / Density % sol: 45 % / Description: HEAVY ATOM DERIVATIVE PHASING
Crystal growpH: 7.5
Details: PROTEIN 19.4 MG/ML IN 0.05 M POTASSIUM PHOSPHATE PH 7.5, 1MM EDTA, 0.4 MM DTT MIXED WITH RESERVOIR 1:1 CONTAINING 1.5-2.1 M AMMONIUM SULFATE, 10 MM COCL2, 0.1 M MES PH 6.5,
PH range: 6.5-7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
119.4 mg/mlprotein1drop
250 mMpotassium phosphate1drop
31 mMEDTA1drop
40.4 mMdithiothreitol1drop
51.5-2.1 Mammonium sulfate1reservoir
610 mM1reservoirCoCl2
70.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 9, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 17903 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.4 / % possible all: 96.2
Reflection
*PLUS
Num. measured all: 118018
Reflection shell
*PLUS
% possible obs: 96.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2→15 Å / σ(F): 0
Details: RESIDUES 129 - 136 ARE IN THE MODEL WITH OCCUPANCIES = 0, BECAUSE THERE IS NO ELECTRON DENSITY FOR THESE RESIDUES; THEY WERE BUILT STEREOCHEMICALLY ONLY.
RfactorNum. reflection% reflection
Rfree0.243 -10 %
Rwork0.192 --
obs0.192 17833 98.8 %
Displacement parametersBiso mean: 32.1 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1561 0 5 106 1672
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 81 10 %
Rwork0.373 720 -
obs--94.4 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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