[English] 日本語
Yorodumi
- PDB-2pnm: Crystal Structure of VP4 protease from infectious pancreatic necr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pnm
TitleCrystal Structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P6122
ComponentsProtease VP4
KeywordsHYDROLASE / protease / Ser/Lys dyad / viral protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / viral capsid / host cell cytoplasm / structural molecule activity / proteolysis / metal ion binding
Similarity search - Function
Ribosomal Protein S5; domain 2 - #110 / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. ...Ribosomal Protein S5; domain 2 - #110 / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Ribosomal Protein S5; domain 2 / Viral coat protein subunit / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesInfectious pancreatic necrosis virus - Sp
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPaetzel, M. / Lee, J. / Feldman, A.R. / Delmas, B.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of the VP4 protease from infectious pancreatic necrosis virus reveals the acyl-enzyme complex for an intermolecular self-cleavage reaction.
Authors: Lee, J. / Feldman, A.R. / Delmas, B. / Paetzel, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Purification, crystallization and preliminary X-ray analysis of truncated and mutant forms of VP4 protease from infectious pancreatic necrosis virus.
Authors: Lee, J. / Feldman, A.R. / Chiu, E. / Chan, C. / Kim, Y.-N. / Delmas, B. / Paetzel, M.
History
DepositionApr 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protease VP4


Theoretical massNumber of molelcules
Total (without water)20,5941
Polymers20,5941
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.953, 76.953, 136.347
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsThis enzymes is a monomer in solution during purification.

-
Components

#1: Protein Protease VP4


Mass: 20593.791 Da / Num. of mol.: 1 / Fragment: VP4hex (residues 524-716) / Mutation: K674A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious pancreatic necrosis virus - Sp
Genus: Aquabirnavirus / Species: Infectious pancreatic necrosis virus / Strain: serotype SP / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q703G9, UniProt: A1XQR0*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 22% PEG 2000 MME, 0.45M Calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→47.7 Å / Num. all: 11248 / Num. obs: 11248 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.5 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 23.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 9.8 / Num. unique all: 1584 / % possible all: 99.8

