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- PDB-1qsu: CRYSTAL STRUCTURE OF THE TRIPLE-HELICAL COLLAGEN-LIKE PEPTIDE, (P... -

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Basic information

Entry
Database: PDB / ID: 1qsu
TitleCRYSTAL STRUCTURE OF THE TRIPLE-HELICAL COLLAGEN-LIKE PEPTIDE, (PRO-HYP-GLY)4-GLU-LYS-GLY(PRO-HYP-GLY)5
ComponentsPROTEIN ((PRO-HYP-GLY)4- GLU-LYS-GLY(PRO-HYP-GLY)5)
KeywordsSTRUCTURAL PROTEIN / TRIPLE HELIX
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsKramer, R.Z. / Venugopal, M. / Bella, J. / Brodsky, B. / Berman, H.M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Staggered molecular packing in crystals of a collagen-like peptide with a single charged pair.
Authors: Kramer, R.Z. / Venugopal, M.G. / Bella, J. / Mayville, P. / Brodsky, B. / Berman, H.M.
History
DepositionJun 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN ((PRO-HYP-GLY)4- GLU-LYS-GLY(PRO-HYP-GLY)5)
B: PROTEIN ((PRO-HYP-GLY)4- GLU-LYS-GLY(PRO-HYP-GLY)5)
C: PROTEIN ((PRO-HYP-GLY)4- GLU-LYS-GLY(PRO-HYP-GLY)5)


Theoretical massNumber of molelcules
Total (without water)8,2173
Polymers8,2173
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-26 kcal/mol
Surface area4900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.326, 26.573, 45.885
Angle α, β, γ (deg.)90.00, 96.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide PROTEIN ((PRO-HYP-GLY)4- GLU-LYS-GLY(PRO-HYP-GLY)5)


Mass: 2738.892 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Collagen-like model sequence.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4K, tris HCl, Li2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlpeptide1drop
215 %PEG40001drop
30.1 MTris-HCl1drop
40.3 M1dropLi2SO4
50.1 MTris1reservoir
60.6 M1reservoirLi2SO4
730 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER / Date: Oct 15, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.75 Å / Num. all: 7286 / % possible obs: 99.97 % / Observed criterion σ(F): 0
Reflection shellResolution: 1.75→1.81 Å / Num. unique all: 718 / % possible all: 99.86
Reflection
*PLUS
Num. obs: 5745
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
MERLOTphasing
CNSrefinement
CAD4data reduction
MOLENdata scaling
RefinementResolution: 1.75→20 Å / Rfactor Rfree error: 0.017 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.227 540 9.9 %RANDOM
Rwork0.18 ---
obs-5480 75.1 %-
Displacement parametersBiso mean: 7.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0.39 Å2
2---0.85 Å20 Å2
3---0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.13 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms569 0 0 153 722
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_improper_angle_d1.24
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 67 10.7 %
Rwork0.286 559 -
obs--53.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2HYP.PAR3
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
LS refinement shell
*PLUS
Rfactor Rfree: 0.296 / Rfactor Rwork: 0.286

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