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- PDB-6t1b: Crystal structure of YlmD from Geobacillus stearothermophilus in ... -

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Basic information

Entry
Database: PDB / ID: 6t1b
TitleCrystal structure of YlmD from Geobacillus stearothermophilus in complex with inosine
ComponentsYlmD
KeywordsHYDROLASE / Purine metabolism / enzyme / deaminase / phosphorylase / nucleoside salvage / zinc-binding protein
Function / homology
Function and homology information


S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / adenosine deaminase / adenosine deaminase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / copper ion binding
Similarity search - Function
CNF1/YfiH-like putative cysteine hydrolases / CNF1/YfiH-like putative cysteine hydrolases / Multi-copper polyphenol oxidoreductase / Multi-copper polyphenol oxidoreductase superfamily / Multi-copper polyphenol oxidoreductase laccase / Cytotoxic necrotizing factor-like, catalytic / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSINE / Purine nucleoside phosphorylase YlmD
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsReikine, S. / Modis, Y.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Wellcome Trust101908/Z/13/Z United Kingdom
Wellcome Trust217191/Z/19/Z United Kingdom
Wellcome Trust106260/Z/14/Z United Kingdom
European Research Council (ERC)HORIZON2020/ERC 648889 United Kingdom
European Research Council (ERC)FP7/2007-2013 260961 United Kingdom
CitationJournal: Cell / Year: 2020
Title: FAMIN Is a Multifunctional Purine Enzyme Enabling the Purine Nucleotide Cycle.
Authors: Cader, M.Z. / de Almeida Rodrigues, R.P. / West, J.A. / Sewell, G.W. / Md-Ibrahim, M.N. / Reikine, S. / Sirago, G. / Unger, L.W. / Iglesias-Romero, A.B. / Ramshorn, K. / Haag, L.M. / ...Authors: Cader, M.Z. / de Almeida Rodrigues, R.P. / West, J.A. / Sewell, G.W. / Md-Ibrahim, M.N. / Reikine, S. / Sirago, G. / Unger, L.W. / Iglesias-Romero, A.B. / Ramshorn, K. / Haag, L.M. / Saveljeva, S. / Ebel, J.F. / Rosenstiel, P. / Kaneider, N.C. / Lee, J.C. / Lawley, T.D. / Bradley, A. / Dougan, G. / Modis, Y. / Griffin, J.L. / Kaser, A.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: 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.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: YlmD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3344
Polymers29,9351
Non-polymers3993
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-37 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.556, 48.483, 134.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein YlmD


Mass: 29934.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P84138
#2: Chemical ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 6000, 0.5 M NaCl, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 9, 2018 / Details: Horizontal and vertical mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→45.62 Å / Num. obs: 85886 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.053 / Net I/σ(I): 12.4
Reflection shellResolution: 1.2→1.243 Å / Redundancy: 6.3 % / Rmerge(I) obs: 3.571 / Num. unique all: 8462 / Num. unique obs: 12741 / CC1/2: 0.377 / Rpim(I) all: 1.521 / Rrim(I) all: 3.889 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDS11data reduction
PHASER1.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T8H

1t8h


Resolution: 1.2→45.615 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1669 4212 4.95 %
Rwork0.1528 56728 -
obs0.1535 85564 69.4 %
all-8239 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.22 Å2 / Biso mean: 23.9947 Å2 / Biso min: 8.58 Å2
Refinement stepCycle: final / Resolution: 1.2→45.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 33 208 2312
Biso mean--35.16 32.85 -
Num. residues----271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.21970.2594270.274853614
1.2197-1.24070.2562340.266562316
1.2407-1.26330.2298330.249270918
1.2633-1.28760.2004430.243280921
1.2876-1.31390.2194570.225998826
1.3139-1.34240.2595660.2374126033
1.3424-1.37370.1892810.23149339
1.3737-1.4080.2374910.2253180547
1.408-1.44610.25391340.2169218557
1.4461-1.48860.23841620.2214311880
1.4886-1.53670.24582140.2151380999
1.5367-1.59160.20021840.19523878100
1.5916-1.65530.17432180.1733844100
1.6553-1.73070.17922150.16233901100
1.7307-1.82190.15772070.15633876100
1.8219-1.93610.15612000.14013896100
1.9361-2.08560.14251840.12913942100
2.0856-2.29540.13371960.13483936100
2.2954-2.62760.15432000.13953942100
2.6276-3.31030.14551880.14174015100
3.3103-45.610.17062230.14394163100

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