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- PDB-4x9s: CRYSTAL STRUCTURE OF HISAP FROM STREPTOMYCES SP. MG1 -

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Basic information

Entry
Database: PDB / ID: 4x9s
TitleCRYSTAL STRUCTURE OF HISAP FROM STREPTOMYCES SP. MG1
ComponentsPhosphoribosyl isomerase A
KeywordsISOMERASE / TIM-BARREL / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
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 sp. Mg1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Biochem. J. / Year: 2016
Title: Co-occurrence of analogous enzymes determines evolution of a novel ( beta alpha )8-isomerase sub-family after non-conserved mutations in flexible loop.
Authors: Verduzco-Castro, E.A. / Michalska, K. / Endres, M. / Juarez-Vazquez, A.L. / Noda-Garcia, L. / Chang, C. / Henry, C.S. / Babnigg, G. / Joachimiak, A. / Barona-Gomez, F.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.3Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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

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Assembly

Deposited unit
A: Phosphoribosyl isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8116
Polymers25,3311
Non-polymers4805
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.547, 69.547, 127.321
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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 / N-(5'-phosphoribosyl)anthranilate isomerase / Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase


Mass: 25330.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Mg1 (bacteria) / Gene: priA, hisA, SSAG_02214 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Gold / References: UniProt: B4V386
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris/HCl, pH 8.5, 1.5 M Li2SO4 and 2 mM rCdRP
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2013 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 41756 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.67
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2 / % possible all: 95.7

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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: 4W9T

4w9t


Resolution: 1.6→28.943 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.26 / Stereochemistry target values: ML / Details: HYDROGEN ATOMS HAVE BEEN ADDED IN RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 1299 3.11 %random
Rwork0.1552 ---
obs0.1562 41715 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→28.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 25 227 1996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111869
X-RAY DIFFRACTIONf_angle_d1.332552
X-RAY DIFFRACTIONf_dihedral_angle_d14.156659
X-RAY DIFFRACTIONf_chiral_restr0.055297
X-RAY DIFFRACTIONf_plane_restr0.006334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6002-1.66420.24451260.23464338X-RAY DIFFRACTION97
1.6642-1.73990.29311370.22064429X-RAY DIFFRACTION100
1.7399-1.83170.22191440.18824466X-RAY DIFFRACTION100
1.8317-1.94640.22341530.16434422X-RAY DIFFRACTION100
1.9464-2.09660.20491520.14934489X-RAY DIFFRACTION100
2.0966-2.30760.15711280.14084514X-RAY DIFFRACTION100
2.3076-2.64130.17311700.14664498X-RAY DIFFRACTION100
2.6413-3.3270.1911440.15674566X-RAY DIFFRACTION100
3.327-28.94760.17151450.14024694X-RAY DIFFRACTION97
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)
10.5724-0.4249-0.05371.68-0.07510.9841-0.0009-0.0090.0087-0.0090.0455-0.10480.0781-0.0138-0.03340.1488-0.0002-0.00490.11960.00550.168514.511317.010248.4855
21.7381.0692-1.01772.8543-1.77191.34330.0860.11690.0256-0.4544-0.1456-0.10610.2990.09650.00630.3230.0222-0.0170.16950.01760.156114.64817.459529.8784
30.61580.02690.12771.52680.08742.18030.0570.05170.0294-0.11110.08760.1412-0.0418-0.2165-0.12060.1392-0.0078-0.00560.12640.03780.18074.206728.066742.0261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 159 )
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 243 )

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