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- PDB-3sqf: Crystal structure of monomeric M-PMV retroviral protease -

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Basic information

Entry
Database: PDB / ID: 3sqf
TitleCrystal structure of monomeric M-PMV retroviral protease
ComponentsProtease
KeywordsHYDROLASE / folded monomer / retroviral protease folded as a monomer / aspartic protease / retroviral protease / retropepsin / D-type retrovirus
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral process / viral nucleocapsid / structural constituent of virion / aspartic-type endopeptidase activity / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / dUTPase-like / dUTPase ...GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesMason-Pfizer monkey virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6324 Å
AuthorsJaskolski, M. / Kazmierczyk, M. / Gilski, M. / Krzywda, S. / Pichova, I. / Zabranska, H. / Khatib, F. / DiMaio, F. / Cooper, S. / Thompson, J. ...Jaskolski, M. / Kazmierczyk, M. / Gilski, M. / Krzywda, S. / Pichova, I. / Zabranska, H. / Khatib, F. / DiMaio, F. / Cooper, S. / Thompson, J. / Popovic, Z. / Baker, D. / Group, Foldit Contenders
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Crystal structure of a monomeric retroviral protease solved by protein folding game players.
Authors: Khatib, F. / DiMaio, F. / Cooper, S. / Kazmierczyk, M. / Gilski, M. / Krzywda, S. / Zabranska, H. / Pichova, I. / Thompson, J. / Popovic, Z. / Jaskolski, M. / Baker, D.
#1: Journal: Virology / Year: 1998
Title: Three active forms of aspartic proteinase from Mason-Pfizer monkey virus.
Authors: Zabransky, A. / Andreansky, M. / Hruskova-Heidingsfeldova, O. / Havlicek, V. / Hunter, E. / Ruml, T. / Pichova, I.
#2: Journal: J.Mol.Biol. / Year: 2003
Title: Three-dimensional structure of a monomeric form of a retroviral protease.
Authors: Veverka, V. / Bauerova, H. / Zabransky, A. / Lang, J. / Ruml, T. / Pichova, I. / Hrabal, R.
#3: Journal: Nature / Year: 1989
Title: Crystal structure of a retroviral protease proves relationship to aspartic protease family.
Authors: Miller, M. / Jaskolski, M. / Rao, J.K. / Leis, J. / Wlodawer, A.
#4: Journal: Science / Year: 1989
Title: Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease.
Authors: Wlodawer, A. / Miller, M. / Jaskolski, M. / Sathyanarayana, B.K. / Baldwin, E. / Weber, I.T. / Selk, L.M. / Clawson, L. / Schneider, J. / Kent, S.B.
History
DepositionJul 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease


Theoretical massNumber of molelcules
Total (without water)25,8002
Polymers25,8002
Non-polymers00
Water2,774154
1
A: Protease


Theoretical massNumber of molelcules
Total (without water)12,9001
Polymers12,9001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protease


Theoretical massNumber of molelcules
Total (without water)12,9001
Polymers12,9001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.76, 86.62, 39.31
Angle α, β, γ (deg.)90.0, 104.6, 90.0
Int Tables number4
Space group name H-MP1211
DetailsThe biologically active assembly of this protein is a homodimer. The present structure corresponds to the polypeptide chain folded as a monomer. This is not the enzymatically competent unit. There are two monomers in the asymmetric unit (chains A and B) but they do not form a biologically active dimer.

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Components

#1: Protein Protease /


Mass: 12899.834 Da / Num. of mol.: 2 / Fragment: 13 kDa form (UNP residues 163-276) / Mutation: C7A, C106A, D26N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mason-Pfizer monkey virus / Gene: pro, prt / Plasmid: pT7Q10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P07570, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.71 Å3/Da / Density % sol: 28.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M imidazole, 1 M sodium acetate, 1.2-fold molar excess (relative to dimeric protein) of Pro-Tyr-Val-Pst-Ala-Met-Thr (inhibitor), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8086 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 13, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8086 Å / Relative weight: 1
ReflectionResolution: 1.63→43.3 Å / Num. all: 21369 / Num. obs: 21369 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 26.01 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.63-1.734.20.7521.914007333796.3
1.73-1.850.4283.6615617326299.7
1.85-20.2436.3714396303599.6
2-2.190.13211.5113374280699.6
2.19-2.450.09914.9912096252399.4
2.45-2.820.06222.1210606222599.7
2.82-3.450.03932.038960188999.5
3.45-4.870.0342.966796146899.5
4.87-43.30.02444.95383182498.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.7_641refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A model generated by Foldit players from the NMR coordinates 1NSO

