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- PDB-1s7z: Structure of Ocr from Bacteriophage T7 -

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Basic information

Entry
Database: PDB / ID: 1s7z
TitleStructure of Ocr from Bacteriophage T7
ComponentsGene 0.3 protein
KeywordsGENE REGULATION / all helical
Function / homology
Function and homology information


symbiont-mediated evasion of host restriction-modification system / symbiont-mediated suppression of host innate immune response
Similarity search - Function
DNA mimic ocr / B-form DNA mimic Ocr / DNA mimic ocr / Protein Ocr / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å
AuthorsWalkinshaw, M.D. / Taylor, P. / Sturrock, S.S. / Atanasiu, C. / Berg, T. / Henderson, R.M. / Edwardson, J.M. / Dryden, D.T.
CitationJournal: Mol.Cell / Year: 2002
Title: Structure of Ocr from Bacteriophage T7, a Protein that Mimics B-Form DNA
Authors: Walkinshaw, M.D. / Taylor, P. / Sturrock, S.S. / Atanasiu, C. / Berg, T. / Henderson, R.M. / Edwardson, J.M. / Dryden, D.T.
History
DepositionJan 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gene 0.3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4994
Polymers14,1001
Non-polymers3993
Water2,126118
1
A: Gene 0.3 protein
hetero molecules

A: Gene 0.3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9988
Polymers28,2012
Non-polymers7976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
2
A: Gene 0.3 protein
hetero molecules

A: Gene 0.3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9988
Polymers28,2012
Non-polymers7976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2280 Å2
ΔGint-180 kcal/mol
Surface area13010 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.777, 37.665, 35.490
Angle α, β, γ (deg.)90.00, 98.42, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe tight (sub nanomolar) dimer in solution is retained in the crystal by a crystallographic two-fold axis The interface is only 250 Angstroms squared for each monomer

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Components

#1: Protein Gene 0.3 protein


Mass: 14100.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: 0.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P03775
#2: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
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: 1.85 Å3/Da / Density % sol: 33.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 32%PEG-8000, 0.1M Tris-HCl, 0.2M caesium chloride, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Sturrock, S.S., (2001) Acta Cryst., D57, 1652.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
132 %PEG80001reservoir
20.1 MTris-HCl1reservoirpH8.2
30.2 M1reservoirCsCl
42.8 %glycerol1reservoir
516 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.87 / Wavelength: 1.2, 0.9777,0.9793
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2000 / Details: channel cut monochromator
RadiationMonochromator: Silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
21.21
30.97771
40.97931
ReflectionResolution: 1.83→38.9 Å / Num. all: 8923 / Num. obs: 8923 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 17.9
Reflection shellResolution: 1.83→1.88 Å / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 13.3 / Rsym value: 0.096 / % possible all: 98.5
Reflection
*PLUS
Highest resolution: 1.8 Å / % possible obs: 99.3 % / Num. measured all: 71916
Reflection shell
*PLUS
% possible obs: 98.5 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.83→38.9 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.888 / SU B: 4.209 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23947 495 5.5 %RANDOM
Rwork0.16975 ---
obs0.17349 8426 96.91 %-
all-8426 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.834 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.48 Å2
2--0.3 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.83→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms876 0 3 118 997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.021893
X-RAY DIFFRACTIONr_bond_other_d0.0010.02762
X-RAY DIFFRACTIONr_angle_refined_deg2.1951.9451213
X-RAY DIFFRACTIONr_angle_other_deg0.95831774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5523105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93615153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021012
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02175
X-RAY DIFFRACTIONr_nbd_refined0.3150.3222
X-RAY DIFFRACTIONr_nbd_other0.2310.3722
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.550
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.4420.55
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.320
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.341
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5030.520
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2981.5529
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4262854
X-RAY DIFFRACTIONr_scbond_it4.63364
X-RAY DIFFRACTIONr_scangle_it6.8954.5359
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.879 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 25
Rwork0.164 427
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.241 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.03
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.2

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