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- PDB-1yud: X-ray Crystal Structure of Protein SO0799 from Shewanella oneiden... -

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Basic information

Entry
Database: PDB / ID: 1yud
TitleX-ray Crystal Structure of Protein SO0799 from Shewanella oneidensis. Northeast Structural Genomics Consortium Target SoR12.
Componentshypothetical protein SO0799Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SoR12 / Q8E1N8 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Cupin domain of unknown function DUF985 / Uncharacterized protein YML079W-like / Cupin superfamily (DUF985) / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cupin_5 domain-containing protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsKuzin, A.P. / Vorobiev, S. / Chen, Y. / Forouhar, F. / Acton, T. / Ma, L.-C. / Xiao, R. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein SO0799 from Shewanella oneidensis
Authors: Kuzin, A.P. / Vorobiev, S. / Chen, Y. / Forouhar, F. / Acton, T. / Ma, L.-C. / Xiao, R. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein SO0799
B: hypothetical protein SO0799
C: hypothetical protein SO0799
D: hypothetical protein SO0799
E: hypothetical protein SO0799
F: hypothetical protein SO0799
G: hypothetical protein SO0799
H: hypothetical protein SO0799
I: hypothetical protein SO0799
J: hypothetical protein SO0799


Theoretical massNumber of molelcules
Total (without water)197,51110
Polymers197,51110
Non-polymers00
Water2,018112
1
A: hypothetical protein SO0799
H: hypothetical protein SO0799


Theoretical massNumber of molelcules
Total (without water)39,5022
Polymers39,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-21 kcal/mol
Surface area14220 Å2
MethodPISA
2
B: hypothetical protein SO0799
C: hypothetical protein SO0799


Theoretical massNumber of molelcules
Total (without water)39,5022
Polymers39,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-22 kcal/mol
Surface area14370 Å2
MethodPISA
3
D: hypothetical protein SO0799
J: hypothetical protein SO0799


Theoretical massNumber of molelcules
Total (without water)39,5022
Polymers39,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-22 kcal/mol
Surface area14250 Å2
MethodPISA
4
E: hypothetical protein SO0799
F: hypothetical protein SO0799


Theoretical massNumber of molelcules
Total (without water)39,5022
Polymers39,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-23 kcal/mol
Surface area14680 Å2
MethodPISA
5
G: hypothetical protein SO0799
I: hypothetical protein SO0799


Theoretical massNumber of molelcules
Total (without water)39,5022
Polymers39,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-22 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.441, 94.100, 117.100
Angle α, β, γ (deg.)90.00, 111.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
hypothetical protein SO0799 / Hypothesis


Mass: 19751.096 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Production host: Escherichia coli (E. coli) / Strain (production host): E.coli BL21(DE3).Magic / References: UniProt: Q8EIN8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Hepes, 22% PEG3350, 200 mM ammonium sulphate, 5 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97624, 0.97895, 0.97020
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.976241
20.978951
30.97021
ReflectionResolution: 2.7→30 Å / Num. all: 105384 / Num. obs: 105384 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 22
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→29.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 240076.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 4268 4.9 %RANDOM
Rwork0.237 ---
obs0.237 87778 81.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.7161 Å2 / ksol: 0.270733 e/Å3
Displacement parametersBiso mean: 66.8 Å2
Baniso -1Baniso -2Baniso -3
1--18.06 Å20 Å2-2.87 Å2
2--22.81 Å20 Å2
3----4.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12650 0 0 112 12762
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.415 439 5.2 %
Rwork0.378 8074 -
obs--47.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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