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- PDB-3enc: Crystal structure of Pyrococcus furiosus PCC1 dimer -

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Basic information

Entry
Database: PDB / ID: 3enc
TitleCrystal structure of Pyrococcus furiosus PCC1 dimer
Componentsprotein PCC1
KeywordsUNKNOWN FUNCTION / dimerization domain / KEOPS / telomere
Function / homologyCTAG/Pcc1 family / Transcription factor Pcc1 / Alpha-D-phosphohexomutase, C-terminal domain / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta / KEOPS complex subunit Pcc1
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6304 Å
AuthorsNeculai, D.
CitationJournal: Mol.Cell / Year: 2008
Title: Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine.
Authors: Mao, D.Y. / Neculai, D. / Downey, M. / Orlicky, S. / Haffani, Y.Z. / Ceccarelli, D.F. / Ho, J.S. / Szilard, R.K. / Zhang, W. / Ho, C.S. / Wan, L. / Fares, C. / Rumpel, S. / Kurinov, I. / ...Authors: Mao, D.Y. / Neculai, D. / Downey, M. / Orlicky, S. / Haffani, Y.Z. / Ceccarelli, D.F. / Ho, J.S. / Szilard, R.K. / Zhang, W. / Ho, C.S. / Wan, L. / Fares, C. / Rumpel, S. / Kurinov, I. / Arrowsmith, C.H. / Durocher, D. / Sicheri, F.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein PCC1
B: protein PCC1


Theoretical massNumber of molelcules
Total (without water)20,0822
Polymers20,0822
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-9 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.810, 78.810, 60.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein protein PCC1 / uncharacterized protein PF2011


Mass: 10041.199 Da / Num. of mol.: 2 / Fragment: pcc1 / Mutation: I12M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF2011 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TZI1

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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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 45% PEG 300 0.1 M Na/K phosphate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 10, 2007 / Details: MIRRORS
RadiationMonochromator: HORIZONTAL BENT SI(111), ASYMMETRICALLY CUT WITH WATER COOLED CU BLOCK
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
Reflection twinType: pseudo-merohedral / Operator: h,-h-k,-l / Fraction: 0.503
ReflectionResolution: 2.6304→68.251 Å / Num. all: 6413 / Num. obs: 6401 / % possible obs: 99.8 % / Observed criterion σ(I): 2.48 / Redundancy: 1.93 % / Rmerge(I) obs: 0.0331 / Rsym value: 0.0305 / Net I/σ(I): 20.16
Reflection shellResolution: 2.6304→2.72 Å / Redundancy: 1.93 % / Rmerge(I) obs: 0.2677 / Mean I/σ(I) obs: 2.86 / Num. unique all: 612 / Rsym value: 0.398 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6304→68.251 Å / Cross valid method: THROUGHOUT / σ(F): 2.06 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 448 7.01 %RANDOM
Rwork0.1921 ---
all0.1944 6413 --
obs0.1921 6390 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 138.453 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2071 Å20 Å2-0 Å2
2---1.2071 Å2-0 Å2
3----39.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6304→68.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1276 0 0 0 1276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091296
X-RAY DIFFRACTIONf_angle_d1.2321744
X-RAY DIFFRACTIONf_chiral_restr0.082202
X-RAY DIFFRACTIONf_plane_restr0.005214
X-RAY DIFFRACTIONf_dihedral_angle_d20.158488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6304-3.0110.28821480.27921966X-RAY DIFFRACTION98
3.011-3.79350.25761490.2391978X-RAY DIFFRACTION98
3.7935-68.27440.20011510.16111998X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 14.1503 Å / Origin y: 24.3766 Å / Origin z: 30.0971 Å
111213212223313233
T0.3106 Å20.1763 Å20.0666 Å2-0.7629 Å2-0.0937 Å2--0.5327 Å2
L-0.276 °21.3019 °2-2.5519 °2-1.5026 °20.8468 °2--3.6317 °2
S-0.0849 Å °0.2239 Å °-0.4186 Å °0.1051 Å °0.2156 Å °0.0218 Å °0.0114 Å °-0.2511 Å °-0.1099 Å °
Refinement TLS groupSelection details: all

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