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- PDB-4w9t: Crystal structure of HisAP from Streptomyces sp. Mg1 -

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Basic information

Entry
Database: PDB / ID: 4w9t
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 / L-histidine biosynthetic process / L-tryptophan biosynthetic process / cytoplasm
Similarity search - Function
HisA/PriA, Actinobacteria / HisA/PriA, bacterial-type / Histidine biosynthesis, HisA-like / 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: 1.57 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
DepositionAug 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
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_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
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 / refine_hist
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)25,7155
Polymers25,3311
Non-polymers3844
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)69.332, 69.332, 126.934
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 Gold / References: UniProt: B4V386
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / 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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2 M (NH4)2SO4, 0.1 M Bis/Tris, protein 10 mg/ml, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 20, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.57→30 Å / Num. all: 43584 / Num. obs: 43584 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 34.9
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.1 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SBC-Collectdata collection
HKL-3000phasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VZW

1vzw


Resolution: 1.57→27.859 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.66 / Stereochemistry target values: ML / Details: HYDROGEN ATOMS HAVE BEEN ADDED IN RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.1835 1249 2.87 %
Rwork0.1545 --
obs0.1553 43540 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→27.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 20 227 1944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111793
X-RAY DIFFRACTIONf_angle_d1.4422446
X-RAY DIFFRACTIONf_dihedral_angle_d14.127635
X-RAY DIFFRACTIONf_chiral_restr0.06289
X-RAY DIFFRACTIONf_plane_restr0.006320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5699-1.63270.29861270.24454558X-RAY DIFFRACTION98
1.6327-1.7070.25691240.22134539X-RAY DIFFRACTION97
1.707-1.7970.22711370.19114537X-RAY DIFFRACTION97
1.797-1.90960.19331370.17474617X-RAY DIFFRACTION98
1.9096-2.0570.18961560.15914681X-RAY DIFFRACTION100
2.057-2.26390.1961410.14674730X-RAY DIFFRACTION100
2.2639-2.59130.18371240.14524782X-RAY DIFFRACTION100
2.5913-3.2640.19041360.15594815X-RAY DIFFRACTION100
3.264-27.86370.16021670.14065032X-RAY DIFFRACTION100
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)
10.7661-0.4074-0.16331.9796-0.00991.0838-0.00830.0284-0.0023-0.04410.0341-0.07630.0581-0.0037-0.03320.19430.0034-0.0090.15150.00790.178914.883516.525548.4774
24.00140.1227-1.24492.0569-2.74754.28950.17870.15290.0053-0.2874-0.19790.08670.22360.1686-0.01830.25860.0259-0.03990.2084-0.00130.14514.409414.870832.2711
30.81360.00880.17412.03170.72453.10020.07870.12130.0197-0.18730.03880.144-0.053-0.1881-0.1020.18270.004-0.02120.15720.03980.19244.87326.373339.4624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 243 )

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