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- PDB-1tcz: Crystal structure of a truncated version of the phage lamda prote... -

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Basic information

Entry
Database: PDB / ID: 1tcz
TitleCrystal structure of a truncated version of the phage lamda protein gpD
ComponentsHead decoration protein
KeywordsVIRAL PROTEIN / phage lamda protein gpD
Function / homology
Function and homology information


viral capsid, decoration / viral DNA genome packaging / host cell cytoplasm
Similarity search - Function
Virus Head Decoration Protein; Chain: A, / Head decoration protein D / Head decoration protein D superfamily / Head decoration protein D / Bacteriophage lambda head decoration protein D / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Capsid decoration protein
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChang, C. / Plueckthun, A. / Wlodawer, A.
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a truncated version of the phage lambda protein gpD.
Authors: Chang, C. / Plueckthun, A. / Wlodawer, A.
History
DepositionMay 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Head decoration protein
B: Head decoration protein
C: Head decoration protein
D: Head decoration protein
E: Head decoration protein
F: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)58,9806
Polymers58,9806
Non-polymers00
Water12,340685
1
A: Head decoration protein
B: Head decoration protein
C: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)29,4903
Polymers29,4903
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-18 kcal/mol
Surface area12380 Å2
MethodPISA
2
D: Head decoration protein
E: Head decoration protein
F: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)29,4903
Polymers29,4903
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-18 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.186, 99.044, 59.321
Angle α, β, γ (deg.)90.00, 119.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Head decoration protein / GPD / Major capsid protein D


Mass: 9829.972 Da / Num. of mol.: 6 / Fragment: N-terminal truncation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: D / Production host: Escherichia coli (E. coli) / References: UniProt: P03712
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl, PEG 4000, Mg acetate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Biso Wilson estimate: 23.5 Å2

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C5E

1c5e


Resolution: 1.85→19.59 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 107673.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 4712 10 %RANDOM
Rwork0.191 ---
obs0.191 46980 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.285 Å2 / ksol: 0.34458 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å21.52 Å2
2--0.64 Å20 Å2
3---1.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-20 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 0 685 4831
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.831.5
X-RAY DIFFRACTIONc_mcangle_it2.562
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_scangle_it3.352.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 671 10.3 %
Rwork0.258 5827 -
obs--78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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