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- PDB-1ei7: TMV COAT PROTEIN REFINED FROM THE 4-LAYER AGGREGATE -

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Basic information

Entry
Database: PDB / ID: 1ei7
TitleTMV COAT PROTEIN REFINED FROM THE 4-LAYER AGGREGATE
ComponentsCOAT PROTEIN
KeywordsVIRUS / disordered loops / Viral protein
Function / homology
Function and homology information


helical viral capsid / structural molecule activity / identical protein binding
Similarity search - Function
Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Capsid protein / Capsid protein
Similarity search - Component
Biological speciesTobacco mosaic virus
MethodX-RAY DIFFRACTION / Resolution: 2.45 Å
AuthorsBhyravbhatla, B. / Watowich, S.J. / Caspar, D.L.
CitationJournal: Biophys.J. / Year: 1998
Title: Refined atomic model of the four-layer aggregate of the tobacco mosaic virus coat protein at 2.4-A resolution.
Authors: Bhyravbhatla, B. / Watowich, S.J. / Caspar, D.L.
History
DepositionFeb 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 20, 2013Group: Refinement description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Oct 31, 2018Group: Data collection / Structure summary / Category: struct_keywords
Item: _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,0112
Polymers35,0112
Non-polymers00
Water6,017334
1
A: COAT PROTEIN
B: COAT PROTEIN
x 34


Theoretical massNumber of molelcules
Total (without water)1,190,36968
Polymers1,190,36968
Non-polymers00
Water1,22568
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation33
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
4
A: COAT PROTEIN
B: COAT PROTEIN
x 17


  • crystal asymmetric unit
  • 595 kDa, 34 polymers
Theoretical massNumber of molelcules
Total (without water)595,18434
Polymers595,18434
Non-polymers00
Water61334
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation16
Unit cell
Length a, b, c (Å)220.845, 171.701, 226.175
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Hermann–Mauguin notation: 17-2 / Schoenflies symbol: D17 (2x17 fold dihedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.93224, -0.00029, 0.36183), (-0.00372, 0.99994, 0.01038), (-0.36181, -0.01103, 0.93218)20.18047, 0.20869, -3.78013
3generate(0.74391, -0.00074, 0.66828), (-0.0105, 0.99986, 0.01279), (-0.66819, -0.01653, 0.7438)37.9883, 0.17812, -14.15205
4generate(0.45365, -0.00612, 0.89116), (-0.01431, 0.9998, 0.01415), (-0.89107, -0.01917, 0.45347)50.65093, 0.5423, -30.45459
5generate(0.09759, -0.01318, 0.99514), (-0.01941, 0.9997, 0.01514), (-0.99504, -0.02079, 0.09731)56.30202, 0.70238, -50.5205
6generate(-0.27098, -0.01954, 0.96239), (-0.02757, 0.99954, 0.01253), (-0.96219, -0.02313, -0.27139)54.35301, 0.3265, -71.2825
7generate(-0.60247, -0.02547, 0.79774), (-0.03286, 0.99943, 0.00709), (-0.79747, -0.02194, -0.60297)45.00132, -0.1332, -89.92058
8generate(-0.84544, -0.03172, 0.53312), (-0.03622, 0.99934, 0.00202), (-0.53283, -0.0176, -0.84604)30.67869, -0.37622, -103.61692
9generate(-0.98129, -0.03713, 0.18894), (-0.03791, 0.99928, -0.00054), (-0.18878, -0.00769, -0.98199)11.05551, -0.25163, -111.4089
10generate(-0.98299, -0.03869, -0.17954), (-0.03856, 0.99925, -0.00418), (0.17956, 0.00282, -0.98374)-9.89218, -0.33599, -111.49278
11generate(-0.85099, -0.0325, -0.52418), (-0.03353, 0.99941, -0.00753), (0.52411, 0.01117, -0.85158)-29.36683, -0.57198, -103.94043
12generate(-0.60598, -0.02966, -0.79492), (-0.02827, 0.99948, -0.01574), (0.79497, 0.01293, -0.60651)-44.43472, -1.14319, -90.03773
13generate(-0.2761, -0.02324, -0.96085), (-0.02051, 0.99962, -0.01828), (0.96091, 0.01466, -0.27648)-53.83889, -1.31207, -71.54736
14generate(0.09036, -0.01551, -0.99579), (-0.01151, 0.9998, -0.01661), (0.99584, 0.01296, 0.09017)-55.79969, -1.3499, -50.95012
15generate(0.44449, -0.00846, -0.89574), (-0.00449, 0.99992, -0.01168), (0.89577, 0.00921, 0.44442)-50.13938, -1.20083, -31.05274
16generate(0.73276, -0.00779, -0.68044), (-0.00252, 0.9999, -0.01415), (0.68048, 0.01208, 0.73267)-37.54948, -0.85093, -14.74149
17generate(0.93234, -0.00558, -0.36155), (0.00141, 0.99993, -0.01179), (0.36159, 0.01048, 0.93228)-20.2436, -0.41613, -3.6987

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Components

#1: Protein COAT PROTEIN


Mass: 17505.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tobacco mosaic virus / Genus: Tobamovirus / References: UniProt: P03570, UniProt: P69687*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2

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Sample preparation

Crystal growTemperature: 300 K / Method: microdialysis / pH: 8
Details: 0.3 M Ammonium Sulfate, 0.1 M Tris/HCl pH 8.0, 14 mg/ml protein concentration, MICRODIALYSIS, temperature 300K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein11
20.2 Mammonium sulfate11
30.1 MTris-HCl11
40.3 Mammonium sulfate12
50.1 MTris-HCl12

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5412
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5412 Å / Relative weight: 1
ReflectionResolution: 2.4→29.9 Å / Num. all: 429646 / Num. obs: 218046 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 6
Reflection shellResolution: 2.45→29.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.094 / % possible all: 65
Reflection
*PLUS
% possible obs: 65.7 % / Num. measured all: 429646

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
X-GENdata reduction
XDSdata scaling
X-PLORphasing
RefinementResolution: 2.45→29.9 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huder
RfactorNum. reflection% reflectionSelection details
Rfree0.225 21804 -random
Rwork0.195 ---
all-429646 --
obs-218046 69 %-
Refinement stepCycle: LAST / Resolution: 2.45→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 0 334 2804
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.97
X-RAY DIFFRACTIONx_bond_d0.01
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 29.9 Å / σ(F): 1 / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.01

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