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- PDB-1nay: GPP-Foldon:X-ray structure -

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Basic information

Entry
Database: PDB / ID: 1nay
TitleGPP-Foldon:X-ray structure
ComponentsCollagen-like peptide
KeywordsSTRUCTURAL PROTEIN / collagen assembly
Function / homology6-Phosphogluconate Dehydrogenase, domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsStetefeld, J.
CitationJournal: Structure / Year: 2003
Title: Collagen Stabilization at Atomic Level. Crystal Structure of Designed (GlyProPro)(10)foldon
Authors: Stetefeld, J. / Frank, S. / Jenny, M. / Schulthess, T. / Kammerer, R.A. / Boudko, S. / Landwehr, R. / Okuyama, K. / Engel, J.
History
DepositionNov 29, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Experimental preparation / Source and taxonomy / Category: exptl_crystal_grow / pdbx_entity_src_syn
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp ..._exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)16,4703
Polymers16,4703
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-54 kcal/mol
Surface area8410 Å2
MethodPISA
2
A: Collagen-like peptide
B: Collagen-like peptide
C: Collagen-like peptide

A: Collagen-like peptide
B: Collagen-like peptide
C: Collagen-like peptide


Theoretical massNumber of molelcules
Total (without water)32,9416
Polymers32,9416
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area17420 Å2
ΔGint-125 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.591, 27.901, 112.274
Angle α, β, γ (deg.)90.00, 105.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Collagen-like peptide / CCP4


Mass: 5490.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
20.1 Msodium acetate1drop
30.2 Mammonium sulfate1drop
425 %PEG40001droppH4.6
550-100 mMmagnesium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 4410 / Biso Wilson estimate: 36.4 Å2
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 95.1 % / Redundancy: 2.2 % / Num. measured all: 25421 / Rmerge(I) obs: 0.107
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.68 Å / % possible obs: 95 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→8 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 639751.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.296 411 10.1 %RANDOM
Rwork0.234 ---
obs0.234 4410 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 112.376 Å2 / ksol: 0.651542 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.49 Å20 Å25.35 Å2
2---0.56 Å20 Å2
3---7.05 Å2
Refine analyzeLuzzati coordinate error free: 0.49 Å / Luzzati sigma a free: 0.53 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 0 121 1287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.75 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 63 9.1 %
Rwork0.299 629 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.73
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.76
LS refinement shell
*PLUS
Rfactor Rfree: 0.376 / Rfactor Rwork: 0.298

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