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- PDB-6j9k: Apo-AcrIIC2 -

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Basic information

Entry
Database: PDB / ID: 6j9k
TitleApo-AcrIIC2
ComponentsAcrIIC2
KeywordsHYDROLASE INHIBITOR / AcrIIC2
Function / homology: / Phage associated protein
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.234 Å
AuthorsZhu, Y.L. / Gao, A. / Serganov, A. / Gao, P.
Funding support United States, China, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM112940 United States
National Science Foundation (China)91753133 China
National Science Foundation (China)31670903 China
CitationJournal: Mol. Cell / Year: 2019
Title: Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type IIC Anti-CRISPR Proteins.
Authors: Zhu, Y. / Gao, A. / Zhan, Q. / Wang, Y. / Feng, H. / Liu, S. / Gao, G. / Serganov, A. / Gao, P.
History
DepositionJan 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AcrIIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5513
Polymers14,5021
Non-polymers492
Water72140
1
A: AcrIIC2
hetero molecules

A: AcrIIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1026
Polymers29,0052
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2910 Å2
ΔGint-30 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.022, 72.022, 105.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-201-

MG

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Components

#1: Protein AcrIIC2


Mass: 14502.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: CIJ84_02100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E2QCQ3, UniProt: A0A425B3G2*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSequence of AcrIIC2 was based on protein sequence of published literature (Pawluk et al., PMID: ...Sequence of AcrIIC2 was based on protein sequence of published literature (Pawluk et al., PMID: 27984730), in which reisdues 'MA' at terminal were reported.

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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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris, ethanol

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 8250 / % possible obs: 98.3 % / Redundancy: 35.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 28.9
Reflection shellResolution: 2.23→2.3 Å / Rmerge(I) obs: 4.078 / Num. unique obs: 599 / % possible all: 81.3

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.234→40.217 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.29
RfactorNum. reflection% reflection
Rfree0.2429 813 10.01 %
Rwork0.2057 --
obs0.2095 8121 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.234→40.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms927 0 2 40 969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01977
X-RAY DIFFRACTIONf_angle_d1.2131323
X-RAY DIFFRACTIONf_dihedral_angle_d13.994375
X-RAY DIFFRACTIONf_chiral_restr0.086134
X-RAY DIFFRACTIONf_plane_restr0.005182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2342-2.37420.35151140.30921022X-RAY DIFFRACTION85
2.3742-2.55750.34811350.27971218X-RAY DIFFRACTION100
2.5575-2.81480.30531350.24321213X-RAY DIFFRACTION100
2.8148-3.22190.26871370.20731227X-RAY DIFFRACTION100
3.2219-4.05870.21781410.18721265X-RAY DIFFRACTION100
4.0587-40.22350.23311510.20131363X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.471-0.07143.49465.6801-0.85825.5117-0.4766-0.1804-0.1263-0.24560.1629-0.16770.12760.38370.1690.42020.11280.09240.381-0.06270.292319.73731.512349.0192
22.0279-6.3606-6.5158.89031.31617.5604-0.44920.3816-2.8489-1.61580.07571.1091.17290.5209-0.03221.10930.0691-0.11360.7199-0.21691.068910.357322.599833.5109
35.2496-2.1355-0.11257.14260.15976.66170.28740.52560.6985-0.9302-0.2734-0.3958-0.56960.483-0.04030.62830.03340.10090.43270.04660.434217.096839.760537.3196
45.86231.0996-0.31622.0194-4.83487.7583-0.0155-0.1684-0.5992-1.5115-0.1809-0.40521.5135-0.26810.09060.90280.09150.05730.6256-0.07670.492117.988322.650939.8217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 118 )

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