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- PDB-5hm2: Crystal structure of the 3C protease from South African Territori... -

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Basic information

Entry
Database: PDB / ID: 5hm2
TitleCrystal structure of the 3C protease from South African Territories type 2 foot-and-mouth disease virus
Components3C proteinasePicornain 3C
KeywordsHYDROLASE / picornavirus / 3C protease / trypsin-like protease
Function / homology
Function and homology information


virion component => GO:0044423 / RNA-protein covalent cross-linking / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding ...virion component => GO:0044423 / RNA-protein covalent cross-linking / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / ATP binding / cytoplasm
Similarity search - Function
Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases ...Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
3C proteinase / p2/P3 polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus - type SAT 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYang, J. / Leen, E.N. / Curry, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustTBD United Kingdom
CitationJournal: Peerj / Year: 2016
Title: Crystal structure of the 3C protease from Southern African Territories type 2 foot-and-mouth disease virus.
Authors: Yang, J. / Leen, E.N. / Maree, F.F. / Curry, S.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2May 25, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C proteinase
B: 3C proteinase
C: 3C proteinase
D: 3C proteinase
E: 3C proteinase


Theoretical massNumber of molelcules
Total (without water)112,0355
Polymers112,0355
Non-polymers00
Water0
1
A: 3C proteinase


Theoretical massNumber of molelcules
Total (without water)22,4071
Polymers22,4071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3C proteinase


Theoretical massNumber of molelcules
Total (without water)22,4071
Polymers22,4071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3C proteinase


Theoretical massNumber of molelcules
Total (without water)22,4071
Polymers22,4071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3C proteinase


Theoretical massNumber of molelcules
Total (without water)22,4071
Polymers22,4071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 3C proteinase


Theoretical massNumber of molelcules
Total (without water)22,4071
Polymers22,4071
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.980, 53.980, 318.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
3C proteinase / Picornain 3C


