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- PDB-8hs8: a bacteria protein complex -

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Basic information

Entry
Database: PDB / ID: 8hs8
Titlea bacteria protein complex
Components
  • CRISPR-associated endonuclease Cas9
  • a protein
KeywordsANTIMICROBIAL PROTEIN / a bacteria protein complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / HNH endonuclease / CRISPR-associated endonuclease Cas9 / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas9 / Uncharacterized protein
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
Haemophilus parainfluenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhang, H. / Li, X.Z. / Song, G.Y.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: a bacteria protein
Authors: Zhang, H. / Li, X.Z. / Song, G.Y.
History
DepositionDec 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas9
B: CRISPR-associated endonuclease Cas9
D: a protein
C: a protein


Theoretical massNumber of molelcules
Total (without water)67,5954
Polymers67,5954
Non-polymers00
Water181
1
A: CRISPR-associated endonuclease Cas9
D: a protein


Theoretical massNumber of molelcules
Total (without water)33,7982
Polymers33,7982
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-11 kcal/mol
Surface area14250 Å2
MethodPISA
2
B: CRISPR-associated endonuclease Cas9

C: a protein


Theoretical massNumber of molelcules
Total (without water)33,7982
Polymers33,7982
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z+1/31
Buried area1620 Å2
ΔGint-7 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.504, 129.504, 44.546
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein CRISPR-associated endonuclease Cas9


Mass: 23812.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: cas9 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0T7L299
#2: Protein a protein


Mass: 9985.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus parainfluenzae (bacteria) / Gene: NCTC10672_00033, NCTC10672_02354 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A377JKY9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, MES/ Sodium hydroxide, Ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→25.72 Å / Num. obs: 1155940 / % possible obs: 99.1 % / Redundancy: 9.9 % / Biso Wilson estimate: 93.75 Å2 / CC1/2: 0.979 / Net I/σ(I): 15.6
Reflection shellResolution: 2.7→2.796 Å / Num. unique obs: 2720 / CC1/2: 0.482

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XVQ,6JDQ

7xvq

6jdq


Resolution: 2.7→22.28 Å / SU ML: 0.5518 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 44.0136
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3038 1011 4.75 %
Rwork0.2675 20270 -
obs0.2693 21281 92.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.25 Å2
Refinement stepCycle: LAST / Resolution: 2.7→22.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4205 0 0 1 4206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00544275
X-RAY DIFFRACTIONf_angle_d0.78675812
X-RAY DIFFRACTIONf_chiral_restr0.0389683
X-RAY DIFFRACTIONf_plane_restr0.0083766
X-RAY DIFFRACTIONf_dihedral_angle_d4.6621602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.840.5358890.41992259X-RAY DIFFRACTION72.16
2.84-3.020.40181460.38992829X-RAY DIFFRACTION90.26
3.02-3.250.45121310.36012943X-RAY DIFFRACTION94.67
3.25-3.580.38562020.34323010X-RAY DIFFRACTION97.69
3.58-4.090.33441520.30693075X-RAY DIFFRACTION98.69
4.09-5.150.31341560.24943093X-RAY DIFFRACTION99.36
5.15-22.280.23161350.20893061X-RAY DIFFRACTION97.26

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