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- PDB-4u28: Crystal structure of apo Phosphoribosyl isomerase A from Streptom... -

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Basic information

Entry
Database: PDB / ID: 4u28
TitleCrystal structure of apo Phosphoribosyl isomerase A from Streptomyces sviceus ATCC 29083
ComponentsPhosphoribosyl isomerase A
KeywordsISOMERASE / 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
PHOSPHATE ION / Phosphoribosyl isomerase A
Similarity search - Component
Biological speciesStreptomyces sviceus ATCC 29083 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.33 Å
AuthorsChang, C. / Verduzco-Castro, E.A. / Endres, M. / Barona-Gomez, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
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 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Feb 11, 2015Group: Other
Revision 1.3Nov 8, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
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 / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)26,1303
Polymers25,9401
Non-polymers1902
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.111, 69.111, 175.036
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

21A-529-

HOH

Detailsbiological unit is the same as asym.

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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: 25939.881 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 (DE3) pGrow7-K / References: UniProt: B5I4P8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 1.8M Na/K phosphate

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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: Nov 2, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. all: 60963 / Num. obs: 57655 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.071 / Χ2: 0.965 / Net I/av σ(I): 26.535 / Net I/σ(I): 10.9 / Num. measured all: 526343
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.33-1.356.70.8341.8227550.76597.9
1.35-1.387.50.74228380.78699.4
1.38-1.48.20.67928340.78599.6
1.4-1.438.40.57628580.7899.8
1.43-1.468.40.46728370.79899.9
1.46-1.58.40.38528630.79899.9
1.5-1.548.30.29328720.81599.9
1.54-1.588.20.25228750.82399.9
1.58-1.628.20.20728450.8399.9
1.62-1.688.20.18128590.81599.8
1.68-1.748.30.1529060.84199.8
1.74-1.818.50.1228510.8799.7
1.81-1.898.70.128870.91199.5
1.89-1.999.10.08228870.95799.4
1.99-2.119.60.07629001.10499.3
2.11-2.2710.20.07728841.34999
2.27-2.5110.07829301.49198.6
2.5-2.8711.90.06329341.30198.2
2.87-3.6112.20.0529481.08897.5
3.61-5011.90.04430920.81694.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.33→26.63 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.412 / SU ML: 0.026 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.043
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.151 2793 5.1 %RANDOM
Rwork0.1271 52240 --
obs0.1283 55033 94.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.37 Å2 / Biso mean: 16.247 Å2 / Biso min: 8.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.33→26.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 10 351 2077
Biso mean--20.51 29.89 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191904
X-RAY DIFFRACTIONr_bond_other_d0.0010.021831
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.9872607
X-RAY DIFFRACTIONr_angle_other_deg0.74734207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1365263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.97424.07481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76815309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.431518
X-RAY DIFFRACTIONr_chiral_restr0.070.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022254
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
X-RAY DIFFRACTIONr_mcbond_it1.3051.3451019
X-RAY DIFFRACTIONr_mcbond_other1.2381.341018
X-RAY DIFFRACTIONr_mcangle_it1.5512.0151293
X-RAY DIFFRACTIONr_rigid_bond_restr1.16633735
X-RAY DIFFRACTIONr_sphericity_free30.031558
X-RAY DIFFRACTIONr_sphericity_bonded8.22153998
LS refinement shellResolution: 1.33→1.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 143 -
Rwork0.225 2428 -
all-2571 -
obs--61.16 %

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