Mass: 22406.910 Da / Num. of mol.: 5 / Mutation: C142A C163A
Source method: isolated from a genetically manipulated source
Details: Gly 1 is a vec
Source: (gene. exp.) Foot-and-mouth disease virus - type SAT 2
Strain: SAT2/GHA/8/91 / Gene: 3C / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1EF85, UniProt: X5CZS0*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% (w/v) PEG-8000, 0.09 M Na-cacodylate pH 7.0, 0.27 M Ca-acetate, 0.01 M Tris pH 8.5, 0.08 M Na-thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.2→53.1 Å / Num. all: 17168 / Num. obs: 17053 / % possible obs: 99.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 66.5 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 5.7
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2j92
Resolution: 3.2→46.748 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2723 822 4.86 %Random selection
Rwork0.2224 ---
obs0.2247 16906 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 119 Å2
Refinement stepCycle: LAST / Resolution: 3.2→46.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7535 0 0 0 7535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067650
X-RAY DIFFRACTIONf_angle_d1.07910328
X-RAY DIFFRACTIONf_dihedral_angle_d13.832757
X-RAY DIFFRACTIONf_chiral_restr0.061200
X-RAY DIFFRACTIONf_plane_restr0.0041333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.40050.32811500.29672676X-RAY DIFFRACTION99
3.4005-3.6630.30851330.26922649X-RAY DIFFRACTION99
3.663-4.03140.31521260.24262667X-RAY DIFFRACTION99
4.0314-4.61430.25261220.1962715X-RAY DIFFRACTION99
4.6143-5.81180.24741460.19432682X-RAY DIFFRACTION99
5.8118-46.7530.24831450.20672695X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
19.61216.2341-0.73964.0036-0.83393.47650.0240.14350.64190.07460.26740.7504-0.76030.3473-0.2031.72940.2044-0.07790.84010.00030.6804-10.577120.6037-34.3034
22.6974-0.577-2.79292.3465-1.15049.39640.11381.04330.6475-0.02880.17150.55930.5508-1.54210.03771.3007-0.1249-0.18550.76930.06840.7073-15.6979.9998-35.5368
32.06671.0160.56840.5936-0.02992.8244-0.7050.7622-0.4556-1.57170.43560.4535-0.4022-0.24080.2941.49160.0426-0.1110.826-0.03240.8675-13.89446.4048-36.9796
48.8619-3.2617-0.79037.2942.02836.4542-1.38450.8656-0.42260.8688-0.50591.12560.8033-0.70161.19841.6103-0.0701-0.23341.3249-0.04610.5703-15.80587.323-45.2829
51.9828-6.60738.68753.9554-5.14696.924-0.24753.1724-1.0927-0.8157-0.2533-0.3861-1.15281.44490.53331.3926-0.01420.13411.04330.00210.65486.62051.0502-35.999
66.60810.94780.35412.24260.3563.1038-0.54670.43691.1054-1.5440.5279-0.0487-0.9076-0.7423-0.13531.80260.09830.12290.88160.1160.7687-6.3816.0728-43.1629
72.9464-1.1919-0.80591.44710.36176.48-0.6359-0.32250.2236-0.94590.9006-1.02620.59051.3271-0.23881.0615-0.06180.2640.9896-0.10170.894910.191217.4761-28.9791
81.9679-0.63930.02786.2441.41752.6581-0.08640.56750.43480.2744-0.4713-0.3762-0.0738-0.56910.55881.70040.14290.06871.13680.02830.524-4.42917.4368-24.2439
96.92813.73020.57262.10790.85241.8745-0.09210.08560.3494-0.2520.14230.5037-0.631-0.6049-0.13841.29380.22570.14450.82770.09810.5054-0.60213.761-24.5157
102.4798-1.52222.1973.19460.82095.2019-0.514-0.57450.2414-0.29590.8547-0.0136-1.3814-0.0917-0.15371.3554-0.1561-0.05570.71310.01220.54-0.999715.25-26.6538
113.6597-0.34653.51486.72193.43315.5683-0.46842.1952-0.9042-0.6862-1.1025-0.1064-0.53851.42731.26712.1753-0.05820.35491.3414-0.0250.74932.74413.357-47.0725
121.4573-0.78080.63273.05760.18695.3978-0.56620.1915-0.13990.13540.0722-0.9949-0.3539-0.16280.48830.9770.29860.06050.7197-0.03440.91516.173-10.5751-13.1409
133.72933.7175-0.73523.4797-0.91664.1563-0.0439-0.33390.86-0.6974-0.178-0.5519-0.57820.59740.10930.76050.1583-0.00320.9984-0.03410.702315.0055-1.4683-15.5494
145.55961.0902-5.27163.84510.6236.9648-0.8903-0.6250.4952-0.52670.59430.01870.4045-0.20920.31270.69130.1031-0.13840.84830.03470.55255.3575-1.1402-18.7687
151.9661.8822-0.2795.6391-3.76897.9403-0.3472-0.4495-0.2991-0.93610.0570.05080.7285-0.56750.11210.90520.199-0.13450.844-0.14490.73684.4125-15.5031-16.7485
162.8028-1.1313-0.89175.3084-1.70032.22170.0690.1223-0.2920.47550.0896-0.04810.05310.8147-0.18170.850.3023-0.06050.94720.04960.64576.4024-8.9627-2.8047
175.1423-0.08480.34125.1418-0.2788.3864-0.06740.5648-0.32910.54040.51930.24371.97880.1692-0.36310.98650.0698-0.04790.61790.07950.64051.6434-13.6765-12.6629
181.4194-0.5560.09514.1809-0.35032.92260.3797-0.85260.19690.137-0.89480.3001-0.2259-0.81910.00591.04290.64810.24941.27550.06261.0102-16.67769.73499.2471
194.30392.0678-0.92352.4611.57814.83970.19370.9096-1.0064-0.2679-0.40180.7655-0.0673-1.37340.0711.0840.4330.07091.16710.10391.0388-15.27441.79152.4916
202.05160.47122.05091.3393-0.11862.4043-0.34270.5448-0.3799-0.74420.2621-0.2764-1.84970.58110.41340.8707-0.04640.04850.8204-0.09770.74616.77512.80536.0436
213.92551.90551.88815.54323.54616.9747-0.9352-0.12310.4763-0.33230.46110.0142-1.59680.18320.38171.21980.28170.06871.02520.05810.5199-5.118115.68195.2239
