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- PDB-5fgy: Structure of human adenovirus 2 protease with cofactor pVIC -

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Basic information

Entry
Database: PDB / ID: 5fgy
TitleStructure of human adenovirus 2 protease with cofactor pVIC
Components
  • Protease
  • pVIC
KeywordsHYDROLASE / protease / cofactor / complex
Function / homology
Function and homology information


adenain / nuclear capsid assembly / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / cysteine-type peptidase activity / virion component / viral capsid / host cell ...adenain / nuclear capsid assembly / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / cysteine-type peptidase activity / virion component / viral capsid / host cell / host cell cytoplasm / cysteine-type endopeptidase activity / host cell nucleus / proteolysis / DNA binding
Similarity search - Function
Peptidase C5, adenain / Adenovirus endoprotease / Minor capsid protein VI / Minor capsid protein VI / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protease / Pre-protein VI
Similarity search - Component
Biological speciesHuman adenovirus C serotype 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDavis, R.R. / Martinez, P. / Hollis, T.
CitationJournal: To Be Published
Title: Structure of human adenovirus 2 protease with cofactor pVIC
Authors: Davis, R.R. / Martinez, P. / Hollis, T.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: pVIC


Theoretical massNumber of molelcules
Total (without water)24,4682
Polymers24,4682
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-7 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.420, 112.420, 49.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protease / Adenain / Adenovirus protease / AVP / Adenovirus proteinase / Endoprotease


Mass: 23114.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus C serotype 2 / Gene: L3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03252, adenain
#2: Protein/peptide pVIC


Mass: 1353.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03274*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: Grew over one week at 4 degrees Celsius in 0.1 M sodium citrate pH 6.4, 1.7 M sodium acetate, 1 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 70 / Detector: CCD / Date: Nov 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→97.36 Å / Num. obs: 20733 / % possible obs: 97.7 % / Redundancy: 5.54 % / Rmerge(I) obs: 0.059 / Rsym value: 0.065 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.46 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 6 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Cootmodel building
MOLREPphasing
d*TREKdata scaling
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AVP

1avp


Resolution: 2.1→97.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.185 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19691 1033 5 %RANDOM
Rwork0.17554 ---
obs0.17663 19700 98.3 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.214 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å2-0 Å2
2--0.48 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→97.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1707 0 0 164 1871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191755
X-RAY DIFFRACTIONr_bond_other_d0.0020.021623
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9422373
X-RAY DIFFRACTIONr_angle_other_deg0.99633731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8775212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9922.61984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38215288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8331515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212008
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02453
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_it1.2421.075854
X-RAY DIFFRACTIONr_mcbond_other1.2421.075853
X-RAY DIFFRACTIONr_mcangle_it1.8471.6031064
X-RAY DIFFRACTIONr_mcangle_other1.8461.6031065
X-RAY DIFFRACTIONr_scbond_it1.9291.3901
X-RAY DIFFRACTIONr_scbond_other1.9291.3901
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9561.8591309
X-RAY DIFFRACTIONr_long_range_B_refined6.40210.352133
X-RAY DIFFRACTIONr_long_range_B_other6.0679.5082054
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 69 -
Rwork0.187 1436 -
obs--95.37 %
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)
11.0706-0.14090.00831.57690.13851.8490.03010.0536-0.0957-0.0056-0.02330.00040.28680.0348-0.00680.10940.0045-0.02030.0153-0.00790.0946-55.46814.9673.915
27.3454-4.1694-9.70362.55125.322513.07690.0459-0.2630.1693-0.09810.1134-0.16310.01010.52-0.15930.14130.00990.00890.2759-0.00770.1856-42.98523.435-0.985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 204
2X-RAY DIFFRACTION2B205 - 215

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