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- PDB-1vzw: Crystal structure of the bifunctional protein Pria -

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Basic information

Entry
Database: PDB / ID: 1vzw
TitleCrystal structure of the bifunctional protein Pria
ComponentsPHOSPHORIBOSYL ISOMERASE A
KeywordsISOMERASE / HISTIDINE BIOSYNTHESIS / TRYPTOPHAN BIOSYNTHESIS
Function / homology
Function and homology information


phosphoribosylanthranilate isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity / phosphoribosylanthranilate isomerase activity / histidine biosynthetic process / tryptophan biosynthetic process / cytoplasm
Similarity search - Function
HisA/PriA, Actinobacteria / Histidine biosynthesis, HisA-like / HisA/PriA, bacterial-type / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Phosphoribosyl isomerase A
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKuper, J. / Wilmanns, M.
CitationJournal: Embo Rep. / Year: 2005
Title: Two-Fold Repeated (Beta-Alpha)(4) Half-Barrels May Provide a Molecular Tool for Dual Substrate Specificity
Authors: Kuper, J. / Doenges, C. / Wilmanns, M.
History
DepositionMay 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHORIBOSYL ISOMERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7874
Polymers25,5031
Non-polymers2843
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.473, 64.473, 102.869
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PHOSPHORIBOSYL ISOMERASE A / 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE ...1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE / PHOSPHORIBOSYLFORMIMINO-5-AMINOIMIDAZOLE CARBOXAMIDE RIBOTIDE ISOMERASE / N-(5'-PHOSPHORIBOSYL)ANTHRANILATE ISOMERASE / PRAI


Mass: 25502.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Plasmid: PTYB4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / Variant (production host): NEB IMPACT CN
References: UniProt: P16250, D-lyxose ketol-isomerase, phosphoribosylanthranilate isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPRAI IS INVOLVED IN BOTH THE HISTIDINE AND TRYPTOPHAN BIOSYNTHETIC PATHWAYS. MEMBER OF THE ...PRAI IS INVOLVED IN BOTH THE HISTIDINE AND TRYPTOPHAN BIOSYNTHETIC PATHWAYS. MEMBER OF THE HISA/HISF FAMILY OF PROTEINS.

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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: 2.5 Å3/Da / Density % sol: 49.6 %
Crystal growpH: 5.5 / Details: 1.6 M NH4SO4 PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.813
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 1.7→34.3 Å / Num. obs: 27751 / % possible obs: 99.7 % / Redundancy: 3.93 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.4463
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.98 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.41 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMV. 6.2.3data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H5Y

1h5y


Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.165 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE CHAIN ATOMS WERE DELETED.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1167 5 %RANDOM
Rwork0.164 ---
obs-22242 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 13.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1633 0 16 226 1875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211680
X-RAY DIFFRACTIONr_bond_other_d0.0020.021569
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.982289
X-RAY DIFFRACTIONr_angle_other_deg0.79833629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0515227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021899
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02312
X-RAY DIFFRACTIONr_nbd_refined0.2010.2303
X-RAY DIFFRACTIONr_nbd_other0.240.21780
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.2990
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2161
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.13451108
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.17661756
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2616572
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0037.5530
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.24 79
Rwork0.196 1638
Refinement TLS params.Method: refined / Origin x: 22.234 Å / Origin y: 22.107 Å / Origin z: 29.669 Å
111213212223313233
T0.0197 Å20.0203 Å2-0.0012 Å2-0.0228 Å2-0.0081 Å2--0.0253 Å2
L0.1299 °2-0.0963 °20.0892 °2-0.0168 °20.0406 °2--0.8272 °2
S0.0042 Å °0.001 Å °-0.013 Å °0.0079 Å °-0.0254 Å °-0.0201 Å °-0.0218 Å °-0.1412 Å °0.0212 Å °

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