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- PDB-4bbd: THE STRUCTURE OF VACCINIA VIRUS N1 R58Y MUTANT -

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Basic information

Entry
Database: PDB / ID: 4bbd
TitleTHE STRUCTURE OF VACCINIA VIRUS N1 R58Y MUTANT
ComponentsN1L
KeywordsVIRAL PROTEIN / BCL-LIKE PROTEIN / APOPTOSIS / VIRULENCE FACTOR
Function / homology
Function and homology information


symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host NF-kappaB cascade / virus-mediated perturbation of host defense response
Similarity search - Function
Orthopoxvirus, Protein N1 / dsDNA poxvirus / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / Apoptosis Regulator Bcl-x / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein OPG035 / N1L
Similarity search - Component
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMaluquer de Motes, C. / Cooray, S. / McGourty, K. / Ren, H. / Bahar, M.W. / Stuart, D.I. / Grimes, J.M. / Graham, S.C. / Smith, G.L.
CitationJournal: Plos Pathog. / Year: 2011
Title: Inhibition of Apoptosis and NF-kappaB Activation by Vaccinia Protein N1 Occur Via Distinct Binding Surfaces and Make Different Contributions to Virulence.
Authors: Maluquer De Motes, C. / Cooray, S. / Ren, H. / Almeida, G.M.F. / Mcgourty, K. / Bahar, M.W. / Stuart, D.I. / Grimes, J.M. / Graham, S.C. / Smith, G.L.
History
DepositionSep 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N1L
B: N1L
C: N1L
D: N1L
E: N1L
F: N1L


Theoretical massNumber of molelcules
Total (without water)90,2356
Polymers90,2356
Non-polymers00
Water00
1
B: N1L
E: N1L


Theoretical massNumber of molelcules
Total (without water)30,0782
Polymers30,0782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-3.1 kcal/mol
Surface area11420 Å2
MethodPISA
2
C: N1L
D: N1L


Theoretical massNumber of molelcules
Total (without water)30,0782
Polymers30,0782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-3.9 kcal/mol
Surface area11370 Å2
MethodPISA
3
A: N1L
F: N1L


Theoretical massNumber of molelcules
Total (without water)30,0782
Polymers30,0782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-3.5 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.560, 110.200, 72.930
Angle α, β, γ (deg.)90.00, 111.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N1L / N1L PROTEIN / VACV-DUKE-037 / VACV026 / VIROKINE


Mass: 15039.105 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: C40S MUTATION WAS INTRODUCED TO AVOID INTERMOLECULAR DISULPHIDE BOND DRIVEN AGGREGATION.
Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q49PX0, UniProt: P21054*PLUS
Sequence detailsR58Y IS FUNCTIONAL MUTATION. C40S MUTATION WAS INTRODUCED TO AVOID INTERMOLECULAR DISULPHIDE BOND ...R58Y IS FUNCTIONAL MUTATION. C40S MUTATION WAS INTRODUCED TO AVOID INTERMOLECULAR DISULPHIDE BOND DRIVEN AGGREGATION (AS PDB ID 2UXE). C-TERMINAL LEHHHHHH SEQUENCE DERIVES FROM EXPRESSION VECTOR.

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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: 2.93 Å3/Da / Density % sol: 57.97 %
Description: SOLVED BY ISOMORPHOUS DIFFERENCE FOURIER SYNTHESIS.
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESAERCH / Detector: CCD / Date: Nov 10, 2008
Details: FOCUSING MIRRORS, ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK- BAEZ GEOMETRY
RadiationMonochromator: HORIZONTALLY DIFFRACTING MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 20904 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 91.12 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 20
Reflection shellResolution: 3→3.05 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
BUSTER-TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I39

2i39


Resolution: 3→42.79 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 1061 5.1 %RANDOM
Rwork0.1763 ---
obs0.1775 20818 --
Displacement parametersBiso mean: 75.91 Å2
Baniso -1Baniso -2Baniso -3
1-8.5699 Å20 Å22.1312 Å2
2--3.3567 Å20 Å2
3----11.9266 Å2
Refine analyzeLuzzati coordinate error obs: 0.431 Å
Refinement stepCycle: LAST / Resolution: 3→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5682 0 0 0 5682
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015769HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.027782HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2150SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes184HARMONIC2
X-RAY DIFFRACTIONt_gen_planes796HARMONIC5
X-RAY DIFFRACTIONt_it5769HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.14
X-RAY DIFFRACTIONt_other_torsion20.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion762SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6827SEMIHARMONIC4
LS refinement shellResolution: 3→3.16 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2943 164 5.52 %
Rwork0.2389 2807 -
all0.2419 2971 -
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)
11.73910.11770.54596.9515-3.5495.96260.06710.361-0.3451-1.47250.02490.41871.14790.2332-0.0920.35820.1728-0.2664-0.2317-0.0804-0.166635.7308-15.3999-16.658
23.16010.4358-1.37775.4303-2.343.37450.0278-0.07620.05250.53660.01990.6869-0.388-0.3755-0.0477-0.0472-0.0110.0668-0.131-0.0456-0.052812.232231.4335-16.9047
35.9608-1.3464-1.68673.02731.01973.7190.30070.81360.5609-0.7145-0.047-0.2508-0.5152-0.3213-0.2536-0.0539-0.00580.0714-0.03150.1064-0.1162-3.82387.17-31.6955
43.3749-0.8945-1.63445.09942.36554.2176-0.0755-0.6903-0.09930.69180.2337-0.12720.47450.3121-0.1581-0.0377-0.0232-0.06110.05590.0351-0.13516.2114-9.0926-17.8813
52.82010.88621.21184.52311.82654.60180.07360.29440.0027-0.03060.0875-0.65510.20790.3908-0.1611-0.0736-0.0212-0.0199-0.13080.0382-0.039534.91226.5359-18.0233
64.78580.3972-0.65512.6918-0.38852.90080.1121-0.40670.29330.3804-0.12530.0949-0.06480.11850.0131-0.06950.0076-0.0371-0.0473-0.03-0.109940.15564.5224-5.7665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1-114
2X-RAY DIFFRACTION2CHAIN B AND RESID 1-114
3X-RAY DIFFRACTION3CHAIN C AND RESID 1-114
4X-RAY DIFFRACTION4CHAIN D AND RESID 1-114
5X-RAY DIFFRACTION5CHAIN E AND RESID 1-114
6X-RAY DIFFRACTION6CHAIN F AND RESID 1-114

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