1nso


Resolution: 1.6324→28.6 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.8579 / SU ML: 0.23 / Isotropic thermal model: Isotropic / Cross valid method: R-free / Stereochemistry target values: Engh & Huber
Details: TLS groups selected according to the TLSMD server. H atoms were added at riding positions.
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1070 5.01 %RANDOM
Rwork0.1694 ---
all0.1715 21365 --
obs0.1715 21365 99.2 %-
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.162 Å2 / ksol: 0.467 e/Å3
Displacement parametersBiso max: 114.59 Å2 / Biso mean: 28.9429 Å2 / Biso min: 9.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.254 Å2-0 Å2-1.3628 Å2
2---5.9528 Å20 Å2
3---6.2068 Å2
Refinement stepCycle: LAST / Resolution: 1.6324→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 0 154 1674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191567
X-RAY DIFFRACTIONf_angle_d1.772138
X-RAY DIFFRACTIONf_chiral_restr0.114242
X-RAY DIFFRACTIONf_plane_restr0.011267
X-RAY DIFFRACTIONf_dihedral_angle_d12.592590
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6324-1.70660.30621290.27092454258396
1.7066-1.79660.27291340.228525412675100
1.7966-1.90920.2621350.207925512686100
1.9092-2.05650.21681340.171625412675100
2.0565-2.26340.21571320.150825292661100
2.2634-2.59070.20511340.172225492683100
2.5907-3.26330.24421360.154325622698100
3.2633-28.58670.15961360.15222568270499
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)
10.5287-0.2989-0.35380.65170.68830.7287-0.0468-0.07290.1971-0.15530.0056-0.0188-0.66590.1386-0.17690.4446-0.03240.02330.2212-0.04640.12853.795723.882622.8697
20.3092-0.09830.41050.9992-0.46020.66010.1116-0.2867-0.2212-0.01720.02090.2014-0.0074-0.0648-0.01740.07520.00470.01040.1768-0.0140.1543.671312.86918.1613
30.60870.62530.25431.28110.00690.40590.12940.04160.00730.2463-0.0226-0.0769-0.06710.0998-0.03410.0981-0.02170.00190.1636-0.02180.10225.761111.535813.5932
40.71550.91690.70821.20750.74891.5105-0.1001-0.06430.1504-0.39070.0204-0.0623-0.4359-0.0709-0.46250.36340.02520.04090.1137-0.01320.084-0.175825.492717.4011
50.0887-0.01010.09330.12480.0160.106-0.0706-0.04930.05460.06230.0376-0.001-0.0508-0.0119-0.19470.43510.1448-0.12390.1622-0.01520.193-9.154825.885615.4677
62.22552.0965-0.60182.0708-0.10762.35380.2312-0.08280.7346-0.0511-0.01670.1175-1.00570.1501-0.13270.2695-0.0240.02510.1297-0.00950.1631-3.287820.84899.9748
70.4338-0.1847-0.14450.07850.06170.04780.14040.05680.1213-0.0660.1179-0.0254-0.168-0.03582.14830.2431-0.08180.0770.2136-0.0050.0615.724717.96285.3593
80.10060.1304-0.0030.55090.05370.3020.10380.1533-0.26230.0331-0.0915-0.0877-0.0259-0.09150.00680.1046-0.00090.00440.2085-0.04950.12153.59299.14183.3876
92.0479-1.8773-1.00211.80030.910.49170.0760.28050.3623-0.6389-0.2620.2335-0.8718-0.2180.10280.28090.0957-0.06320.2477-0.01090.1672-5.797515.6914-1.6813
100.3523-0.073-0.08980.85970.17290.23820.07370.0964-0.0915-0.0953-0.06230.1489-0.0233-0.02090.0450.66460.1358-0.06820.2424-0.05260.2548-10.044226.29822.8054
110.3702-0.0172-1.16090.4269-0.15573.7461-0.30920.15560.1057-0.3607-0.077-0.07980.0538-0.51260.23780.86080.0456-0.01740.451-0.02770.314-4.971726.8229-3.3843
120.37170.05420.22610.29870.19310.2257-0.06390.08620.208-0.52810.0622-0.0618-0.6147-0.20370.00550.39530.06180.03620.19-0.00340.1468-4.416319.37-0.3678
