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- PDB-7msl: Structure of anti-CRISPR AcrIIC4 from Haemophilus parainfluenzae -

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Basic information

Entry
Database: PDB / ID: 7msl
TitleStructure of anti-CRISPR AcrIIC4 from Haemophilus parainfluenzae
ComponentsAcrIIC4
KeywordsVIRAL PROTEIN / Anti-CRISPR proteins / AcrIIC4 / a Haemophilus parainfluenzae prophage
Function / homologyIODIDE ION / Uncharacterized protein
Function and homology information
Biological speciesHaemophilus parainfluenzae (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.73 Å
AuthorsPan, C. / Maxwell, K.L. / Moraes, T.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-06546 Canada
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural and Mechanistic Insight into CRISPR-Cas9 Inhibition by Anti-CRISPR Protein AcrIIC4 Hpa.
Authors: Hwang, S. / Pan, C. / Garcia, B. / Davidson, A.R. / Moraes, T.F. / Maxwell, K.L.
History
DepositionMay 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AcrIIC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7124
Polymers10,3321
Non-polymers3813
Water59433
1
A: AcrIIC4
hetero molecules

A: AcrIIC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4258
Polymers20,6632
Non-polymers7616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area5540 Å2
ΔGint-44 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.450, 82.450, 27.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-233-

HOH

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Components

#1: Protein AcrIIC4


Mass: 10331.721 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 BL21(DE3) (bacteria) / References: UniProt: A0A377JKY9
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 35% PEG 600, 0.1M NaHPO4/citric acid pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: CCD / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.73→36.87 Å / Num. obs: 10268 / % possible obs: 99.92 % / Redundancy: 2 % / Biso Wilson estimate: 23.55 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.32
Reflection shellResolution: 1.73→1.8 Å / Num. unique obs: 990 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.73→36.87 Å / SU ML: 0.2102 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.2669 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2736 1027 10.01 %
Rwork0.2388 9235 -
obs0.2422 10262 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.5 Å2
Refinement stepCycle: LAST / Resolution: 1.73→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms700 0 3 33 736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038715
X-RAY DIFFRACTIONf_angle_d0.5361958
X-RAY DIFFRACTIONf_chiral_restr0.0343105
X-RAY DIFFRACTIONf_plane_restr0.0033125
X-RAY DIFFRACTIONf_dihedral_angle_d17.8706447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.830.36621420.34261281X-RAY DIFFRACTION99.93
1.83-1.940.31171430.29791287X-RAY DIFFRACTION100
1.94-2.090.2741440.23911289X-RAY DIFFRACTION100
2.09-2.30.26591460.21941310X-RAY DIFFRACTION99.93
2.3-2.630.26181440.20751301X-RAY DIFFRACTION99.93
2.63-3.320.26321490.23791337X-RAY DIFFRACTION100
3.32-36.870.26841590.23391430X-RAY DIFFRACTION99.81
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)
16.10030179824-3.25033988178-0.1039612511487.569715267240.90928964680.993998905680.0158176529181-0.08297499594870.007732911538380.1097949470510.1281866724170.363377635534-0.0189401005403-0.0289225651548-0.1373626559280.137128977054-0.01444170622910.007846591363040.177209709165-0.03494083104430.12824174801950.629000562613.8565334718.23527487937
25.92730205848-5.000081375111.2857062254.49960404196-1.223662702830.9912640070320.2568030459630.12579064962-0.631391426821-0.755935036408-0.2422289764940.4502704985390.1704151800420.05430308698960.001767813554480.2061708786280.002603201673270.005932750370480.204303027316-0.02239025158690.19609104946129.016358010356.93348331476.17170003157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:49)
2X-RAY DIFFRACTION2(chain A and resid 50:88)

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