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→25.52 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.271 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 538 4.8 %RANDOM
Rwork0.182 ---
all0.2 11248 --
obs0.184 11186 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.945 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 0 159 1496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221367
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9831869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.84827.36857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25515212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.175151
X-RAY DIFFRACTIONr_chiral_restr0.10.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021042
X-RAY DIFFRACTIONr_nbd_refined0.2140.2606
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2944
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.217
X-RAY DIFFRACTIONr_mcbond_it0.9241.5927
X-RAY DIFFRACTIONr_mcangle_it1.43421454
X-RAY DIFFRACTIONr_scbond_it2.0013490
X-RAY DIFFRACTIONr_scangle_it2.914.5415
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 44 -
Rwork0.17 750 -
obs-794 99.75 %
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)
110.4332-0.906819.16676.0134-13.790259.98020.4811.9647-0.06330.2684-2.5608-1.80740.78323.55422.07980.03350.0847-0.0650.14950.04950.211221.1153-10.925-4.3224
22.38961.77720.75752.8574-1.03522.44430.1001-0.01050.01160.15650.0027-0.02750.02010.0445-0.10280.05080.0037-0.0350.0215-0.00260.0496.3221-15.6809-9.9954
321.53561.566711.747110.50826.72970.81780.3417-1.4331.13321.1197-0.96140.0476-3.71581.17460.61970.4876-0.44970.00370.21790.0425-0.08211.1988-16.21327.9786
48.05950.978-3.3921.5605-0.18517.48040.2814-0.2098-0.3623-0.05630.0966-0.26220.37710.2344-0.3780.0806-0.0323-0.0750.0022-0.01840.03868.0194-20.9752-7.9427
57.90793.20076.502110.12866.464915.15350.09760.7854-0.1886-0.54690.5139-0.2051-0.15061.1165-0.61140.02330.009-0.04310.0166-0.0650.016316.233-16.0001-5.911
62.24082.87822.10894.05741.86143.97620.37130.0955-0.62610.33470.2165-0.40040.86310.5275-0.58780.13840.0878-0.1945-0.0539-0.06710.11915.4114-27.9351-2.6099
70.2742-0.24911.27266.8589-4.42387.51690.42050.2228-0.64340.20060.3691-0.3181.23480.1234-0.78960.25330.0739-0.2735-0.1646-0.09520.149611.0429-35.9201-6.4777
811.5063-2.84425.36310.9494-1.19272.50140.5030.7434-0.4375-0.5226-0.0522-0.61540.25250.3035-0.45080.06910.0027-0.04710.0218-0.01140.069310.2576-22.1995-8.4629
94.39322.13867.80813.5074-0.278820.6267-0.17890.10870.26840.01050.08760.3391-0.352-0.21190.0913-0.0120.0025-0.0213-0.02810.02090.06150.3128-10.962-13.2234
104.2008-0.07128.69350.17630.518320.52150.0901-0.1353-0.01520.10590.12420.0515-0.0443-0.3097-0.21430.014-0.0319-0.036-0.00470.00130.08268.7852-11.5491-2.9362
111.6482-0.18840.42852.84180.86711.25290.7128-0.5875-0.24820.5985-0.35950.07511.0652-0.2901-0.35330.2005-0.0807-0.169-0.05340.05740.00987.4994-25.27873.6909
123.63381.14981.19613.25452.80277.06250.19130.2187-0.76510.01020.0719-0.13530.822-0.0926-0.26320.1879-0.0532-0.1793-0.09020.02680.1092.9733-32.224-9.0907
1328.9802-8.1801-6.45859.30942.326615.2791-0.0211.3867-0.4489-0.3337-0.20440.15930.9058-0.33910.22540.1597-0.078-0.10930.07160.02980.0452-0.7621-24.1751-16.0097
142.2150.22310.87871.67081.91982.38320.5006-0.4407-0.47440.5837-0.12190.15650.8075-0.4158-0.37860.2342-0.1834-0.1283-0.01150.0802-0.0231-1.8673-30.176-2.5554
157.4756-7.2353-3.41313.6332.60769.61950.2075-0.7762-1.05560.81890.38940.06351.52630.0577-0.59680.3068-0.2748-0.2624-0.10290.16310.0433-1.9529-36.13881.2816
163.8597-5.85572.31313.5516-4.59681.63950.5263-0.6711-0.02711.0681-0.1090.6112-0.0408-0.8693-0.41730.0568-0.16060.04420.20440.0142-0.0619-6.986-18.43312.5434
1714.01946.69280.577810.4409-4.61873.330.0552-0.15560.55420.4880.01820.3365-0.1288-0.6572-0.07340.006-0.04420.01180.11620.0185-0.031-6.8078-17.3037-4.3581
181.13850.88851.46054.7595-1.73033.89970.5289-0.4723-0.35590.36680.01060.56770.7695-1.0494-0.53950.1096-0.2543-0.0130.15270.0784-0.0105-10.0336-28.51770.5611
196.1249-1.70673.32577.35580.54566.90280.7375-0.614-0.56380.0094-0.16480.75430.5926-0.8481-0.57280.1199-0.2286-0.1875-0.03610.10340.109-8.8069-33.8536-7.9715
2016.03231.052512.87522.7602-2.285622.86470.1082-0.20690.82790.2932-0.11640.29920.2567-1.69940.00830.0727-0.1911-0.10380.00940.0714-0.057-10.9331-26.7777-14.012
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11524 - 5281 - 5
22529 - 5456 - 22
33546 - 55823 - 35
44559 - 56736 - 44
55568 - 57345 - 50
66574 - 59451 - 71
77595 - 60272 - 79
88603 - 61080 - 87
99611 - 61888 - 95
1010619 - 62596 - 102
1111626 - 634103 - 111
1212635 - 645112 - 122
1313646 - 651123 - 128
1414652 - 659129 - 136
1515660 - 671137 - 148
1616672 - 679149 - 156
1717680 - 685157 - 162
1818686 - 693163 - 170
1919694 - 705171 - 182
2020706 - 711183 - 188

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more