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- PDB-3c9i: Structure of P22 Tail-Needle GP26 Bound to Xenon Gas -

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Basic information

Entry
Database: PDB / ID: 3c9i
TitleStructure of P22 Tail-Needle GP26 Bound to Xenon Gas
ComponentsTail needle protein gp26
KeywordsVIRAL PROTEIN / P22 / Tail-Needle / Xenon / Coiled-Coil / Protein Fiber / Coiled coil / Late protein
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, short tail mechanism / virus tail / symbiont genome entry into host cell via pore formation in plasma membrane
Similarity search - Function
Helix Hairpins - #940 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
XENON / Tail needle protein gp26
Similarity search - Component
Biological speciesBacteriophage P22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCingolani, G. / Olia, A.S.
CitationJournal: Protein Sci. / Year: 2009
Title: Structural plasticity of the phage P22 tail needle gp26 probed with xenon gas.
Authors: Olia, A.S. / Casjens, S. / Cingolani, G.
History
DepositionFeb 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tail needle protein gp26
B: Tail needle protein gp26
C: Tail needle protein gp26
D: Tail needle protein gp26
E: Tail needle protein gp26
F: Tail needle protein gp26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,83224
Polymers153,8436
Non-polymers1,98918
Water28,6441590
1
A: Tail needle protein gp26
B: Tail needle protein gp26
C: Tail needle protein gp26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,91612
Polymers76,9213
Non-polymers9959
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30440 Å2
ΔGint-183.1 kcal/mol
Surface area31660 Å2
MethodPISA
2
D: Tail needle protein gp26
E: Tail needle protein gp26
F: Tail needle protein gp26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,91612
Polymers76,9213
Non-polymers9959
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28380 Å2
ΔGint-170.4 kcal/mol
Surface area31060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.539, 114.531, 172.045
Angle α, β, γ (deg.)90.00, 91.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tail needle protein gp26 / Packaged DNA stabilization protein


Mass: 25640.424 Da / Num. of mol.: 6 / Mutation: L222M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage P22 (virus) / Gene: 26 / Plasmid: pET-15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P35837
#2: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Xe
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1590 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 298 K / pH: 4.6
Details: 18% PEG 4000, 0.1M Ammonium Sulfate, 0.1M Ammonium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179
DetectorType: ADSC Q-270 / Detector: CCD / Date: Nov 2, 2007
Details: HORIZONTAL BENT SI(111), ASYMMETRICALLY CUT WITH WATER COOLED CU BLOCK. RH-COATED SI MIRROR FOR VERTICAL FOCUSING
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 103949 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 22.38 Å2 / Rsym value: 0.083 / Net I/σ(I): 11.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 1.3 / % possible all: 74.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2POH

2poh


Resolution: 1.95→20 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.269 4368 -RANDOM
Rwork0.234 ---
obs0.234 100919 92.5 %-
all-109083 --
Displacement parametersBiso mean: 40.42 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10243 0 18 1590 11851
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.18
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.95→1.99 Å /
RfactorNum. reflection
Rfree0.37 31
Rwork0.3674 -

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