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- PDB-1ocy: Structure of the receptor-binding domain of the bacteriophage T4 ... -

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Basic information

Entry
Database: PDB / ID: 1ocy
TitleStructure of the receptor-binding domain of the bacteriophage T4 short tail fibre
ComponentsBACTERIOPHAGE T4 SHORT TAIL FIBRE
KeywordsSTRUCTURAL PROTEIN / FIBROUS PROTEIN / LIPO-POLYSACCHARIDE BINDING / BACTERIOPHAGE STRUCTURAL PROTEIN / BASEPLATE PROTEIN / GENE PRODUCT 12
Function / homology
Function and homology information


virus tail, baseplate / virus tail, fiber / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / metal ion binding
Similarity search - Function
receptor-binding domain of the bacteriophage t4 short tail fibre, domain 2 / receptor-binding domain of the bacteriophage t4 short tail fibre, domain 2 / heat- and protease-stable fragment of the bacteriophage t4 short fibre, domain 3 / Phage tail collar domain / Bacteriophage T4, Gp12 / Short tail fibre protein, C-terminal / Short tail fibre protein, C-terminal superfamily / Phage short tail fibre protein gp12, middle domain / Short tail fibre protein receptor-binding domain / Phage tail collar domain superfamily ...receptor-binding domain of the bacteriophage t4 short tail fibre, domain 2 / receptor-binding domain of the bacteriophage t4 short tail fibre, domain 2 / heat- and protease-stable fragment of the bacteriophage t4 short fibre, domain 3 / Phage tail collar domain / Bacteriophage T4, Gp12 / Short tail fibre protein, C-terminal / Short tail fibre protein, C-terminal superfamily / Phage short tail fibre protein gp12, middle domain / Short tail fibre protein receptor-binding domain / Phage tail collar domain superfamily / Phage tail collar domain / Phage Tail Collar Domain / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Short tail fiber protein gp12 / Gp12
Similarity search - Component
Biological speciesBACTERIOPHAGE T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.5 Å
AuthorsThomassen, E. / Gielen, G. / Schuetz, M. / Miller, S. / van Raaij, M.J.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The Structure of the Receptor-Binding Domain of the Bacteriophage T4 Short Tail Fibre Reveals a Knitted Trimeric Metal-Binding Fold
Authors: Thomassen, E. / Gielen, G. / Schuetz, M. / Schoehn, G. / Abrahams, J.P. / Miller, S. / van Raaij, M.J.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of a Heat- and Protease-Stable Part of the Bacteriophage T4 Short Tail Fibre
Authors: van Raaij, M.J. / Schoehn, G. / Burda, M.R. / Miller, S.
#2: Journal: Biol.Chem. / Year: 2001
Title: Identification and Crystallisation of a Heat- and Protease-Stable Fragment of the Bacteriophage T4 Short Tail Fibre
Authors: van Raaij, M.J. / Schoehn, G. / Jaquinod, M. / Ashman, K. / Burda, M.R. / Miller, S.
#3: Journal: Biol.Chem. / Year: 2000
Title: Stability of Bacteriophage T4 Short Tail Fiber
Authors: Burda, M.R. / Hindennach, I. / Miller, S.
#4: Journal: Eur.J.Biochem. / Year: 1999
Title: Folding of Coliphage T4 Short Tail Fiber in Vitro. Analysing the Role of a Bacteriophage-Encoded Chaperone
Authors: Burda, M.R. / Miller, S.
History
DepositionFeb 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.page_last / _citation_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BACTERIOPHAGE T4 SHORT TAIL FIBRE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2955
Polymers21,8451
Non-polymers4504
Water9,296516
1
A: BACTERIOPHAGE T4 SHORT TAIL FIBRE
hetero molecules

A: BACTERIOPHAGE T4 SHORT TAIL FIBRE
hetero molecules

A: BACTERIOPHAGE T4 SHORT TAIL FIBRE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,88415
Polymers65,5353
Non-polymers1,34912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.782, 50.782, 435.647
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1530-

SO4

21A-1531-

ZN

31A-2264-

HOH

41A-2275-

HOH

51A-2354-

HOH

61A-2355-

HOH

71A-2447-

HOH

81A-2452-

HOH

91A-2515-

HOH

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Components

#1: Protein BACTERIOPHAGE T4 SHORT TAIL FIBRE


Mass: 21845.139 Da / Num. of mol.: 1 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 330-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE T4 (virus) / Strain: D
Description: VARIANT AS PRESENT IN LABORATORY OF S. MILLER. CO-EXPRESSION WITH GP57 CHAPERONE
Plasmid: PET21+ / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): DE3 / References: UniProt: Q38160, UniProt: P10930*PLUS
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsT4D STRAIN VARIANT, SEQUENCE ANALYSIS OF EXPRESSION PLASMID PERFORMED IN THE LABORATORY OF S. MILLER

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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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growpH: 5.6
Details: 15-25 % (V/V),2-METHYLPROPANE-2-OL (TERTIARY BUTANOL), 100 MM SODIUM CITRATE PH 5.6, 10% (V/V) GLYCEROL,10 MM HEPES, 150 MM SODIUM CHLORIDE
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 mg/mlprotein1drop
215-35 %(v/v)tertiary butanol1reservoir
3100 mMsodium citrate1reservoirpH5.6
40-10 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9464
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9464 Å / Relative weight: 1
ReflectionResolution: 1.5→15 Å / Num. obs: 96264 / % possible obs: 89.8 % / Redundancy: 6.56 % / Biso Wilson estimate: 14.103 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 4.122
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.37 / % possible all: 53.3
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 15 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
% possible obs: 53.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.284

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.5→15 Å / SU B: 0.5303 / SU ML: 0.0194 / Cross valid method: THROUGHOUT / ESU R: 0.0375 / ESU R Free: 0.0354
Details: RESIDUES 85-329 COULD NOT BE MODELLED DUE TO DISORDER
RfactorNum. reflection% reflectionSelection details
Rfree0.1516 1922 2.066 %RANDOM
Rwork0.1434 ---
obs-94341 89.7582 %-
Displacement parametersBiso mean: 23.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 24 516 2077
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor Rfree: 0.152 / Rfactor Rwork: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.018
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.6
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.58 Å / Rfactor Rfree: 0.22 / Num. reflection Rfree: 116 / Rfactor Rwork: 0.2 / Num. reflection obs: 6339

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