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- PDB-2wkd: Crystal structure of a double Ile-to-Met mutant of protein ORF34 ... -

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Basic information

Entry
Database: PDB / ID: 2wkd
TitleCrystal structure of a double Ile-to-Met mutant of protein ORF34 from lactococcus phage p2
ComponentsORF34P2
KeywordsDNA BINDING PROTEIN / SSB / SINGLE-STRANDED DNA BINDING
Function / homologyLactococcus phage single-stranded DNA binding protein / Lactococcus phage single-stranded DNA binding protein / Lactococcus phage SSB superfamily / Lactococcus phage single-stranded DNA binding protein / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / SSB protein
Function and homology information
Biological speciesLACTOCOCCUS PHAGE P2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsScaltriti, E. / Cambillau, C. / Ortiz-Lombardia, M.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Structure and Function of Phage P2 Orf34(P2), a New Type of Single-Stranded DNA Binding Protein.
Authors: Scaltriti, E. / Tegoni, M. / Rivetti, C. / Launay, H. / Masson, J.Y. / Magadan, A.H. / Tremblay, D. / Moineau, S. / Ramoni, R. / Lichiere, J. / Campanacci, V. / Cambillau, C. / Ortiz-Lombardia, M.
History
DepositionJun 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 29, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF34P2


Theoretical massNumber of molelcules
Total (without water)13,0671
Polymers13,0671
Non-polymers00
Water46826
1
A: ORF34P2

A: ORF34P2


Theoretical massNumber of molelcules
Total (without water)26,1342
Polymers26,1342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1890 Å2
ΔGint-5.6 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.740, 75.740, 88.040
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-2003-

HOH

21A-2006-

HOH

31A-2018-

HOH

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Components

#1: Protein ORF34P2


Mass: 13067.198 Da / Num. of mol.: 1 / Fragment: RESIDUES 15-131 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS PHAGE P2 (virus) / Plasmid: PETG-20A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA (DE3) PLYSS / References: UniProt: Q09WL7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 62 TO MSE ENGINEERED RESIDUE IN CHAIN A, LEU 68 TO MSE
Has protein modificationY

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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: 4.22 Å3/Da / Density % sol: 70.9 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.2
Details: PROTEIN AT 7 MG/ML IN 10 MM TRIS, 300 MM NACL, 1 MM TCEP, PH 8.0 WAS CRYSTALLIZED BY SITTING-DROP VAPOUR DIFFUSION AGAINST 0.1 M HEPES PH 7.2, 60% MME-PEG550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→88.04 Å / Num. obs: 9205 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.18 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.79
Reflection shellResolution: 2.1→2.12 Å / Redundancy: 10.54 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.77 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
TRUNCATEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→44.02 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.471 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 918 10.08 %RANDOM
Rwork0.2386 ---
obs0.24 9182 99.783 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 55.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.152 Å21.576 Å20 Å2
2--3.152 Å20 Å2
3----4.728 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms610 0 0 26 636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022618
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.949832
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.932576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8122524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68815111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.773152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021440
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2208
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2419
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.234
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6261.5390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.532637
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3153228
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5434.5195
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 67 -
Rwork0.307 591 -
obs--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)
14.3768-0.2883-6.37592.4517-0.617710.7160.37560.26380.2304-0.0658-0.25220.0063-0.609-0.1977-0.12340.0594-0.00680.03480.0809-0.01250.117227.866740.7297-11.5124
210.1362-6.0087-4.0675.9042.57744.40850.15680.1040.47020.0899-0.03310.0056-0.49770.1584-0.12380.1275-0.05750.0390.038-0.00130.064433.871241.0312-11.6056
34.74782.15470.49121.1231.40029.74910.214-0.22370.25260.0045-0.10530.0935-0.66860.0693-0.10880.11660.00370.08040.1752-0.04330.093129.700137.9781-12.0228
43.86884.37933.51810.12465.376411.77450.4853-0.28220.0730.4027-0.296-0.3820.16360.6314-0.18930.0766-0.05350.0360.2305-0.04770.084430.579736.9456-5.3845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 15
2X-RAY DIFFRACTION2A16 - 35
3X-RAY DIFFRACTION3A40 - 63
4X-RAY DIFFRACTION4A64 - 88

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