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- PDB-7a67: Pcc1Pcc2 complex -

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Basic information

Entry
Database: PDB / ID: 7a67
TitlePcc1Pcc2 complex
Components
  • KEOPS complex subunit Pcc1
  • Pcc2
KeywordsSTRUCTURAL PROTEIN / t6A synthases
Function / homologyCTAG/Pcc1 family / Transcription factor Pcc1 / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / cytoplasm / KEOPS complex subunit Pcc1
Function and homology information
Biological speciesPyrococcus abyssi (archaea)
Pyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsMissoury, S. / Tilbeurgh, V.H.
CitationJournal: To Be Published
Title: Pcc1Pcc2 structure
Authors: Missoury, S. / Tilbeurgh, V.H.
History
DepositionAug 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KEOPS complex subunit Pcc1
B: Pcc2


Theoretical massNumber of molelcules
Total (without water)20,7522
Polymers20,7522
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-11 kcal/mol
Surface area8260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.898, 69.898, 92.751
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein KEOPS complex subunit Pcc1


Mass: 10408.970 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Strain: GE5 / Orsay / Gene: pcc1, PYRAB02750, PAB3073
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9V1Z9
#2: Protein Pcc2


Mass: 10342.880 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 6000 and 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980066 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980066 Å / Relative weight: 1
ReflectionResolution: 3.17→34.95 Å / Num. obs: 4659 / % possible obs: 98.4 % / Redundancy: 18.751 % / Biso Wilson estimate: 90.58 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.212 / Rrim(I) all: 0.218 / Χ2: 1.105 / Net I/σ(I): 10.93 / Num. measured all: 87363
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.17-3.3617.4881.7961.54118577456780.8591.84791
3.36-3.5919.6971.0013.36135326886870.9641.02899.9
3.59-3.8819.1410.6864.98127296666650.9790.70599.8
3.88-4.2420.1150.418.69119085925920.9940.421100
4.24-4.7319.5230.21113.33107185505490.9970.21799.8
4.73-5.4518.2740.21314.8792655075070.9930.22100
5.45-6.6418.0070.20715.875274184180.9940.213100
6.64-9.2417.5520.10627.0960383443440.9980.11100
9.24-34.9517.3010.0737.9337892232190.9980.07398.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ENC

3enc


Resolution: 3.18→34.95 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.442
RfactorNum. reflection% reflectionSelection details
Rfree0.25 435 9.86 %RANDOM
Rwork0.185 ---
obs0.192 4411 94 %-
Displacement parametersBiso max: 136.84 Å2 / Biso mean: 60.74 Å2 / Biso min: 15.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.6277 Å20 Å20 Å2
2--1.6277 Å20 Å2
3----3.2554 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 3.18→34.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 0 8 1324
Biso mean---24.65 -
Num. residues----164
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d481SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes222HARMONIC5
X-RAY DIFFRACTIONt_it1336HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion179SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1639SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1336HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1809HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion24.76
LS refinement shellResolution: 3.18→3.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 21
RfactorNum. reflection% reflection
Rfree0.4884 24 11.37 %
Rwork0.2358 187 -
all0.2623 211 -
obs--55.44 %

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