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- PDB-4mjk: Crystal structure of a CRISPR protein from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 4mjk
TitleCrystal structure of a CRISPR protein from Archaeoglobus fulgidus
ComponentsCRISPR protein
KeywordsPROTEIN BINDING / CASCADE / CRISPR protein
Function / homologyAlpha-Beta Plaits - #3120 / CRISPR-associated protein, Cas5a type / CRISPR-associated protein, Cas5 / CRISPR-associated protein (Cas_Cas5) / maintenance of CRISPR repeat elements / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.953 Å
AuthorsHuang, Q.Q.
CitationJournal: To be Published
Title: Crystal structure of a CRISPR protein from Archaeoglobus fulgidus
Authors: Huang, Q.Q.
History
DepositionSep 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR protein
B: CRISPR protein


Theoretical massNumber of molelcules
Total (without water)59,4642
Polymers59,4642
Non-polymers00
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-12 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.251, 87.524, 140.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CRISPR protein


Mass: 29731.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_1872 / Production host: Escherichia coli (E. coli) / References: UniProt: O28407
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% ethanol, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 5, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.953→33.474 Å / Num. obs: 34700

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.953→33.474 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 1926 5.24 %random
Rwork0.1947 ---
obs0.1959 68918 94.13 %-
all-73215 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.423 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4837 Å2-0 Å20 Å2
2---1.1787 Å20 Å2
3---1.6624 Å2
Refinement stepCycle: LAST / Resolution: 1.953→33.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 0 232 3953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083800
X-RAY DIFFRACTIONf_angle_d1.1085132
X-RAY DIFFRACTIONf_dihedral_angle_d13.8451400
X-RAY DIFFRACTIONf_chiral_restr0.078574
X-RAY DIFFRACTIONf_plane_restr0.005643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9527-1.97840.2105800.19231321X-RAY DIFFRACTION50
1.9784-2.00550.31290.2292357X-RAY DIFFRACTION86
2.0055-2.03420.2391270.21042373X-RAY DIFFRACTION90
2.0342-2.06450.2381290.21492406X-RAY DIFFRACTION90
2.0645-2.09680.21221430.20332411X-RAY DIFFRACTION90
2.0968-2.13110.2621290.20512480X-RAY DIFFRACTION92
2.1311-2.16790.25121320.21142445X-RAY DIFFRACTION93
2.1679-2.20730.21241470.20192550X-RAY DIFFRACTION94
2.2073-2.24970.25941420.18252540X-RAY DIFFRACTION96
2.2497-2.29570.23941390.18952542X-RAY DIFFRACTION95
2.2957-2.34560.19361440.18792578X-RAY DIFFRACTION95
2.3456-2.40010.29161380.18922504X-RAY DIFFRACTION96
2.4001-2.46010.24911450.19642551X-RAY DIFFRACTION96
2.4601-2.52660.25521410.18822610X-RAY DIFFRACTION97
2.5266-2.60090.24261430.19582567X-RAY DIFFRACTION97
2.6009-2.68480.2491450.19692615X-RAY DIFFRACTION98
2.6848-2.78080.20531480.18312613X-RAY DIFFRACTION98
2.7808-2.8920.22361390.1842611X-RAY DIFFRACTION98
2.892-3.02360.18231480.17242642X-RAY DIFFRACTION99
3.0236-3.18290.17531490.17182623X-RAY DIFFRACTION99
3.1829-3.38210.19871450.17012660X-RAY DIFFRACTION99
3.3821-3.6430.18351410.17112661X-RAY DIFFRACTION100
3.643-4.0090.19211430.17192669X-RAY DIFFRACTION100
4.009-4.58790.18891490.18372667X-RAY DIFFRACTION100
4.5879-5.77540.17631510.21522654X-RAY DIFFRACTION100
5.7754-33.47890.28781460.27352656X-RAY DIFFRACTION99

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