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- PDB-2x4j: Crystal structure of ORF137 from Pyrobaculum spherical virus -

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Basic information

Entry
Database: PDB / ID: 2x4j
TitleCrystal structure of ORF137 from Pyrobaculum spherical virus
ComponentsHYPOTHETICAL PROTEIN ORF137
KeywordsVIRAL PROTEIN
Function / homologySH3 type barrels. - #600 / Domain of unknown function DUF5608 / Domain of unknown function DUF5607 / Domain of unknown function (DUF5607) / Domain of unknown function (DUF5608) / SH3 type barrels. / Roll / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesPYROBACULUM SPHERICAL VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.62 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionFeb 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 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 / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN ORF137


Theoretical massNumber of molelcules
Total (without water)14,9671
Polymers14,9671
Non-polymers00
Water79344
1
A: HYPOTHETICAL PROTEIN ORF137

A: HYPOTHETICAL PROTEIN ORF137

A: HYPOTHETICAL PROTEIN ORF137


Theoretical massNumber of molelcules
Total (without water)44,9023
Polymers44,9023
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area3320 Å2
ΔGint-18.3 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.770, 89.770, 36.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein HYPOTHETICAL PROTEIN ORF137


Mass: 14967.177 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROBACULUM SPHERICAL VIRUS / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6ZYJ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.89 Å3/Da / Density % sol: 34.9 % / Description: NONE
Crystal growpH: 7
Details: 23% PEG3350, 0.37M MA-SCN, 0.23M MGCL2, 0.1M MES, PH 7.0. CRYSTAL CRYOPROTECTED WITH 40% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.6
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 15, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6 Å / Relative weight: 1
ReflectionResolution: 1.62→44.9 Å / Num. obs: 22381 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2
Reflection shellResolution: 1.62→1.74 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.7 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
SCALEPACKdata scaling
SHELXCDESOLVE RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.62→44.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.902 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20241 665 5.1 %RANDOM
Rwork0.16791 ---
obs0.16964 12476 94.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.001 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.14 Å20 Å2
2---0.29 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.62→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 0 44 897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.022870
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1581.9651178
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7315107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.20924.41234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65615154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.257153
X-RAY DIFFRACTIONr_chiral_restr0.150.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021632
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1271.5536
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0952869
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7593334
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.8374.5309
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.7673870
X-RAY DIFFRACTIONr_sphericity_free10.352344
X-RAY DIFFRACTIONr_sphericity_bonded4.3473853
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 38 -
Rwork0.3 701 -
obs--70.05 %
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)
115.5570.20521.39093.03620.05680.12910.1105-0.2322-0.28110.4449-0.09140.26270.0425-0.0065-0.01910.26960.03110.01130.15160.06430.245714.97-14.94823.537
26.9307-4.38564.10696.8454-5.44158.0784-0.17010.3989-0.4801-0.33220.0706-0.10420.1554-0.23940.09950.1068-0.03030.03020.1394-0.06320.088713.309-9.4699.708
34.0391-1.63361.56572.57850.67829.9761-0.05390.137-0.23020.01640.0124-0.22590.3080.28520.04160.0605-0.02210.02080.07740.00170.118919.087-8.23415.53
44.7643-0.16140.53551.21472.2534.73460.0005-0.1690.00910.1661-0.07160.04050.2683-0.17170.07120.1330.00690.00690.13240.02930.09414.386-4.70724.482
53.52120.017-0.59760.90240.07770.6004-0.0675-0.0071-0.2115-0.0638-0.0007-0.04730.07820.02680.06820.1103-0.00030.01720.1277-0.01130.091916.136-5.81315.176
63.77871.7246-0.0874.81851.6211.7439-0.0204-0.3593-0.19240.42490.02-0.19010.10650.10880.00040.11230.0188-0.02490.1430.00870.078917.551-3.23624.674
74.94171.26660.03411.1420.54390.92510.09670.06760.34020.04160.0025-0.053-0.026-0.002-0.09920.1072-0.00310.00790.1218-0.00120.110618.185.9813.908
813.371410.35311.446611.24632.06574.5623-0.41220.6360.2625-0.53740.34710.1743-0.1461-0.0250.06510.08470.0251-0.00920.11880.04090.093112.4726.6548.714
97.09633.459-3.22713.3241-3.22795.50690.1095-0.54870.44080.28530.04770.0833-0.22080.0285-0.15720.11310.0319-0.00210.1819-0.03880.121613.25310.1622.563
1012.4344-2.1871-1.78512.2386-6.557111.8750.14510.80081.1718-0.7194-0.1817-0.2472-0.07950.23740.03660.1357-0.0269-0.00280.11960.08720.242813.9616.64711.909
110.1791-0.2887-0.5337.3773-2.30393.7565-0.0187-0.00370.01010.0078-0.12390.04450.10650.09760.14260.08970.02880.01020.15310.02490.13337.3037.11918.337
123.4134-1.1266-1.22162.4260.44841.02080.00730.06610.1298-0.07070.071-0.29860.0176-0.1231-0.07820.1132-0.00750.00990.1265-0.0010.087719.5530.513.812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 21
2X-RAY DIFFRACTION2A22 - 31
3X-RAY DIFFRACTION3A32 - 41
4X-RAY DIFFRACTION4A42 - 47
5X-RAY DIFFRACTION5A48 - 64
6X-RAY DIFFRACTION6A65 - 85
7X-RAY DIFFRACTION7A86 - 96
8X-RAY DIFFRACTION8A97 - 104
9X-RAY DIFFRACTION9A105 - 113
10X-RAY DIFFRACTION10A114 - 121
11X-RAY DIFFRACTION11A122 - 129
12X-RAY DIFFRACTION12A130 - 136

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