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- PDB-3ipn: Crystal Structure of fluorine and methyl modified collagen: (mepF... -

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Basic information

Entry
Database: PDB / ID: 3ipn
TitleCrystal Structure of fluorine and methyl modified collagen: (mepFlpgly)7
ComponentsNon-natural Collagen
KeywordsSTRUCTURAL PROTEIN / Collagen / Fluorinated methylated collagen / nonnatural amino acid
Function / homologyCARBONATE ION
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsSatyshur, K.A. / Shoulders, M.D. / Raines, R.T. / Forest, K.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Stereoelectronic and steric effects in side chains preorganize a protein main chain.
Authors: Shoulders, M.D. / Satyshur, K.A. / Forest, K.T. / Raines, R.T.
History
DepositionAug 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-natural Collagen
B: Non-natural Collagen
C: Non-natural Collagen
D: Non-natural Collagen
E: Non-natural Collagen
F: Non-natural Collagen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,24710
Polymers12,0076
Non-polymers2404
Water3,207178
1
A: Non-natural Collagen
B: Non-natural Collagen
C: Non-natural Collagen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1235
Polymers6,0033
Non-polymers1202
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Non-natural Collagen
E: Non-natural Collagen
F: Non-natural Collagen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1235
Polymers6,0033
Non-polymers1202
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.4, 25.3, 61.9
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Non-natural Collagen


Mass: 2001.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Chemically synthesized from modified amino acids
#2: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1.72 Å3/Da / Density % sol: 28.67 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 3.4
Details: 15% acetic acid to dissolve the collagen, peg4000, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2007 / Details: Diamond 111 and compound beryllium lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 21822 / Num. obs: 21822 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 8.6 Å2 / Rsym value: 0.0894 / Net I/σ(I): 9.9
Reflection shellResolution: 1.21→1.35 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 4151 / Rsym value: 0.146 / % possible all: 60.4

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Processing

Software
NameClassification
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K6F, truncated to 21 amino acids

1k6f


Resolution: 1.21→10 Å / Num. parameters: 8976 / Num. restraintsaints: 10805 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.5 PERCENTAGE POINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 1115 -RANDOM
all0.1866 20642 --
obs-20642 82.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 997
Refinement stepCycle: LAST / Resolution: 1.21→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms800 0 16 178 994
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0325
X-RAY DIFFRACTIONs_zero_chiral_vol0.075
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.047
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0.053

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