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- PDB-4cx8: Monomeric pseudorabies virus protease pUL26N at 2.5 A resolution -

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Basic information

Entry
Database: PDB / ID: 4cx8
TitleMonomeric pseudorabies virus protease pUL26N at 2.5 A resolution
ComponentsPSEUDORABIES VIRUS PROTEASE
KeywordsVIRAL PROTEIN / ASSEMBLIN / UL26 / PRV
Function / homology
Function and homology information


assemblin / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding
Similarity search - Function
Serine Protease, Human Cytomegalovirus Protease; Chain A / Herpesvirus/Caudovirus protease domain / Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21) / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Capsid scaffolding protein
Similarity search - Component
Biological speciesSUID HERPESVIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsZuehlsdorf, M. / Werten, S. / Palm, G.J. / Hinrichs, W.
CitationJournal: Plos Pathog. / Year: 2015
Title: Dimerization-Induced Allosteric Changes of the Oxyanion-Hole Loop Activate the Pseudorabies Virus Assemblin Pul26N, a Herpesvirus Serine Protease.
Authors: Zuhlsdorf, M. / Werten, S. / Klupp, B.G. / Palm, G.J. / Mettenleiter, T.C. / Hinrichs, W.
History
DepositionApr 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references / Other / Structure summary
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Aug 12, 2015Group: Database references
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PSEUDORABIES VIRUS PROTEASE
B: PSEUDORABIES VIRUS PROTEASE


Theoretical massNumber of molelcules
Total (without water)53,2912
Polymers53,2912
Non-polymers00
Water88349
1
A: PSEUDORABIES VIRUS PROTEASE


Theoretical massNumber of molelcules
Total (without water)26,6451
Polymers26,6451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PSEUDORABIES VIRUS PROTEASE


Theoretical massNumber of molelcules
Total (without water)26,6451
Polymers26,6451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.437, 101.337, 130.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.606, -0.1438, 0.7824), (-0.06811, -0.9893, -0.1291), (0.7926, 0.02495, -0.6093)
Vector: -26.42, -10.67, 54.19)

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Components

#1: Protein PSEUDORABIES VIRUS PROTEASE


Mass: 26645.357 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-224
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL (HIS)6-TAG WITH THROMBIN-LINKER / Source: (gene. exp.) SUID HERPESVIRUS 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83417, assemblin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.5 Å3/Da / Density % sol: 50.91 %
Description: STARTING MODEL FOR DIMERIC PRV PROTEASE IS WWPDB ENTRY 1AT3
Crystal growpH: 8 / Details: 0.1 M TRIS PH 8, 14% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.53→80 Å / Num. obs: 18230 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 55.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.29
Reflection shellResolution: 2.53→2.68 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.06 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DIMERIC PRV PROTEASE, YET TO BE DEPOSITED

Resolution: 2.53→79.94 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.912 / SU B: 21.997 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.423 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25215 878 4.8 %RANDOM
Rwork0.19819 ---
obs0.20078 17352 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å20 Å20 Å2
2--1.45 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.53→79.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 0 49 3172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193189
X-RAY DIFFRACTIONr_bond_other_d0.0020.023048
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.9854354
X-RAY DIFFRACTIONr_angle_other_deg0.87736944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4365412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.61321.364132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93615454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8921538
X-RAY DIFFRACTIONr_chiral_restr0.0860.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02726
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4422.2921666
X-RAY DIFFRACTIONr_mcbond_other1.4432.2931665
X-RAY DIFFRACTIONr_mcangle_it2.3733.4332072
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4512.3821523
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.527→2.593 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 62 -
Rwork0.334 1129 -
obs--88.35 %
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)
13.4468-2.9636-0.59468.6238-0.78144.5866-0.1308-0.34840.6240.20930.30270.3336-0.8621-0.669-0.17190.33070.0369-0.00970.2804-0.10370.2454-11.8184-5.53812.7368
26.7729-4.4447-0.53155.03121.31742.4048-0.4462-0.73760.03270.54750.31850.2123-0.1092-0.08850.12780.20820.01420.01230.2539-0.05290.0341-6.8121-15.944815.8577
35.7555-1.10752.14774.9745-0.72755.4271-0.3009-0.30070.62720.5920.2797-0.3878-0.62430.09370.02120.24150.0354-0.01920.1739-0.09240.1095-3.9145-11.79612.1064
44.91880.43882.69991.59941.67087.784-0.0231-0.3233-1.06470.36840.07530.35690.6116-0.3974-0.05220.2384-0.01890.10070.23260.05730.3752-12.4019-24.66696.8744
54.91775.86144.99039.32815.83817.41740.2476-0.22680.30960.1251-0.60110.56780.2365-0.65270.35350.32350.0190.06440.5587-0.28470.1811-25.3113-6.519538.0211
61.07470.58061.81135.26065.20826.6835-0.01020.0969-0.0079-0.21-0.09120.1582-0.18020.02270.10140.21770.047-0.02230.4648-0.20810.1779-17.61192.456639.7905
76.7597-0.75681.04313.91995.45418.41810.1892-0.04980.2198-0.1604-0.1127-0.0774-0.32050.1172-0.07650.3597-0.0599-0.02340.7468-0.23870.3087-14.33722.615340.4317
86.8238-6.6497-4.5889.34659.724612.762-0.4538-0.0061-0.35270.3043-0.08010.4944-0.0191-0.36080.53390.55160.07490.13151.0548-0.3320.746-33.928510.409750.4634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 42
2X-RAY DIFFRACTION2A43 - 129
3X-RAY DIFFRACTION3A130 - 187
4X-RAY DIFFRACTION4A188 - 224
5X-RAY DIFFRACTION5B2 - 32
6X-RAY DIFFRACTION6B33 - 165
7X-RAY DIFFRACTION7B166 - 212
8X-RAY DIFFRACTION8B213 - 223

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