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- PDB-1y81: Conserved hypothetical protein Pfu-723267-001 from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 1y81
TitleConserved hypothetical protein Pfu-723267-001 from Pyrococcus furiosus
Componentsconserved hypothetical protein
Keywordsstructural genomics / unknown function / conserved hypothetical protein / Pyrococcus furiosus / hyperthermophile / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


CoA binding domain / CoA binding domain / CoA-binding / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / THIOCYANATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / sad / Resolution: 1.701 Å
AuthorsZhao, M. / Chang, J. / Habel, J. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. ...Zhao, M. / Chang, J. / Habel, J. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Tempel, W. / Zhou, 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-723267-001 from Pyrococcus furiosus
Authors: Zhao, M. / Chang, J. / Habel, J. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Tempel, W. / Zhou, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney ...Authors: Zhao, M. / Chang, J. / Habel, J. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Tempel, W. / Zhou, 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 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: 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
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. ...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: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,48811
Polymers15,6621
Non-polymers82610
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.146, 79.146, 36.402
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein conserved hypothetical protein


Mass: 15661.961 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: Q8U2V3
#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 291 K / Method: modified microbatch
Details: 0.3M sodium thiocyanate, 35% w/v PEG 3350, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 14818 / % possible obs: 83.1 % / Rmerge(I) obs: 0.054 / Χ2: 1.424
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2% possible all
1.59-1.650.3713540.99720.1
1.65-1.710.3328370.97547.1
1.71-1.790.2712701.04472.5
1.79-1.890.22916291.0891.8
1.89-20.16417371.20798.5
2-2.160.12217761.375100
2.16-2.380.08917671.459100
2.38-2.720.06918001.588100
2.72-3.430.05417911.708100
3.43-500.03918571.46899.8

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Phasing

PhasingMethod: sad
Phasing MADD res high: 2.2 Å / D res low: 20 Å / FOM : 0.43 / Reflection: 6722
Phasing MAD shell
Resolution (Å)FOM Reflection
7.62-200.44349
4.91-7.620.45569
3.87-4.910.43716
3.3-3.870.45835
2.92-3.30.46937
2.64-2.920.451030
2.44-2.640.421109
2.27-2.440.351177
Phasing dmFOM : 0.66 / FOM acentric: 0.66 / FOM centric: 0.71 / Reflection: 7765 / Reflection acentric: 7127 / Reflection centric: 638
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6-19.7870.910.910.8234527273
3.8-60.910.920.851050927123
3-3.80.850.850.8112971184113
2.6-30.740.740.741308121098
2.3-2.60.590.590.623192171148
2.1-2.30.320.310.421446136383

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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: 1.701→68.519 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.23 / SU B: 2.468 / SU ML: 0.082 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 488 3.542 %RANDOM
Rwork0.2226 ---
all0.223 ---
obs0.22334 13777 94.942 %-
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: 24.266 Å2
Baniso -1Baniso -2Baniso -3
1--0.953 Å2-0.476 Å20 Å2
2---0.953 Å20 Å2
3---1.429 Å2
Refinement stepCycle: LAST / Resolution: 1.701→68.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms886 0 59 23 968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022957
X-RAY DIFFRACTIONr_angle_refined_deg1.3252.0441301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2775115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9625.13537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09815148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.365152
X-RAY DIFFRACTIONr_chiral_restr0.0740.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02703
X-RAY DIFFRACTIONr_nbd_refined0.2640.2457
X-RAY DIFFRACTIONr_nbtor_refined0.30.2657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0450.21
X-RAY DIFFRACTIONr_mcbond_it1.8442578
X-RAY DIFFRACTIONr_mcangle_it2.7663929
X-RAY DIFFRACTIONr_scbond_it2.162380
X-RAY DIFFRACTIONr_scangle_it3.2973372
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 (%)
1.701-1.7450.442300.34664107964.319
1.745-1.7920.332270.313776100779.742
1.792-1.8440.261380.279884102490.039
1.844-1.9010.274300.26390996996.904
1.901-1.9630.234310.24590194398.834
1.963-2.0320.292330.23906939100
2.032-2.1090.201320.232851883100
2.109-2.1950.282300.225820850100
2.195-2.2920.272300.231799829100
2.292-2.4040.239340.229749783100
2.404-2.5340.313200.234727747100
2.534-2.6880.275220.249689711100
2.688-2.8730.239220.24646668100
2.873-3.1020.236210.244599620100
3.102-3.3980.186270.219542569100
3.398-3.7980.245190.185513532100
3.798-4.3830.199160.173452468100
4.383-5.3630.19580.164388396100
5.363-7.5610.285110.262298309100
7.561-68.5190.24170.21817618598.919

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