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- PDB-5jbl: Structure of the bacteriophage T4 capsid assembly protease, gp21. -

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Basic information

Entry
Database: PDB / ID: 5jbl
TitleStructure of the bacteriophage T4 capsid assembly protease, gp21.
ComponentsProhead core protein protease
KeywordsHYDROLASE / protease pentamer / phage T4 / prohead
Function / homologyPeptidase U9, T4 prohead protease / Prohead core protein serine protease / viral procapsid maturation / virion component => GO:0044423 / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / Prohead core protein protease
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.943 Å
AuthorsFokine, A. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
CitationJournal: Structure / Year: 2016
Title: Common Evolutionary Origin of Procapsid Proteases, Phage Tail Tubes, and Tubes of Bacterial Type VI Secretion Systems.
Authors: Fokine, A. / Rossmann, M.G.
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Prohead core protein protease
B: Prohead core protein protease
C: Prohead core protein protease
D: Prohead core protein protease
E: Prohead core protein protease


Theoretical massNumber of molelcules
Total (without water)126,0425
Polymers126,0425
Non-polymers00
Water11,169620
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-48 kcal/mol
Surface area35190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.745, 124.041, 88.959
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Prohead core protein protease / Protein Gp21


Mass: 25208.447 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: The catalytic residues Ser140 and His85 of the gp21 protease were mutated to alanines. In addition Met45 was mutated to Leu.
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 21 / Production host: Escherichia coli (E. coli) / References: UniProt: P06807, EC: 3.4.99.-
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 1.83 Å3/Da / Density % sol: 32.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.3 M Ammonium sulfate, 0.1 M Hepes pH 7.5, and 0.1 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.94→42 Å / Num. obs: 61875 / % possible obs: 93 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.9
Reflection shellResolution: 1.94→1.98 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / % possible all: 76

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.943→41.869 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.75
RfactorNum. reflection% reflection
Rfree0.2047 2355 3.81 %
Rwork0.1719 --
obs0.1731 61875 92.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.943→41.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6413 0 0 620 7033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076547
X-RAY DIFFRACTIONf_angle_d0.8528888
X-RAY DIFFRACTIONf_dihedral_angle_d14.1273904
X-RAY DIFFRACTIONf_chiral_restr0.059962
X-RAY DIFFRACTIONf_plane_restr0.0061170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9425-1.98220.29441170.21612869X-RAY DIFFRACTION76
1.9822-2.02530.21691290.19223376X-RAY DIFFRACTION91
2.0253-2.07240.25981360.17683497X-RAY DIFFRACTION92
2.0724-2.12420.17931120.16993498X-RAY DIFFRACTION93
2.1242-2.18160.22341700.20043514X-RAY DIFFRACTION94
2.1816-2.24580.271980.26963418X-RAY DIFFRACTION91
2.2458-2.31830.38981820.30043382X-RAY DIFFRACTION90
2.3183-2.40120.23271000.17653613X-RAY DIFFRACTION96
2.4012-2.49730.21511950.17253529X-RAY DIFFRACTION95
2.4973-2.61090.1991940.17173678X-RAY DIFFRACTION96
2.6109-2.74860.16831940.15783501X-RAY DIFFRACTION96
2.7486-2.92070.2114970.17153657X-RAY DIFFRACTION96
2.9207-3.14620.18721880.16513599X-RAY DIFFRACTION96
3.1462-3.46270.2086950.15883674X-RAY DIFFRACTION96
3.4627-3.96340.1761880.15093520X-RAY DIFFRACTION95
3.9634-4.99210.1286940.1293626X-RAY DIFFRACTION95
4.9921-41.87870.16281660.16663569X-RAY DIFFRACTION93
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)
11.88020.6390.15952.5757-0.5021.62250.0884-0.26-0.25250.0813-0.0270.07790.1093-0.1098-0.01660.1169-0.00070.00090.15880.05190.1412-3.988-18.7192-4.9322
21.654-0.0889-0.39271.0942-0.18481.7494-0.1084-0.4930.15640.20540.11420.045-0.0493-0.0126-0.00540.18140.0607-0.00630.2648-0.04610.1135-4.171711.4751.3533
31.948-0.72590.27641.96710.0651.4554-0.1127-0.06620.36850.04840.022-0.0832-0.1658-0.09720.07770.1479-0.0024-0.03130.1016-0.02360.1625-4.017426.2546-25.0694
42.356-0.33420.57942.2151-0.4672.0748-0.02290.3742-0.0114-0.30640.0030.0856-0.0326-0.02670.01440.1789-0.02340.00820.1439-0.01140.0968-4.0545.9082-47.6451
52.08530.68040.90592.0740.73461.99280.08210.1042-0.2742-0.1165-0.00360.01620.132-0.0631-0.02650.1429-0.0060.00720.0977-0.01070.1526-3.9945-22.0034-35.0578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E

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