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- PDB-2vep: Crystal Structure Of The Full Length Bifunctional Enzyme Pria -

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Basic information

Entry
Database: PDB / ID: 2vep
TitleCrystal Structure Of The Full Length Bifunctional Enzyme Pria
ComponentsPHOSPHORIBOSYL ISOMERASE A
KeywordsISOMERASE / AROMATIC AMINO ACID BIOSYNTHESIS / EVOLUTION OF SUBSTRATE SPECIFICITY / TRYPTOPHAN BIOSYNTHESIS / HISTIDINE BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS / PRIA / (BETA-ALPHA)8-BARREL
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 / MAD / Resolution: 1.8 Å
AuthorsWright, H. / Noda-Garcia, L. / Ochoa-Leyva, A. / Hodgson, D.A. / Fulop, V. / Barona-Gomez, F.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: The Structure/Function Relationship of a Dual Substrate (Betaalpha)(8)-Isomerase
Authors: Wright, H. / Noda-Garcia, L. / Ochoa-Leyva, A. / Hodgson, D.A. / Fulop, V. / Barona-Gomez, F.
History
DepositionOct 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
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)25,6953
Polymers25,5031
Non-polymers1922
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.140, 65.140, 104.670
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 ...(1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE) / PRAI / PHOSPHORIBOSYLFORMIMINO-5-AMINOIMIDAZOLE CARBOXAMIDE RIBOTIDE ISOMERASE / N-(5'-PHOSPHORIBOSYL) ANTHRANILATE ISOMERASE


Mass: 25502.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Strain: SCO2050 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P16250, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPRIA IS INVOLVED IN BOTH THE HISTIDINE AND TRYPTOPHAN BIOSYNTHETIC PATHWAYS. MEMBER OF THE ...PRIA IS INVOLVED IN BOTH THE HISTIDINE AND TRYPTOPHAN BIOSYNTHETIC PATHWAYS. MEMBER OF THE HISA/TRPF 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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 4.8
Details: 1.50 M AMMONIUM SULFATE AND 100 MM SODIUM CITRATE PH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 10, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→39 Å / Num. obs: 23394 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.8→38.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.561 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 923 3.9 %RANDOM
Rwork0.18 ---
obs0.181 22471 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 10 204 1976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221792
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9812437
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2895239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15624.30672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50915290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5391514
X-RAY DIFFRACTIONr_chiral_restr0.1120.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021338
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2838
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21221
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2167
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.991.51206
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57521867
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.583659
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0214.5570
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
Rfree0.276 67
Rwork0.211 1571
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4975-0.3572-0.12340.5286-0.2391.3271-0.00410.055-0.011-0.01020.00110.05760.0337-0.07580.003-0.0093-0.0092-0.008-0.0101-0.0058-0.026324.487824.481422.6488
20.6259-0.5503-0.14060.9938-0.43641.42150.0001-0.001-0.0390.02870.03040.11790.0298-0.1391-0.0305-0.0216-0.0096-0.0019-0.0003-0.0057-0.014521.096321.393836.6743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 123
2X-RAY DIFFRACTION2A124 - 240

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