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- PDB-2x5c: Crystal structure of hypothetical protein ORF131 from Pyrobaculum... -

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Basic information

Entry
Database: PDB / ID: 2x5c
TitleCrystal structure of hypothetical protein ORF131 from Pyrobaculum Spherical Virus
ComponentsHYPOTHETICAL PROTEIN ORF131
KeywordsVIRAL PROTEIN
Function / homologyAlpha-Beta Plaits - #3590 / : / PSV_Hypothetical protein ORF131-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / metal ion binding / Alpha Beta / PSV hypothetical protein ORF131-like domain-containing protein
Function and homology information
Biological speciesPYROBACULUM SPHERICAL VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genom. / 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 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Non-polymer description / Other / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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.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_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: HYPOTHETICAL PROTEIN ORF131
B: HYPOTHETICAL PROTEIN ORF131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6215
Polymers29,3982
Non-polymers2233
Water2,072115
1
A: HYPOTHETICAL PROTEIN ORF131
hetero molecules

A: HYPOTHETICAL PROTEIN ORF131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5294
Polymers29,3982
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-y+1,-x+1,-z+1/31
Buried area3170 Å2
ΔGint-39.8 kcal/mol
Surface area10980 Å2
MethodPISA
2
B: HYPOTHETICAL PROTEIN ORF131
hetero molecules

B: HYPOTHETICAL PROTEIN ORF131
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7136
Polymers29,3982
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area3640 Å2
ΔGint-34.3 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.880, 53.880, 127.459
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

21B-2043-

HOH

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Components

#1: Protein HYPOTHETICAL PROTEIN ORF131


Mass: 14699.056 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROBACULUM SPHERICAL VIRUS / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q6ZYH1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.8 Å3/Da / Density % sol: 32.3 % / Description: NONE
Crystal growpH: 8.5
Details: 6.545% ISOPROPANOL, 0.1M TRIS-HCL, PH8.5. THE CRYOPROTECTANT USED WAS 30% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.6
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 11, 2006 / 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: 1.8→19 Å / Num. obs: 19587 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.68 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXCDESOLVE RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→18.824 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 23.78 / Stereochemistry target values: ML / Details: THE STRUCTURE IS ORDERED FROM RESIDUE 29 TO 127
RfactorNum. reflection% reflection
Rfree0.2268 1001 5.1 %
Rwork0.1917 --
obs0.1935 19587 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.254 Å2 / ksol: 0.433 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0158 Å20 Å20 Å2
2---0.0158 Å2-0 Å2
3---0.0316 Å2
Refinement stepCycle: LAST / Resolution: 1.8→18.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1587 0 8 115 1710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181628
X-RAY DIFFRACTIONf_angle_d1.5432178
X-RAY DIFFRACTIONf_dihedral_angle_d16.899615
X-RAY DIFFRACTIONf_chiral_restr0.104233
X-RAY DIFFRACTIONf_plane_restr0.007276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8003-1.89510.29061210.27292380X-RAY DIFFRACTION89
1.8951-2.01370.31481480.2432648X-RAY DIFFRACTION99
2.0137-2.1690.22991530.19942686X-RAY DIFFRACTION100
2.169-2.38690.2581450.18222680X-RAY DIFFRACTION100
2.3869-2.73140.22391440.18112706X-RAY DIFFRACTION100
2.7314-3.43780.22891350.17222728X-RAY DIFFRACTION100
3.4378-18.82540.20211550.19022758X-RAY DIFFRACTION99
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)
13.20310.15590.11433.01612.10731.53620.16660.0385-0.7157-0.06550.0449-0.27150.021-0.0897-0.07660.1746-0.05-0.04220.1327-0.0560.155719.36368.380213.1418
24.65930.7574-1.9052.52171.60142.2877-0.14970.1937-1.3971-0.35080.2199-0.7975-0.23890.4530.06940.3-0.07010.02920.35830.02190.492523.4451-0.200711.7564
31.2594-1.1384-1.29271.59910.14343.0854-0.7457-0.89540.2853-0.4232-0.5024-0.45490.38120.66770.94990.17740.0290.1050.44330.15820.748224.0452-3.895315.1124
40.57571.09520.3364.21491.24050.24780.3448-0.39410.03721.0931-0.45080.25970.4095-0.22410.0630.2773-0.05140.00170.2917-0.04120.137716.485814.880424.6481
51.2980.73010.36110.93520.3392.2346-0.46050.19410.5046-0.1964-0.11330.6464-0.3938-0.81980.55240.3173-0.0114-0.05970.3023-0.15620.318421.093335.094126.1772
61.2830.0590.16794.55570.21711.7035-0.0154-0.30460.19870.50010.1106-0.091-0.1869-0.2589-0.00640.27450.0791-0.02390.2888-0.07260.2395-8.10769.16787.1665
73.7412-0.59151.20354.058-0.42110.5001-0.191-0.57420.38970.11930.1512-0.9596-0.2234-0.18380.00440.28070.10090.0080.3286-0.08810.4189-2.569416.93894.3239
85.2195-2.4412-0.41272.20690.38782.0087-0.28390.09761.5072-0.36510.5057-1.23550.21670.6605-0.12050.15540.03740.01530.3084-0.17530.4782-0.400119.46553.4478
91.8939-1.6029-0.65743.85230.46210.48170.25630.4249-0.3447-0.7783-0.47940.7051-0.0816-0.25670.1650.20770.0346-0.05270.2236-0.11520.2136-9.0453-1.8245-4.3366
101.75671.1615-0.02792.4739-2.01962.79360.3836-0.5272-0.44130.5978-0.2632-0.31760.4239-0.1223-0.05030.5882-0.0760.11930.27630.06580.2946-3.1159-20.86134.9096
110.00560.0001-0.00280.00010.00020.0014-0.0856-2.85581.33930.0834-0.015-1.7311-0.71761.3143-0.30120.95480.09310.0860.5654-0.02760.66491.90554.6013-4.1286
12000000-027033.1649152.32-27033.1500-49152.32000.44440.0580.07050.58560.35421.568424.4428-7.458417.925
130000000-1077.89701077.897501550.93740-1550.93700.36540.06230.17270.36490.00321.087-0.914823.379-1.8045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 29:51)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 52:76)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 77:91)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 92:115)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 116:127)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 29:49)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 50:72)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 73:88)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 89:122)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 123:129)
11X-RAY DIFFRACTION11(CHAIN E AND RESID 1:1)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 1128:1128)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 1131:1131)

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