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- PDB-4x2r: Crystal structure of PriA from Actinomyces urogenitalis -

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Basic information

Entry
Database: PDB / ID: 4x2r
TitleCrystal structure of PriA from Actinomyces urogenitalis
Components1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
KeywordsISOMERASE / TIM barrel / tryptophan/histidine synthesis / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


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 / 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
PHOSPHATE ION / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Similarity search - Component
Biological speciesActinomyces urogenitalis DSM 15434 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsMICHALSKA, K. / VERDUZCO-CASTRO, E.A. / ENDRES, M. / BARONA-GOMEZ, F. / JOACHIMIAK, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: Elife / Year: 2017
Title: Evolution of substrate specificity in a retained enzyme driven by gene loss.
Authors: Juarez-Vazquez, A.L. / Edirisinghe, J.N. / Verduzco-Castro, E.A. / Michalska, K. / Wu, C. / Noda-Garcia, L. / Babnigg, G. / Endres, M. / Medina-Ruiz, S. / Santoyo-Flores, J. / Carrillo- ...Authors: Juarez-Vazquez, A.L. / Edirisinghe, J.N. / Verduzco-Castro, E.A. / Michalska, K. / Wu, C. / Noda-Garcia, L. / Babnigg, G. / Endres, M. / Medina-Ruiz, S. / Santoyo-Flores, J. / Carrillo-Tripp, M. / Ton-That, H. / Joachimiak, A. / Henry, C.S. / Barona-Gomez, F.
History
DepositionNov 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5106
Polymers25,9091
Non-polymers6015
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.020, 76.020, 43.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase / Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase


Mass: 25909.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomyces urogenitalis DSM 15434 (bacteria)
Gene: hisA, HMPREF0058_1848 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21) Gold(DE3)
References: UniProt: C0W7K4, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Li2SO4, 0.1 M CAPS:NaOH pH 10.5, 1.2 M/NaH2PO4, 0.8 M K2HPO4, cryo 2.4 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.05→30 Å / Num. obs: 114288 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.35
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.88 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VZW

1vzw


Resolution: 1.05→28.531 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.49 / Stereochemistry target values: ML / Details: Hydrogen atoms have been added in riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.141 1145 1 %random
Rwork0.1226 ---
obs0.1228 114252 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→28.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 34 295 2095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141978
X-RAY DIFFRACTIONf_angle_d1.6032718
X-RAY DIFFRACTIONf_dihedral_angle_d13.315720
X-RAY DIFFRACTIONf_chiral_restr0.101318
X-RAY DIFFRACTIONf_plane_restr0.009364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0501-1.09790.22121510.190913578X-RAY DIFFRACTION96
1.0979-1.15580.14461320.131214172X-RAY DIFFRACTION100
1.1558-1.22820.10781620.100714143X-RAY DIFFRACTION100
1.2282-1.3230.12881540.090414128X-RAY DIFFRACTION100
1.323-1.45610.10621280.085214204X-RAY DIFFRACTION100
1.4561-1.66680.1091460.087614231X-RAY DIFFRACTION100
1.6668-2.09990.11261380.119214259X-RAY DIFFRACTION100
2.0999-28.54110.17261340.139914392X-RAY DIFFRACTION99

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