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- PDB-4tx9: Crystal structure of HisAp from Streptomyces sviceus with degrade... -

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Basic information

Entry
Database: PDB / ID: 4tx9
TitleCrystal structure of HisAp from Streptomyces sviceus with degraded ProFAR
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
AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / Phosphoribosyl isomerase A
Similarity search - Component
Biological speciesStreptomyces sviceus ATCC 29083 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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
DepositionJul 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _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 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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: Phosphoribosyl isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7424
Polymers26,2121
Non-polymers5303
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.546, 72.546, 143.286
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: 26212.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sviceus ATCC 29083 (bacteria)
Gene: priA, hisA, SSEG_10012 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: B5I4P8
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AMZ / AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / AICAR / AICA ribonucleotide


Mass: 338.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N4O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 3.61 Å3/Da / Density % sol: 65.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M NaCl, 0.1 M imidazole/HCl, 0.4 M Na2HPO4/1.6 M K2HPO4, 10mg/ml protein, 2 mM ProFAR

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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: 51524 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 20.31 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 27.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.97 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1613)refinement
HKL-3000phasing
HKL-3000data collection
HKL-3000data scaling
HKL-3000data reduction
SHELXmodel building
MLPHAREphasing
DMmodel building
ARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→26.84 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 16.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1805 1319 2.56 %random
Rwork0.1521 ---
obs0.1529 51456 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→26.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 32 336 2187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141930
X-RAY DIFFRACTIONf_angle_d1.6212633
X-RAY DIFFRACTIONf_dihedral_angle_d14.865704
X-RAY DIFFRACTIONf_chiral_restr0.062305
X-RAY DIFFRACTIONf_plane_restr0.008345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.660.26391470.22945457X-RAY DIFFRACTION99
1.66-1.740.25771330.20515468X-RAY DIFFRACTION100
1.74-1.830.21221570.17265487X-RAY DIFFRACTION100
1.83-1.940.20591410.15455504X-RAY DIFFRACTION100
1.94-2.090.17761480.1495516X-RAY DIFFRACTION100
2.09-2.30.17891350.13645571X-RAY DIFFRACTION100
2.3-2.640.16541420.14435602X-RAY DIFFRACTION100
2.64-3.320.17971490.15635658X-RAY DIFFRACTION100
3.32-26.840.16531670.14255874X-RAY DIFFRACTION99
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)
13.4301-0.35050.22142.58580.32761.77860.2206-0.5018-0.65320.7067-0.17450.00780.31780.2948-0.11310.3179-0.0701-0.07080.25430.04560.235135.82154.370231.7763
21.55070.44730.3383.504-0.06081.63380.02250.2291-0.1095-0.17680.002-0.0706-0.04840.0775-0.02520.1085-0.0019-0.01910.1809-0.03460.094335.430415.149814.4254
35.88674.4703-1.0933.4889-1.45274.1893-0.30350.58950.3573-0.37870.41780.9132-0.1603-0.6204-0.1170.15940.0206-0.04630.2855-0.03360.221723.708917.397211.2596
42.1088-0.57330.21062.26280.45861.4264-0.0142-0.0441-0.02790.0053-0.1320.19690.0004-0.22860.15480.101-0.0148-0.01750.2064-0.03970.16622.794919.109622.9515
55.37610.6402-0.02573.0984-0.24762.2446-0.1684-0.4756-0.07960.1243-0.02990.4852-0.0373-0.55350.17990.1293-0.00730.00480.2871-0.0750.184721.225222.290231.2096
64.46290.45733.29194.66770.72186.4739-0.17830.14410.3625-0.20410.0346-0.0339-0.3433-0.03130.14720.1625-0.0211-0.0360.13980.00020.182836.77230.757327.9555
71.92793.9028-0.36217.9013-0.78985.73650.2472-0.66770.62080.5237-0.32290.6463-0.4142-0.54310.13730.2192-0.00960.02160.2636-0.08320.209329.331126.817540.2765
81.43650.2177-0.06291.90840.63942.17440.0633-0.0586-0.15530.21090.0207-0.16910.18790.0667-0.06230.1425-0.0144-0.04060.1392-0.00730.15340.426411.660430.2264
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 114 )
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 135 )
6X-RAY DIFFRACTION6chain 'A' and (resid 136 through 151 )
7X-RAY DIFFRACTION7chain 'A' and (resid 152 through 162 )
8X-RAY DIFFRACTION8chain 'A' and (resid 163 through 245 )

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