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- PDB-2x30: Crystal structure of the r139n mutant of a bifunctional enzyme pria -

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Basic information

Entry
Database: PDB / ID: 2x30
TitleCrystal structure of the r139n mutant of a bifunctional enzyme pria
ComponentsPHOSPHORIBOSYL ISOMERASE A
KeywordsISOMERASE / AROMATIC AMINO ACID BIOSYNTHESIS / TRYPTOPHAN BIOSYNTHESIS / CONFORMATIONAL DIVERSITY / DUAL-SUBSTRATE SPECIFICITY / HISTIDINE BIOSYNTHESIS / LOOPS MOTION / HISA / TRPF
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: 1.95 Å
AuthorsNoda-Garcia, L. / Camacho-Zarco, A.R. / Verdel-Aranda, K. / Wright, H. / Soberon, X. / Fulop, V. / Barona-Gomez, F.
CitationJournal: Protein Sci. / Year: 2010
Title: Identification and Analysis of Residues Contained on Beta --> Alpha Loops of the Dual-Substrate (Betaalpha)(8) Phosphoribosyl Isomerase a (Pria) Specific for its Phosphoribosyl Anthranilate Isomerase Activity.
Authors: Noda-Garcia, L. / Camacho-Zarco, A.R. / Verdel-Aranda, K. / Wright, H. / Soberon, X. / Fulop, V. / Barona-Gomez, F.
History
DepositionJan 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2010Provider: 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
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORIBOSYL ISOMERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2553
Polymers25,0631
Non-polymers1922
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.600, 63.600, 102.900
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: 25063.154 Da / Num. of mol.: 1 / Mutation: YES
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.: 126 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 139 TO ASN

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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: BM16 / Wavelength: 1.0074
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 24, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0074 Å / Relative weight: 1
ReflectionResolution: 1.95→28 Å / Num. obs: 18061 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 23
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VEP

2vep


Resolution: 1.95→27.52 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.504 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 696 3.9 %RANDOM
Rwork0.216 ---
obs0.21816 17365 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.217 Å2
Baniso -1Baniso -2Baniso -3
1-3.1 Å21.55 Å20 Å2
2--3.1 Å20 Å2
3----4.65 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 10 126 1845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221739
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9772365
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2924.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55215278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0831513
X-RAY DIFFRACTIONr_chiral_restr0.090.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021293
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2772
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21158
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.691.51177
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13421812
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.553638
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2424.5553
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 39 -
Rwork0.359 1269 -
obs--99.85 %
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)
11.9933-1.51351.14481.3921-1.02943.7106-0.3112-0.1711-0.02330.26140.22020.0768-0.5016-0.04130.0910.10930.0552-0.0096-0.0319-0.0177-0.126323.32624.4122.858
20.8986-0.71921.14251.9655-1.71567.1429-0.1443-0.2238-0.04410.11010.10430.0524-0.6119-1.33290.040.00220.2187-0.01230.3437-0.054-0.146419.53320.57436.534
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 123
2X-RAY DIFFRACTION2A124 - 240

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