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

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Basic information

Entry
Database: PDB / ID: 2drx
TitleStructure Analysis of (POG)4-(LOG)2-(POG)4
Componentscollagen like peptide
KeywordsSTRUCTURAL PROTEIN / collagen / triple helix / Leu
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: collagen like peptide
B: collagen like peptide
C: collagen like peptide


Theoretical massNumber of molelcules
Total (without water)8,1693
Polymers8,1693
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-25 kcal/mol
Surface area5040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.894, 22.751, 46.372
Angle α, β, γ (deg.)90.00, 107.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide collagen like peptide


Mass: 2722.914 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: Two LEU-Hyp-Gly guest triplets sandwiched by host Pro-Hyp-Gly sequence; This host triplet is very popular in the collagen sequence.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 1.83 Å3/Da / Density % sol: 32.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 13.5% PEG 2000, 0.05M citrate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2004 / Details: mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 11974 / Num. obs: 10986 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 10.5
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.294 / Num. unique all: 1183 / % possible all: 99.7

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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: 1.4→8 Å / Num. parameters: 4655 / Num. restraintsaints: 5584
Isotropic thermal model: anisotropic for peptide, isotropic for water
Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.214 657 -RANDOM
Rwork0.16 ---
all-10254 --
obs-10911 85.5 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 482.5 / Occupancy sum non hydrogen: 720.5
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms558 0 0 170 728
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0255
X-RAY DIFFRACTIONs_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.027
X-RAY DIFFRACTIONs_approx_iso_adps0.038
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.4-1.460.196X-RAY DIFFRACTION10570.103
1.46-1.530.206X-RAY DIFFRACTION10300.1
1.53-1.60.184X-RAY DIFFRACTION10010.097
1.6-1.690.164X-RAY DIFFRACTION10410.102
1.69-1.810.158X-RAY DIFFRACTION10070.098
1.81-1.950.157X-RAY DIFFRACTION10320.101

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