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- PDB-7xvo: a bacteria protein complex -

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Basic information

Entry
Database: PDB / ID: 7xvo
Titlea bacteria protein complex
Components
  • CRISPR-associated endonuclease Cas9
  • Uncharacterized 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
Uncharacterized protein / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
Haemophilus parainfluenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionMay 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas9
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)33,0672
Polymers33,0672
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-5 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.210, 127.210, 44.384
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein CRISPR-associated endonuclease Cas9


Mass: 23081.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: cas9 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8I1A9C6, Hydrolases; Acting on ester bonds
#2: Protein Uncharacterized protein


Mass: 9985.316 Da / Num. of mol.: 1
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.: 105 / 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: 60.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 2-Propanol, Sodium citrate tribasic dihydrate, Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→63.6 Å / Num. obs: 28150 / % possible obs: 99.93 % / Redundancy: 2 % / Biso Wilson estimate: 41.14 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.39
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 2777 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JDV

6jdv


Resolution: 2→31.8 Å / SU ML: 0.2891 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.4219
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2598 1434 5.1 %
Rwork0.2307 26690 -
obs0.2322 28124 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.93 Å2
Refinement stepCycle: LAST / Resolution: 2→31.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 0 105 2419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292351
X-RAY DIFFRACTIONf_angle_d0.63443151
X-RAY DIFFRACTIONf_chiral_restr0.0397348
X-RAY DIFFRACTIONf_plane_restr0.0051405
X-RAY DIFFRACTIONf_dihedral_angle_d4.6784308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.35771460.30342635X-RAY DIFFRACTION99.96
2.07-2.150.33191520.27622627X-RAY DIFFRACTION99.93
2.15-2.250.29461080.27322682X-RAY DIFFRACTION100
2.25-2.370.26321510.25322643X-RAY DIFFRACTION100
2.37-2.520.29071540.26842627X-RAY DIFFRACTION99.96
2.52-2.710.27721470.24272670X-RAY DIFFRACTION99.96
2.71-2.980.25931310.25152686X-RAY DIFFRACTION100
2.98-3.410.24281590.24362657X-RAY DIFFRACTION100
3.42-4.30.24031590.21212672X-RAY DIFFRACTION100
4.3-31.80.25571270.20452791X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -44.6059307099 Å / Origin y: 17.1656743512 Å / Origin z: -1.94223982305 Å
111213212223313233
T0.374899212814 Å20.00165722701662 Å2-0.0374110923255 Å2-0.28620064703 Å2-0.0166082407812 Å2--0.310421214654 Å2
L0.55254140985 °21.23161372718 °20.0255717120527 °2-3.02614886212 °20.112714613714 °2---0.0216412165484 °2
S-0.0760678796626 Å °-0.0468441691127 Å °0.00433403099937 Å °-0.132178621872 Å °0.0236439768113 Å °-0.117328825462 Å °-0.0346700964774 Å °0.226585034654 Å °0.0541698628372 Å °
Refinement TLS groupSelection details: all

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