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- PDB-1yb3: Conserved hypothetical protein Pfu-178653-001 from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 1yb3
TitleConserved hypothetical protein Pfu-178653-001 from Pyrococcus furiosus
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / PSI / conserved hypothetical protein / Pyrococcus furiosus / hyperthermophile / SECSG / The Southeast Collaboratory for Structural Genomics
Function / homologyProtein of unknown function DUF3201 / Protein of unknown function (DUF3201) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / sad / Resolution: 1.6 Å
AuthorsHabel, J. / Zhou, W. / Chang, J. / Zhao, M. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Horanyi, P. ...Habel, J. / Zhou, W. / Chang, J. / Zhao, M. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Tempel, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney Jr., F.E. / Adams, M.W.W. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Conserved hypothetical protein Pfu-178653-001 from Pyrococcus furiosus
Authors: Habel, J. / Zhou, W. / Chang, J. / Zhao, M. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Tempel, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney ...Authors: Habel, J. / Zhou, W. / Chang, J. / Zhao, M. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Tempel, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney Jr., F.E. / Adams, M.W.W. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C.
History
DepositionDec 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)21,0192
Polymers21,0191
Non-polymers01
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein

A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)42,0384
Polymers42,0382
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2170 Å2
ΔGint-24 kcal/mol
Surface area15470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)109.134, 44.388, 55.326
Angle α, β, γ (deg.)90.00, 118.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein hypothetical protein /


Mass: 21019.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U4C0
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 291 K / Method: modified microbatch / pH: 3.6
Details: 12% w/v PEG 4000, 0.2M sodium chloride, 0.2M magnesium chloride, 0.1M sodium citrate, pH 3.6, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 26254 / % possible obs: 84.8 % / Rmerge(I) obs: 0.052 / Χ2: 1.337
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2Diffraction-ID% possible all
1.6-1.660.21810661.013134.6
1.66-1.720.215951.132151.6
1.72-1.80.19523560.915177.3
1.8-1.90.16529251.026195
1.9-2.020.12830221.157197.6
2.02-2.170.08530071.308197.9
2.17-2.390.06730311.5198
2.39-2.740.05830491.54198.3
2.74-3.450.04930741.822198.4
3.45-500.04231291.231198.2

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Phasing

PhasingMethod: sad
Phasing MADD res high: 2.4 Å / D res low: 20 Å / FOM : 0.39 / Reflection: 9009
Phasing MAD shell
Resolution (Å)FOM Reflection
8.22-200.42470
5.33-8.220.44764
4.21-5.330.4968
3.59-4.210.441125
3.18-3.590.451254
2.88-3.180.411367
2.66-2.880.381487
2.48-2.660.281574

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
MAR345data collection
ISASphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAS / Resolution: 1.6→48.45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.217 / SU B: 1.663 / SU ML: 0.06 / SU R Cruickshank DPI: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 1312 4.997 %RANDOM
Rwork0.2039 ---
all0.205 ---
obs0.20521 26254 84.792 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.965 Å2
Baniso -1Baniso -2Baniso -3
1--1.491 Å20 Å2-0.15 Å2
2--0.988 Å20 Å2
3---0.359 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 1 102 1495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221461
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9541974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.315165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.9832588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03415258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.644157
X-RAY DIFFRACTIONr_chiral_restr0.0870.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021150
X-RAY DIFFRACTIONr_nbd_refined0.1940.2642
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21009
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.27
X-RAY DIFFRACTIONr_mcbond_it2.3732873
X-RAY DIFFRACTIONr_mcangle_it3.0431352
X-RAY DIFFRACTIONr_scbond_it2.4372690
X-RAY DIFFRACTIONr_scangle_it3.6373622
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.6390.324390.282718227633.26
1.639-1.6840.326440.283910220943.187
1.684-1.7330.308590.2861223216759.16
1.733-1.7860.337780.2721536208977.262
1.786-1.8450.29890.2571774202791.909
1.845-1.9090.284860.2221811195796.934
1.909-1.9810.231950.2161746188897.511
1.981-2.0620.27860.2011703183297.653
2.062-2.1540.218920.1961632176197.899
2.154-2.2590.245910.1961555167798.151
2.259-2.380.237720.2021498160198.064
2.38-2.5240.236690.2121407150398.204
2.524-2.6980.264670.2231335142798.248
2.698-2.9140.227720.221236133198.272
2.914-3.1910.216670.2051150123498.622
3.191-3.5650.205480.1911038110198.638
3.565-4.1130.185540.18192199298.286
4.113-5.0280.174480.15678684898.349
5.028-7.0730.263340.20762065699.695
7.073-48.450.24220.21734338794.315

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