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- PDB-6f1s: C-terminal domain of CglI restriction endonuclease H subunit -

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Basic information

Entry
Database: PDB / ID: 6f1s
TitleC-terminal domain of CglI restriction endonuclease H subunit
ComponentsCglIIR protein
KeywordsHYDROLASE / restriction endonuclease / NTPase
Function / homologyPutative endonuclease, Z1 domain / Z1 domain / P-loop containing nucleoside triphosphate hydrolase / FORMIC ACID / CglIIR protein
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsTamulaitiene, G. / Grigaitis, R. / Zaremba, M. / Silanskas, A.
Funding supportLithuania, 1items
OrganizationGrant numberCountry
Research Council of LithuaniaMIP-56/2015Lithuania
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor.
Authors: Toliusis, P. / Tamulaitiene, G. / Grigaitis, R. / Tuminauskaite, D. / Silanskas, A. / Manakova, E. / Venclovas, C. / Szczelkun, M.D. / Siksnys, V. / Zaremba, M.
History
DepositionNov 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Mar 7, 2018Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 4, 2018Group: Data collection / Database references / Refinement description
Category: citation / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _software.name
Revision 1.4Jan 16, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CglIIR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0323
Polymers19,9241
Non-polymers1082
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer (Zaremba et al., Nucleic Acids Res, 2014)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint3 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.704, 75.704, 95.044
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein CglIIR protein


Mass: 19924.193 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag / Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cglIIR / Plasmid: pLATE31 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H7C664
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.98 Å3/Da / Density % sol: 37.81 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystallization buffer was 0.1 M Tris-HCl (pH 8.5), 27% PEG3350, 7% Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9802, 0.9803, 0.9779
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98021
20.98031
30.97791
ReflectionResolution: 2.4→53.967 Å / Num. all: 6654 / Num. obs: 6654 / % possible obs: 98.6 % / Redundancy: 36.9 % / Rpim(I) all: 0.013 / Rrim(I) all: 0.082 / Rsym value: 0.066 / Net I/av σ(I): 9.2 / Net I/σ(I): 51.3 / Num. measured all: 245242
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.4-2.5335.10.2582.68740.0450.270.25891.5
2.53-2.6838.70.1843.88930.0310.1980.18499.8
2.68-2.8738.50.1285.38430.0230.1430.12899.8
2.87-3.138.80.0917.47950.0170.1070.09199.8
3.1-3.3937.60.065107440.0130.0790.065100
3.39-3.7936.90.05312.16840.0110.0660.05399.9
3.79-4.3836.30.04413.76000.0090.0570.044100
4.38-5.3736.60.0414.55270.0090.0560.04100
5.37-7.5934.40.04114.44250.0110.070.04199.8
7.59-53.96728.90.03813.72690.0090.0530.03899.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
SHELXDEphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.4→38.477 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.63 / Phase error: 20.17
RfactorNum. reflection% reflection
Rfree0.2147 1105 9.38 %
Rwork0.1719 --
obs0.1759 6635 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.16 Å2 / Biso mean: 29.2845 Å2 / Biso min: 8.31 Å2
Refinement stepCycle: final / Resolution: 2.4→38.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 7 68 1183
Biso mean--36.16 31.04 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041135
X-RAY DIFFRACTIONf_angle_d0.7941544
X-RAY DIFFRACTIONf_chiral_restr0.032182
X-RAY DIFFRACTIONf_plane_restr0.003200
X-RAY DIFFRACTIONf_dihedral_angle_d11.801412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.50930.28971420.21991223136590
2.5093-2.64160.22791420.20413411483100
2.6416-2.8070.22911500.186913421492100
2.807-3.02370.2461260.188313541480100
3.0237-3.32780.27611250.184113651490100
3.3278-3.8090.20521420.165513501492100
3.809-4.79750.1611260.142113521478100
4.7975-38.48210.18681520.158713511503100
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)
10.64810.30030.01380.31650.05010.2971-0.22450.3918-0.1091-0.2782-0.0157-0.38930.03180.117-0.14490.22820.06740.00130.2442-0.08260.2706-18.902344.938513.2593
20.41740.4517-0.5430.59470.31961.7544-0.03040.0546-0.0542-0.0876-0.0143-0.01640.00520.1014-0.14480.1061-0.00670.03820.0963-0.04560.1219-20.470648.823618.0101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 478:496)A478 - 496
2X-RAY DIFFRACTION2(chain A and resid 497:623)A497 - 623

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