130.3485-0.03990.08520.07760.28551.50260.07490.0786-0.2866-0.11660.1996-0.0314-0.10550.2408-0.04720.11690.01050.00550.1758-0.01130.1259-5.36269.786810.8431
140.875-0.7161-0.23451.2377-0.67031.2018-0.0757-0.20460.3196-0.06380.0219-0.3670.10520.4682-0.05570.1160.00650.01480.2136-0.0180.15041.823310.242424.7728
150.00430.086-0.0532.6588-2.45462.7352-0.0161-0.1902-0.0395-0.15290.0472-0.06750.2484-0.11240.02480.06610.0114-0.00940.1799-0.02810.0805-4.51549.306220.0598
160.6066-0.37230.25830.89011.39493.7620.0158-0.04890.0094-0.3629-0.03380.1095-0.5116-0.0231-0.1080.17390.07060.00890.1562-0.01460.0892-5.217316.90276.539
170.630.2550.10340.2442-0.15220.28340.13290.05980.18320.06780.00910.0198-0.17770.07440.37590.4561-0.08470.22710.2089-0.01130.23473.458925.52983.7523
181.0402-0.34791.34260.9303-0.92222.0075-0.1935-0.01440.0594-0.11680.16960.0325-0.769-0.15-0.00250.2471-0.00290.04180.1334-0.04390.1115-1.81822.761714.4926
190.09310.36550.26241.42671.02620.739-0.0851-0.01790.1367-0.0946-0.1471-0.012-0.39880.10550.09950.21380.04320.03550.1773-0.01310.1924-7.685618.539518.6358
201.48411.0026-0.95840.9229-0.18691.49250.00060.11220.37410.2658-0.3489-0.2026-0.186-0.09330.10370.1902-0.0252-0.03170.11180.00810.2536-6.365616.436124.8802
210.61510.0124-0.0390.142-0.12110.7692-0.079-0.0779-0.03150.01280.04650.02390.0897-0.0665-0.2480.3881-0.0872-0.00610.1690.02260.08210.409933.342322.9352
220.12070.1982-0.07261.4491.16011.50340.0645-0.10420.03170.03670.1705-0.36560.14690.13760.20710.05190.0205-0.00990.15530.01580.1303-0.199644.924218.1596
230.73620.30420.54931.4845-0.02410.88640.11670.119-0.0480.0381-0.1057-0.2438-0.0842-0.019-0.00830.1072-0.00530.02560.16940.00520.1135-1.969248.652413.4358
241.1844-1.07380.35180.9755-0.32520.1049-0.0945-0.0865-0.08740.01540.0301-0.070.51560.0919-0.10560.23890.01560.0070.08990.01730.08951.432335.599616.3125
250.1215-0.16680.00520.56970.1570.0787-0.0731-0.0775-0.04810.13680.0640.0220.05260.01680.07580.44610.13920.10380.12420.00390.170312.480832.743614.5079
260.1226-0.2849-0.61310.88371.13643.4368-0.1049-0.0334-0.05480.23650.0789-0.04480.22030.21040.09460.2638-0.0562-0.02660.11460.01760.09423.234837.07388.9686
271.6634-0.4897-0.46260.14620.09490.81440.12570.00020.0658-0.14820.06040.06430.499-0.26540.10130.1664-0.0241-0.01320.17760.03870.0914-1.016544.7474.2211
280.40010.01880.69061.805-1.8013.0580.17580.0236-0.3742-0.582-0.2369-0.43240.612-0.09020.07820.21670.05950.0440.26170.00660.19429.549642.3586-1.7768
290.218-0.13480.34691.1278-0.50280.63190.15310.10140.04520.0393-0.04880.07910.02570.1109-0.02710.49520.2040.10220.36580.13710.402615.352234.34061.1023
301.01550.8071-0.9970.719-1.13482.49370.10060.27630.0358-0.2876-0.0677-0.0720.3447-0.1114-0.04820.55540.1023-0.03710.29080.05930.214810.941327.82864.0439
310.348-0.0374-0.58190.1747-0.54833.1899-0.25170.250.035-0.26090.17350.06260.3210.14610.04940.95670.03390.1330.522-0.08910.3947.500232.1106-3.945
321.2531-1.5053-0.42691.84470.84313.32930.15610.2275-0.2201-0.0004-0.37610.07130.7409-0.26850.01650.23260.0462-0.02420.1911-0.02710.14868.647440.61791.5881
331.10950.5681-0.44071.14390.14870.34040.04490.3680.0206-0.1830.1186-0.0554-0.09590.02890.41740.06380.02570.02610.18430.01560.09978.888148.401111.4307
