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- PDB-1ycy: Conserved hypothetical protein Pfu-1806301-001 from Pyrococcus fu... -

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Basic information

Entry
Database: PDB / ID: 1ycy
TitleConserved hypothetical protein Pfu-1806301-001 from Pyrococcus furiosus
ComponentsConserved hypothetical protein
Keywordsstructural genomics / unknown function / Southeast Collaboratory for Structural Genomics / SECSG / Protein Structure Initiative / PSI / conserved hypothetical protein / Pyrococcus furiosus / hyperthermophile
Function / homologySH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / sad / Resolution: 2.8 Å
AuthorsHuang, L. / Liu, Z.-J. / Lee, D. / Tempel, W. / Chang, J. / Zhao, M. / Habel, J. / Xu, H. / Chen, L. / Nguyen, D. ...Huang, L. / Liu, Z.-J. / Lee, D. / Tempel, W. / Chang, J. / Zhao, M. / Habel, J. / Xu, H. / Chen, L. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Zhou, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney Jr., F.E. / Adams, M.W.W. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Conserved hypothetical protein Pfu-1806301-001 from Pyrococcus furiosus
Authors: Huang, L. / Liu, Z.-J. / Lee, D. / Tempel, W. / Chang, J. / Zhao, M. / Habel, J. / Xu, H. / Chen, L. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Zhou, W. / Lin, D. / Zhang, H. ...Authors: Huang, L. / Liu, Z.-J. / Lee, D. / Tempel, W. / Chang, J. / Zhao, M. / Habel, J. / Xu, H. / Chen, L. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Zhou, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney Jr., F.E. / Adams, M.W.W. / Rose, J.P. / Wang, B.-C.
History
DepositionDec 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved hypothetical protein
B: Conserved hypothetical protein
C: Conserved hypothetical protein
D: Conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)32,6674
Polymers32,6674
Non-polymers00
Water0
1
A: Conserved hypothetical protein
B: Conserved hypothetical protein
C: Conserved hypothetical protein
D: Conserved hypothetical protein

A: Conserved hypothetical protein
B: Conserved hypothetical protein
C: Conserved hypothetical protein
D: Conserved hypothetical protein

A: Conserved hypothetical protein
B: Conserved hypothetical protein
C: Conserved hypothetical protein
D: Conserved hypothetical protein

A: Conserved hypothetical protein
B: Conserved hypothetical protein
C: Conserved hypothetical protein
D: Conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)130,66916
Polymers130,66916
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_766-x+2,-x+y+1,-z+4/31
crystal symmetry operation4_765-x+2,-y+1,z1
crystal symmetry operation12_556x,x-y,-z+4/31
Buried area25500 Å2
ΔGint-219.8 kcal/mol
Surface area38710 Å2
MethodPISA
2
A: Conserved hypothetical protein
B: Conserved hypothetical protein
C: Conserved hypothetical protein
D: Conserved hypothetical protein

A: Conserved hypothetical protein
B: Conserved hypothetical protein
C: Conserved hypothetical protein
D: Conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)65,3358
Polymers65,3358
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_766-x+2,-x+y+1,-z+4/31
Buried area8770 Å2
ΔGint-94.5 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.958, 82.958, 189.782
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: SER / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 5 - 70 / Label seq-ID: 5 - 70

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Conserved hypothetical protein


Mass: 8166.827 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZN2

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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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 291 K / pH: 4.5
Details: 20% w/v PEG 3000, 0.1M sodium acetate, 0.01M NAD, pH 4.5, modified microbatch, temperature 291K, pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9785
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 11111 / % possible obs: 95 % / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.67→2.77 Å / Rmerge(I) obs: 0.294 / % possible all: 61.6

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Phasing

PhasingMethod: sad
Phasing MADD res high: 3 Å / D res low: 20 Å / FOM : 0.36 / Reflection: 8118
Phasing MAD shell
Resolution (Å)FOM Reflection
9.91-200.29504
6.56-9.910.43729
5.22-6.560.44897
4.46-5.220.421023
3.96-4.460.41136
3.6-3.960.371218
3.32-3.60.331281
3.09-3.320.251330
Phasing dmFOM : 0.58 / FOM acentric: 0.61 / FOM centric: 0.49 / Reflection: 8880 / Reflection acentric: 6932 / Reflection centric: 1948
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.3-19.9530.90.90.73431220211
5.2-8.30.740.830.541284882402
4.1-5.20.80.860.6315521176376
3.6-4.10.680.730.515171210307
3.1-3.60.480.510.3425892151438
2.9-3.10.220.230.1915071293214

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
MAR345data collection
MolProbitymodel building
RefinementMethod to determine structure: SAS / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / ESU R Free: 0.385 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.311 518 5.172 %THIN SHELLS
Rwork0.281 ---
obs-10016 100 %-
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: 55.52 Å2
Baniso -1Baniso -2Baniso -3
1-3.246 Å21.623 Å20 Å2
2--3.246 Å20 Å2
3----4.869 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 0 0 1797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221817
X-RAY DIFFRACTIONr_bond_other_d0.0010.021771
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9642460
X-RAY DIFFRACTIONr_angle_other_deg0.73834010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4535240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.3442556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83215298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.463154
X-RAY DIFFRACTIONr_chiral_restr0.070.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021988
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02344
X-RAY DIFFRACTIONr_nbd_refined0.2210.2380
X-RAY DIFFRACTIONr_nbd_other0.1720.21740
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2862
X-RAY DIFFRACTIONr_nbtor_other0.0890.21221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0550.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.65121264
X-RAY DIFFRACTIONr_mcbond_other0.6362528
X-RAY DIFFRACTIONr_mcangle_it3.40131896
X-RAY DIFFRACTIONr_scbond_it1.9492681
X-RAY DIFFRACTIONr_scangle_it2.8483564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 868 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.240.5
2Bmedium positional0.230.5
3Cmedium positional0.260.5
4Dmedium positional0.260.5
1Amedium thermal0.412
2Bmedium thermal0.372
3Cmedium thermal0.422
4Dmedium thermal0.442
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 37 -
Rwork0.381 621 -
obs--100 %

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