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- PDB-6nko: Crystal structure of ForH -

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Basic information

Entry
Database: PDB / ID: 6nko
TitleCrystal structure of ForH
ComponentsForH
KeywordsUNKNOWN FUNCTION / Apo structure / Formycin A
Function / homology
Function and homology information


phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process / cytosol
Similarity search - Function
Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AICAR transformylase
Similarity search - Component
Biological speciesStreptomyces kaniharaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsZheng, J. / Irani, S. / Zhang, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
Welch Foundation United States
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Identification of the Formycin A Biosynthetic Gene Cluster from Streptomyces kaniharaensis Illustrates the Interplay between Biological Pyrazolopyrimidine Formation and de Novo Purine Biosynthesis.
Authors: Wang, S.A. / Ko, Y. / Zeng, J. / Geng, Y. / Ren, D. / Ogasawara, Y. / Irani, S. / Zhang, Y. / Liu, H.W.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: ForH
B: ForH
C: ForH
D: ForH


Theoretical massNumber of molelcules
Total (without water)92,7704
Polymers92,7704
Non-polymers00
Water2,270126
1
A: ForH


Theoretical massNumber of molelcules
Total (without water)23,1921
Polymers23,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ForH


Theoretical massNumber of molelcules
Total (without water)23,1921
Polymers23,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ForH


Theoretical massNumber of molelcules
Total (without water)23,1921
Polymers23,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ForH


Theoretical massNumber of molelcules
Total (without water)23,1921
Polymers23,1921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: ForH
D: ForH


Theoretical massNumber of molelcules
Total (without water)46,3852
Polymers46,3852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-21 kcal/mol
Surface area16110 Å2
MethodPISA
6
B: ForH
C: ForH


Theoretical massNumber of molelcules
Total (without water)46,3852
Polymers46,3852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-24 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.218, 111.401, 163.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
ForH


Mass: 23192.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces kaniharaensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V8H038*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 22, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 41344 / % possible obs: 100 % / Redundancy: 6.5 % / Net I/σ(I): 15.14
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 4551

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M9N

1m9n


Resolution: 2.403→48.93 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.65
RfactorNum. reflection% reflection
Rfree0.2616 1864 5 %
Rwork0.2117 --
obs0.2142 37263 89.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.403→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 0 126 5940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045915
X-RAY DIFFRACTIONf_angle_d0.6348020
X-RAY DIFFRACTIONf_dihedral_angle_d5.0713596
X-RAY DIFFRACTIONf_chiral_restr0.045910
X-RAY DIFFRACTIONf_plane_restr0.0041062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4032-2.46810.36961370.2662605X-RAY DIFFRACTION88
2.4681-2.54070.30831460.25152786X-RAY DIFFRACTION93
2.5407-2.62280.31861460.24872775X-RAY DIFFRACTION93
2.6228-2.71650.31551480.24322790X-RAY DIFFRACTION92
2.7165-2.82520.34851420.24332703X-RAY DIFFRACTION91
2.8252-2.95380.31211440.22882726X-RAY DIFFRACTION91
2.9538-3.10950.26871440.22452752X-RAY DIFFRACTION91
3.1095-3.30430.25771450.22722740X-RAY DIFFRACTION91
3.3043-3.55930.27411440.21912747X-RAY DIFFRACTION90
3.5593-3.91740.20871420.18942694X-RAY DIFFRACTION89
3.9174-4.48390.23721420.18212703X-RAY DIFFRACTION88
4.4839-5.64790.20521430.19182711X-RAY DIFFRACTION88
5.6479-48.94050.28041410.20912667X-RAY DIFFRACTION82

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