340.8571-0.0155-0.57930.26290.68452.1252-0.0720.0473-0.05760.0942-0.05260.1344-0.1055-0.1297-0.04750.10370.01140.03140.19880.02550.09621.65347.465624.7459
350.27980.43210.37691.51780.54820.51080.0607-0.12710.1917-0.08670.01230.1081-0.05960.20040.00770.06240.02940.01560.16640.00570.12297.659849.401821.5593
360.87260.2671.61212.603-2.0415.52610.1202-0.139-0.1625-0.4866-0.2223-0.07030.5452-0.07110.12530.1580.06120.0190.194-0.00310.11588.873441.58927.7681
370.18480.16850.08710.15350.08090.0440.0253-0.03890.0057-0.0007-0.05950.04130.0314-0.08440.0930.5938-0.0019-0.32550.1731-0.140.21450.040532.18813.8286
380.1244-0.1032-0.39442.37991.11181.5203-0.01380.2134-0.0499-0.2750.21760.10890.7383-0.19680.20960.2716-0.0438-0.02160.14460.04520.1112.877135.238213.7494
390.81230.4078-0.37530.2042-0.18850.1751-0.05530.23190.037-0.1116-0.15670.02360.75430.24120.00550.25520.1009-0.02860.2125-0.02080.169512.021137.917318.2093
401.51020.0872-1.60830.33260.00721.7428-0.3153-0.0216-0.28540.0833-0.33870.04360.2405-0.19220.29670.162-0.00010.04150.1770.00390.258510.475342.320324.2038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 9:12)A9 - 12
2X-RAY DIFFRACTION2(chain A and resid 13:16)A13 - 16
3X-RAY DIFFRACTION3(chain A and resid 17:22)A17 - 22
4X-RAY DIFFRACTION4(chain A and resid 23:26)A23 - 26
5X-RAY DIFFRACTION5(chain A and resid 27:30)A27 - 30
6X-RAY DIFFRACTION6(chain A and resid 31:34)A31 - 34
7X-RAY DIFFRACTION7(chain A and resid 35:39)A35 - 39
8X-RAY DIFFRACTION8(chain A and resid 40:44)A40 - 44
9X-RAY DIFFRACTION9(chain A and resid 45:48)A45 - 48
10X-RAY DIFFRACTION10(chain A and resid 49:55)A49 - 55
11X-RAY DIFFRACTION11(chain A and resid 56:59)A56 - 59
12X-RAY DIFFRACTION12(chain A and resid 60:63)A60 - 63
13X-RAY DIFFRACTION13(chain A and resid 64:70)A64 - 70
14X-RAY DIFFRACTION14(chain A and resid 71:74)A71 - 74
15X-RAY DIFFRACTION15(chain A and resid 75:80)A75 - 80
16X-RAY DIFFRACTION16(chain A and resid 81:84)A81 - 84
17X-RAY DIFFRACTION17(chain A and resid 85:89)A85 - 89
18X-RAY DIFFRACTION18(chain A and resid 90:95)A90 - 95
19X-RAY DIFFRACTION19(chain A and resid 96:99)A96 - 99
20X-RAY DIFFRACTION20(chain A and resid 100:103)A100 - 103
21X-RAY DIFFRACTION21(chain B and resid 9:12)B9 - 12
22X-RAY DIFFRACTION22(chain B and resid 13:16)B13 - 16
23X-RAY DIFFRACTION23(chain B and resid 17:20)B17 - 20
24X-RAY DIFFRACTION24(chain B and resid 21:26)B21 - 26
25X-RAY DIFFRACTION25(chain B and resid 27:31)B27 - 31
26X-RAY DIFFRACTION26(chain B and resid 32:35)B32 - 35
27X-RAY DIFFRACTION27(chain B and resid 36:44)B36 - 44
28X-RAY DIFFRACTION28(chain B and resid 45:48)B45 - 48
29X-RAY DIFFRACTION29(chain B and resid 49:52)B49 - 52
30X-RAY DIFFRACTION30(chain B and resid 53:56)B53 - 56
31X-RAY DIFFRACTION31(chain B and resid 57:60)B57 - 60
32X-RAY DIFFRACTION32(chain B and resid 61:64)B61 - 64
33X-RAY DIFFRACTION33(chain B and resid 65:70)B65 - 70
34X-RAY DIFFRACTION34(chain B and resid 71:74)B71 - 74
35X-RAY DIFFRACTION35(chain B and resid 75:79)B75 - 79
36X-RAY DIFFRACTION36(chain B and resid 80:84)B80 - 84
37X-RAY DIFFRACTION37(chain B and resid 85:89)B85 - 89
38X-RAY DIFFRACTION38(chain B and resid 90:94)B90 - 94
39X-RAY DIFFRACTION39(chain B and resid 95:99)B95 - 99
40X-RAY DIFFRACTION40(chain B and resid 100:102)B100 - 102

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