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- PDB-4reg: Crystal Structure Analysis of PF0642 -

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Basic information

Entry
Database: PDB / ID: 4reg
TitleCrystal Structure Analysis of PF0642
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION
Function / homologyCRISPR-associated protein Cas7/Cst2/DevR, subtype I-a/Apern / CRISPR-associated protein Cas7/Cst2/DevR / : / CRISPR-associated negative auto-regulator DevR/Csa2 / defense response to virus / Type I-A CRISPR-associated protein Cas7/Csa2
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.494 Å
AuthorsHe, J.H. / Zhou, H. / Liu, X.P.
CitationJournal: To be Published
Title: Structural and functional characterization of PF0642
Authors: He, J.H. / Zhou, H. / Liu, X.P.
History
DepositionSep 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)37,3621
Polymers37,3621
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.259, 79.259, 136.103
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Uncharacterized protein


Mass: 37361.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0642 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U333
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.3 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 4000,0.2M Ammonium citrate tribasic , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98038 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98038 Å / Relative weight: 1
ReflectionResolution: 2.494→50 Å / Num. all: 344551 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.56 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PS0

3ps0


Resolution: 2.494→45.368 Å / SU ML: 0.35 / σ(F): 1.37 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2652 875 4.94 %
Rwork0.2113 --
obs0.2141 17709 99.43 %
all-17707 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.494→45.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 0 44 2233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162229
X-RAY DIFFRACTIONf_angle_d1.9033017
X-RAY DIFFRACTIONf_dihedral_angle_d17.181813
X-RAY DIFFRACTIONf_chiral_restr0.073351
X-RAY DIFFRACTIONf_plane_restr0.009384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4942-2.65040.32071480.23552730X-RAY DIFFRACTION99
2.6504-2.8550.32331230.22842781X-RAY DIFFRACTION100
2.855-3.14230.28251290.22812801X-RAY DIFFRACTION100
3.1423-3.59680.28761340.21082824X-RAY DIFFRACTION100
3.5968-4.5310.23621690.18072801X-RAY DIFFRACTION100
4.531-45.37520.24811720.21972897X-RAY DIFFRACTION98

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