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- PDB-2drt: Structure Analysis of (POG)4-LOG-(POG)5 -

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Basic information

Entry
Database: PDB / ID: 2drt
TitleStructure Analysis of (POG)4-LOG-(POG)5
Componentscollagen like peptide
KeywordsSTRUCTURAL PROTEIN / collagen / triple helix / Leu
Function / homologyETHANOL
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOkuyama, K.
CitationJournal: Biopolymers / Year: 2007
Title: Unique side chain conformation of a leu residue in a triple-helical structure
Authors: Okuyama, K. / Narita, H. / Kawaguchi, T. / Noguchi, K. / Tanaka, Y. / Nishino, N.
History
DepositionJun 14, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: collagen like peptide
B: collagen like peptide
C: collagen like peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2596
Polymers8,1213
Non-polymers1383
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-23 kcal/mol
Surface area4990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)14.092, 24.748, 84.449
Angle α, β, γ (deg.)90.00, 91.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide collagen like peptide


Mass: 2706.871 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: Leu-Hyp-Gly guest triplet sandwiched by host Pro-Hyp-Gly sequence; This host triplet is very popular in the collagen sequence.
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1.81 Å3/Da / Density % sol: 31.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 12.5% PEG 400, 0.05M acetate buffer, 5.0% Ethanol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2003 / Details: mirror
RadiationMonochromator: fixed-exit double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 8327 / Num. obs: 7797 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 5.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.316 / Num. unique all: 767 / % possible all: 99.6

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
ADSCdata collection
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V4F

1v4f


Resolution: 1.6→8 Å / Num. parameters: 2879 / Num. restraintsaints: 2487 / Isotropic thermal model: Isotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 353 -RANDOM
Rwork0.159 ---
all-6667 --
obs-7020 84.3 %-
Displacement parametersBiso mean: 22.3 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 468.5 / Occupancy sum non hydrogen: 714
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms549 0 0 170 719
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0286
X-RAY DIFFRACTIONs_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.074
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.6-1.670.216X-RAY DIFFRACTION6850.102
1.67-1.740.211X-RAY DIFFRACTION6480.097
1.74-1.830.195X-RAY DIFFRACTION7040.106
1.83-1.930.182X-RAY DIFFRACTION6460.097
1.93-2.050.171X-RAY DIFFRACTION6740.101
2.05-2.210.147X-RAY DIFFRACTION6410.096

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