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- PDB-4d1f: Crystal structure of the fiber head domain of the Atadenovirus sn... -

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Basic information

Entry
Database: PDB / ID: 4d1f
TitleCrystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1, native, first P212121 crystal form
ComponentsFIBER PROTEINFibrous protein
KeywordsVIRAL PROTEIN
Function / homologyAdenovirus fibre protein / Attachment protein shaft domain superfamily / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / Fiber protein
Function and homology information
Biological speciesSNAKE ADENOVIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSingh, A.K. / van Raaij, M.J.
Citation
Journal: PLoS ONE / Year: 2014
Title: Crystal structure of the fibre head domain of the Atadenovirus Snake Adenovirus 1.
Authors: Singh, A.K. / Menendez-Conejero, R. / San Martin, C. / van Raaij, M.J.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Crystallization of the C-terminal domain of the fibre protein from snake adenovirus 1, an atadenovirus.
Authors: Singh, A.K. / Menendez-Conejero, R. / San Martin, C. / van Raaij, M.J.
#2: Journal: Archives of Virology / Year: 1993
Title: Physicochemical Properties and Cytopathogenicity of an Adenovirus-Like Agent Isolated from Corn Snake (Elaphe Guttata).
Authors: Juhasz, A. / Ahne, W.
#3: Journal: Virus Res. / Year: 2008
Title: Completion of the Genome Analysis of Snake Adenovirus Type 1, a Representative of the Reptilian Lineage within the Novel Genus Atadenovirus.
Authors: Farkas, S.L. / Harrach, B. / Benko, M.
History
DepositionMay 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBER PROTEIN
B: FIBER PROTEIN
C: FIBER PROTEIN
D: FIBER PROTEIN
E: FIBER PROTEIN
F: FIBER PROTEIN
G: FIBER PROTEIN
H: FIBER PROTEIN
I: FIBER PROTEIN
J: FIBER PROTEIN
K: FIBER PROTEIN
L: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,53313
Polymers184,44112
Non-polymers921
Water3,945219
1
D: FIBER PROTEIN
E: FIBER PROTEIN
F: FIBER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2024
Polymers46,1103
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-22.8 kcal/mol
Surface area13240 Å2
MethodPISA
2
J: FIBER PROTEIN
K: FIBER PROTEIN
L: FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)46,1103
Polymers46,1103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-21.5 kcal/mol
Surface area13590 Å2
MethodPISA
3
A: FIBER PROTEIN
B: FIBER PROTEIN
C: FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)46,1103
Polymers46,1103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-22.3 kcal/mol
Surface area13400 Å2
MethodPISA
4
G: FIBER PROTEIN
H: FIBER PROTEIN
I: FIBER PROTEIN


Theoretical massNumber of molelcules
Total (without water)46,1103
Polymers46,1103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-21.9 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.660, 122.450, 133.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLNGLNAA240 - 24940 - 49
21THRTHRGLNGLNBB240 - 24940 - 49
31THRTHRGLNGLNCC240 - 24940 - 49
41THRTHRGLNGLNDD240 - 24940 - 49
51THRTHRGLNGLNEE240 - 24940 - 49
61THRTHRGLNGLNFF240 - 24940 - 49
71THRTHRGLNGLNGG240 - 24940 - 49
81THRTHRGLNGLNHH240 - 24940 - 49
91THRTHRGLNGLNII240 - 24940 - 49
101THRTHRGLNGLNJJ240 - 24940 - 49
111THRTHRGLNGLNKK240 - 24940 - 49
121THRTHRGLNGLNLL240 - 24940 - 49
12SERSERGLUGLUAA255 - 34455 - 144
22SERSERGLUGLUBB255 - 34455 - 144
32SERSERGLUGLUCC255 - 34455 - 144
42SERSERGLUGLUDD255 - 34455 - 144
52SERSERGLUGLUEE255 - 34455 - 144
62SERSERGLUGLUFF255 - 34455 - 144
72SERSERGLUGLUGG255 - 34455 - 144
82SERSERGLUGLUHH255 - 34455 - 144
92SERSERGLUGLUII255 - 34455 - 144
102SERSERGLUGLUJJ255 - 34455 - 144
112SERSERGLUGLUKK255 - 34455 - 144
122SERSERGLUGLULL255 - 34455 - 144

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Components

#1: Protein
FIBER PROTEIN / Fibrous protein / SPIKE / PROTEIN IV / FIBER PROTEIN OF THE ATADENOVIRUS SNAKE ADENOVIRUS 1


Mass: 15370.116 Da / Num. of mol.: 12 / Fragment: FIBER HEAD DOMAIN, RESIDUES 234-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SNAKE ADENOVIRUS 1
Description: SNAKE ADENOVIRUS 1 (SNADV1) WAS FIRST ISOLATED FROM THE CORN SNAKE ELAPHE GUTTATA, JUHASZ & AHNE, 1993, SEE ADDITIONAL REFERENCE 2.
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CB96
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE C-TERMINAL PART OF THE SEQUENCE IS DIFFERENT, WE BELIEVE THE DATABASE SEQUENCE IS WRONG.

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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: 1.8 Å3/Da / Density % sol: 31 % / Description: NONE
Crystal growpH: 7.5
Details: 10 MM TRIS-HCL, 1.7 M AMMONIUM SULFATE, 0.085 M HEPES SODIUM SALT PH 7.5, 1.7%(V/V) PEG 400, 15%(V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2012 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 36484 / % possible obs: 99.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 9 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D0V

4d0v


Resolution: 2.7→29.89 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / SU B: 15.523 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24736 2057 5.9 %THIN SHELLS
Rwork0.21227 ---
obs0.21442 32882 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.454 Å2
Baniso -1Baniso -2Baniso -3
1-5.98 Å20 Å20 Å2
2---2.06 Å20 Å2
3----3.91 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9574 0 6 219 9799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229784
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.97913243
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31151255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35523.939396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.72151569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9451548
X-RAY DIFFRACTIONr_chiral_restr0.0780.21495
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217372
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.23320
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.26671
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2328
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3870.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3180.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.87726252
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93449970
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.82883532
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.68123273
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 757 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.050.05
3Ctight positional0.050.05
4Dtight positional0.040.05
5Etight positional0.050.05
6Ftight positional0.050.05
7Gtight positional0.050.05
8Htight positional0.040.05
9Itight positional0.040.05
10Jtight positional0.040.05
11Ktight positional0.050.05
12Ltight positional0.050.05
1Atight thermal0.10.5
2Btight thermal0.110.5
3Ctight thermal0.110.5
4Dtight thermal0.090.5
5Etight thermal0.10.5
6Ftight thermal0.10.5
7Gtight thermal0.10.5
8Htight thermal0.090.5
9Itight thermal0.090.5
10Jtight thermal0.110.5
11Ktight thermal0.120.5
12Ltight thermal0.10.5
LS refinement shellResolution: 2.7→2.862 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.34 329 -
Rwork0.316 5194 -
obs--99.8 %

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