224.5529-1.78360.7285.1111.65876.1119-0.0105-0.05140.61190.59170.08220.2451-0.1834-1.0112-0.1181.26130.37750.21250.93460.07260.6569-6.30619.37218.8116
234.0157-0.1092-0.11472.80110.12998.1422-0.4221-0.21520.28020.64020.7323-0.0017-0.82490.7503-0.12631.24140.20820.1040.6421-0.05780.6316-2.371514.86188.8911
241.37110.5221.06463.00110.68174.0320.52750.66470.04070.0846-0.2052-1.46391.24120.95711.42531.80121.2633-0.30922.53640.0285-1.229420.7521-9.440329.5956
253.20661.47732.71025.58032.23448.1282-0.7956-0.4413-0.38950.31940.2947-1.1222-0.89472.21640.42170.74720.6482-0.07831.83430.29420.77119.11331.05129.0288
266.94450.09831.10883.7095-0.86875.2091-1.06770.44311.32750.57280.3421-0.62990.17432.29750.36231.10530.5854-0.05621.90120.03220.746316.6952.597522.9603
273.43162.679-4.43613.1128-1.83528.28851.07440.78710.51-0.3572-0.14290.07671.261-1.1094-0.97111.05540.2583-0.01591.08180.06080.7869-3.2177-3.019427.6426
283.63111.2704-0.25249.3403-2.38313.9429-0.25830.1067-1.0872-0.2205-0.6115-1.79511.80881.84370.51391.60430.73730.0581.6728-0.18070.832815.9072-10.361719.6634
296.30050.4822-1.04243.82961.08720.4993-1.15840.6064-1.03831.04060.41840.53921.1753-0.89890.06891.36020.1611-0.03631.21340.06730.95571.1253-19.079135.3022
303.2635-0.79940.08942.9860.00092.00260.1650.3039-0.31580.460.1273-0.11730.43020.9185-0.34581.62370.5715-0.10861.89790.00080.667713.5756-10.788939.665
316.8254-1.48321.17298.7697-0.24892.79650.13221.32870.1048-0.00630.713-0.47220.61560.1392-0.92351.26520.5619-0.06171.5222-0.04540.51763.0509-1.232639.0942
323.8137-1.7679-2.17862.0186-1.42385.9058-0.0917-1.1531-0.95550.0203-0.28470.07560.34141.37340.24421.31190.5954-0.07471.19870.15090.775111.664-13.81637.2953
332.08460.12450.03892.3765-0.25834.1768-0.1830.1266-0.1608-0.4202-0.6137-0.00821.50680.42040.31081.32820.6294-0.0781.16170.1220.83756.4719-9.607728.262
340.989-0.25920.05271.253-1.09553.36340.12310.2540.22040.1559-0.31370.37720.0422-0.951-0.18650.72780.28020.03441.45260.08020.7283-19.74161.281749.225
354.99755.7821.49016.58892.19195.32960.05210.3437-0.49530.56520.4207-0.15270.722-1.201-0.49561.11240.37990.08971.77360.08930.6914-13.64-5.65346.7534
364.33593.75894.494.86421.33266.7887-0.83541.9097-1.1614-0.92231.0363-0.4594-0.25310.6036-0.03661.00140.23860.04351.4832-0.04040.5817-5.4472-0.154443.8526
370.9792-0.1254-0.51224.562.77745.72460.2261-0.1450.4056-0.0087-0.14260.1832-0.4496-0.1982-0.06041.05370.31180.14891.43490.1360.6902-11.594411.31147.1814
385.8739-1.4901-0.89193.54150.95874.1833-0.0169-0.16710.38710.91970.1730.19010.031-0.893-0.1811.20050.31260.11991.20310.02730.6338-11.28366.163660.0868
394.76940.217-1.22314.6772-0.40182.076-0.05010.11610.303-0.3013-0.4042-0.3299-1.47790.53220.51051.46390.22390.0071.23270.07740.6012-8.1399.888650.0756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 70 )
5X-RAY DIFFRACTION5chain 'A' and (resid 71 through 82 )
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 102 )
7X-RAY DIFFRACTION7chain 'A' and (resid 103 through 113 )
8X-RAY DIFFRACTION8chain 'A' and (resid 114 through 138 )
9X-RAY DIFFRACTION9chain 'A' and (resid 139 through 155 )
10X-RAY DIFFRACTION10chain 'A' and (resid 156 through 195 )
11X-RAY DIFFRACTION11chain 'A' and (resid 196 through 207 )
12X-RAY DIFFRACTION12chain 'B' and (resid 7 through 39 )
13X-RAY DIFFRACTION13chain 'B' and (resid 40 through 59 )
14X-RAY DIFFRACTION14chain 'B' and (resid 60 through 84 )
15X-RAY DIFFRACTION15chain 'B' and (resid 85 through 113 )
16X-RAY DIFFRACTION16chain 'B' and (resid 114 through 165 )
17X-RAY DIFFRACTION17chain 'B' and (resid 166 through 207 )
18X-RAY DIFFRACTION18chain 'C' and (resid 7 through 37 )
19X-RAY DIFFRACTION19chain 'C' and (resid 38 through 70 )
20X-RAY DIFFRACTION20chain 'C' and (resid 71 through 82 )
21X-RAY DIFFRACTION21chain 'C' and (resid 83 through 113 )
22X-RAY DIFFRACTION22chain 'C' and (resid 114 through 165 )
23X-RAY DIFFRACTION23chain 'C' and (resid 166 through 207 )
24X-RAY DIFFRACTION24chain 'D' and (resid 7 through 23 )
25X-RAY DIFFRACTION25chain 'D' and (resid 24 through 37 )
26X-RAY DIFFRACTION26chain 'D' and (resid 38 through 70 )
27X-RAY DIFFRACTION27chain 'D' and (resid 71 through 84 )
28X-RAY DIFFRACTION28chain 'D' and (resid 85 through 102 )
29X-RAY DIFFRACTION29chain 'D' and (resid 103 through 113 )
30X-RAY DIFFRACTION30chain 'D' and (resid 114 through 138 )
31X-RAY DIFFRACTION31chain 'D' and (resid 139 through 155 )
32X-RAY DIFFRACTION32chain 'D' and (resid 156 through 176 )
33X-RAY DIFFRACTION33chain 'D' and (resid 177 through 207 )
34X-RAY DIFFRACTION34chain 'E' and (resid 7 through 39 )
35X-RAY DIFFRACTION35chain 'E' and (resid 40 through 59 )
36X-RAY DIFFRACTION36chain 'E' and (resid 60 through 82 )
37X-RAY DIFFRACTION37chain 'E' and (resid 83 through 113 )
38X-RAY DIFFRACTION38chain 'E' and (resid 114 through 173 )
39X-RAY DIFFRACTION39chain 'E' and (resid 174 through 207 )

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