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- PDB-1c5e: BACTERIOPHAGE LAMBDA HEAD PROTEIN D -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1c5e
TitleBACTERIOPHAGE LAMBDA HEAD PROTEIN D
ComponentsHEAD DECORATION PROTEIN
KeywordsVIRAL PROTEIN / BACTERIOPHAGE LAMBDA / HEAD PROTEIN D / PROTEIN CRYSTAL STRUCTURE / VIRUS ASSEMBLY / PHAGE DISPLAY
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 / MAD / Resolution: 1.1 Å
AuthorsYang, F. / Forrer, P. / Dauter, Z. / Pluckthun, A. / Wlodawer, A.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Novel fold and capsid-binding properties of the lambda-phage display platform protein gpD.
Authors: Yang, F. / Forrer, P. / Dauter, Z. / Conway, J.F. / Cheng, N. / Cerritelli, M.E. / Steven, A.C. / Pluckthun, A. / Wlodawer, A.
History
DepositionNov 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: HEAD DECORATION PROTEIN
B: HEAD DECORATION PROTEIN
C: HEAD DECORATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6745
Polymers29,4903
Non-polymers1842
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-15 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.580, 69.070, 45.590
Angle α, β, γ (deg.)90.00, 104.32, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.254172, 0.010299, 0.967104), (-0.911654, 0.331324, -0.243127), (-0.322929, -0.943461, -0.074824)29.27348, 35.04161, 26.58102
2given(-0.226471, -0.922287, -0.313205), (-0.001972, 0.321993, -0.94674), (0.974016, -0.213792, -0.07474)48.23424, 13.84381, -19.08689

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Components

#1: Protein HEAD DECORATION PROTEIN / GPD / MAJOR CAPSID PROTEIN D


Mass: 9829.972 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / References: UniProt: P03712
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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 Å3/Da / Density % sol: 39 %
Crystal growpH: 6.5 / Details: 28% PEG 4000, 0.1 M BIS-TRIS PH 6.5, 10 % GLYCEROL
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 mMTris1drop
328 %PEG40001reservoir
40.1 MBis-Tris1reservoir
510 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 109996 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rsym value: 4.6
Reflection shellResolution: 1.1→1.12 Å / Rsym value: 25.6 / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 20 Å / Num. measured all: 635194 / Rmerge(I) obs: 0.046

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MAD / Resolution: 1.1→10 Å / Num. parameters: 21691 / Num. restraintsaints: 26304 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.1328 5346 5.1 %RANDOM
all0.0982 104260 --
obs0.0986 -94.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 2051 / Occupancy sum non hydrogen: 2394
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 12 309 2394
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.118
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0.119
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.0982 / Rfactor Rwork: 0.099
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_chiral_restr / Dev ideal: 0.087

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