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- PDB-3d8l: Crystal structure of ORF12 from the lactococcus lactis bacterioph... -

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Basic information

Entry
Database: PDB / ID: 3d8l
TitleCrystal structure of ORF12 from the lactococcus lactis bacteriophage p2
ComponentsORF12
KeywordsVIRAL PROTEIN / lactococcal phage p2 / ORF12
Function / homologyUncharacterised protein, phage p2 ORF12 / Phage p2 ORF12 / : / Lactococcus lactis phage p2, ORF12 / viral tail assembly / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha / Chaperone protein gp12
Function and homology information
Biological speciesLactococcus phage p2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsSiponen, M.I. / Spinelli, S. / Lichiere, J. / Moineau, S. / Cambillau, C. / Campanacci, V.
CitationJournal: J.Bacteriol. / Year: 2009
Title: Crystal structure of ORF12 from Lactococcus lactis phage p2 identifies a tape measure protein chaperone
Authors: Siponen, M. / Sciara, G. / Villion, M. / Spinelli, S. / Cambillau, C. / Moineau, S. / Campanacci, V.
History
DepositionMay 23, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 21, 2016Group: Database references / Source and taxonomy
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF12
B: ORF12
C: ORF12


Theoretical massNumber of molelcules
Total (without water)31,6983
Polymers31,6983
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ORF12


Theoretical massNumber of molelcules
Total (without water)10,5661
Polymers10,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: ORF12


Theoretical massNumber of molelcules
Total (without water)10,5661
Polymers10,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: ORF12


Theoretical massNumber of molelcules
Total (without water)10,5661
Polymers10,5661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.318, 158.318, 99.524
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYAA1 - 911 - 91
2GLYGLYBB1 - 911 - 91
3GLNGLNCC4 - 914 - 91

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Components

#1: Protein ORF12


Mass: 10566.008 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage p2 (virus) / Gene: ORF12 / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: D3WAD0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.79 Å3/Da / Density % sol: 67.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.1M HEPES, 15.9% PEG600, pH6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2007 / Details: tyroidal mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.9→35 Å / Num. all: 10739 / Num. obs: 10739 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 21.4 % / Biso Wilson estimate: 71.6 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 29.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 20 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 6.4 / Num. unique all: 10739 / Rsym value: 0.441 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 33.831 / SU ML: 0.271 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.763 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25319 515 4.8 %RANDOM
Rwork0.20264 ---
obs0.20503 10218 99.98 %-
all-10218 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.215 Å2
Baniso -1Baniso -2Baniso -3
1--3.96 Å2-1.98 Å20 Å2
2---3.96 Å20 Å2
3---5.94 Å2
Refine analyzeLuzzati coordinate error free: 0.347 Å
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 0 4 2215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222244
X-RAY DIFFRACTIONr_bond_other_d0.0010.021584
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9722992
X-RAY DIFFRACTIONr_angle_other_deg0.92133878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7775267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.08726.053114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.42415461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.325156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022457
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined0.2380.2619
X-RAY DIFFRACTIONr_nbd_other0.1930.21601
X-RAY DIFFRACTIONr_nbtor_refined0.2010.21158
X-RAY DIFFRACTIONr_nbtor_other0.0980.21221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3160.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6261.51698
X-RAY DIFFRACTIONr_mcbond_other0.0861.5554
X-RAY DIFFRACTIONr_mcangle_it0.76922128
X-RAY DIFFRACTIONr_scbond_it1.19631084
X-RAY DIFFRACTIONr_scangle_it1.814.5864
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1243 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.410.5
2Bmedium positional0.470.5
3Cmedium positional0.460.5
1Amedium thermal0.422
2Bmedium thermal0.42
3Cmedium thermal0.362
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 36 -
Rwork0.335 755 -
obs-36 100 %
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)
19.9507-1.51891.70547.9449-1.30813.8763-0.05280.1741-0.4135-0.2401-0.06140.3580.5907-0.23220.1142-0.1173-0.0390.0126-0.2257-0.0591-0.244364.23231.22562.957
210.16431.04523.56616.65792.50726.36580.0696-0.2943-0.4578-0.0787-0.33340.18140.3634-0.64720.2638-0.1784-0.12370.0571-0.0331-0.1012-0.218852.38533.6992.143
38.68552.50281.720312.46844.73779.0440.3104-0.1977-0.22070.0282-0.0738-0.2311-0.310.6368-0.2366-0.1327-0.1497-0.00350.0589-0.0611-0.242230.32725.49880.832
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 911 - 91
2X-RAY DIFFRACTION2BB1 - 911 - 91
3X-RAY DIFFRACTION3CC4 - 914 - 91

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