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- PDB-1t8h: 1.8 A CRYSTAL STRUCTURE OF AN UNCHARACTERIZED B. STEAROTHERMOPHIL... -

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Basic information

Entry
Database: PDB / ID: 1t8h
Title1.8 A CRYSTAL STRUCTURE OF AN UNCHARACTERIZED B. STEAROTHERMOPHILUS PROTEIN
ComponentsYlmD protein sequence homologue
KeywordsStructural Genomics / Unknown Function / RBSTP0554 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


adenosine deaminase / 2'-deoxyadenosine deaminase activity / S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / adenosine deaminase activity / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / 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
BETA-MERCAPTOETHANOL / Purine nucleoside phosphorylase YlmD
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsMinasov, G. / Shuvalova, L. / Mondragon, A. / Taneja, B. / Moy, S.F. / Collart, F.R. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.8 A CRYSTAL STRUCTURE OF AN UNCHARACTERIZED B. STEAROTHERMOPHILUS PROTEIN
Authors: Minasov, G. / Shuvalova, L. / Mondragon, A. / Taneja, B. / Moy, S.F. / Collart, F.R. / Anderson, W.F.
History
DepositionMay 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Remark 999sequence There was no suitable sequence database reference available at the time to processing this file

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Structure visualization

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Assembly

Deposited unit
A: YlmD protein sequence homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3724
Polymers30,1501
Non-polymers2223
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.970, 48.879, 135.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein YlmD protein sequence homologue


Mass: 30150.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: RBSTP0554 / Plasmid: PMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P84138
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 0.5M NaCl, 5mM beta-mercaptoethanol, 25% PEG 6K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.97985 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2003
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97985 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. all: 23429 / Num. obs: 23429 / % possible obs: 81.2 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.62
Reflection shellResolution: 1.75→1.88 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 9.2 / Num. unique all: 3509 / % possible all: 64.4

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Cristallographic conjugate gradient refinement using maximum likelihood target for amplitudes. The residue Asp 124 has unusual Phi and Psi angles. The author maintains that this conformation ...Details: Cristallographic conjugate gradient refinement using maximum likelihood target for amplitudes. The residue Asp 124 has unusual Phi and Psi angles. The author maintains that this conformation is important for the function of the protein
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2207 8.3 %Random
Rwork0.18 ---
all-22062 --
obs-22062 83.1 %-
Displacement parametersBiso mean: 25.76 Å2
Baniso -1Baniso -2Baniso -3
1--10.105 Å20 Å20 Å2
2--2.025 Å20 Å2
3---8.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 9 250 2355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.927
X-RAY DIFFRACTIONc_mcbond_it1.728
X-RAY DIFFRACTIONc_mcangle_it2.485
X-RAY DIFFRACTIONc_scbond_it2.653
X-RAY DIFFRACTIONc_scangle_it3.675
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2895 176 0.0684 %
Rwork0.2639 1578 -
obs-1754 0.6777 %

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