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- PDB-3uc8: Trp-cage cyclo-TC1 - tetragonal crystal form -

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Basic information

Entry
Database: PDB / ID: 3uc8
TitleTrp-cage cyclo-TC1 - tetragonal crystal form
Componentscyclo-TC1
KeywordsDE NOVO PROTEIN / miniprotein / Trp-cage / cyclic peptide / multimer / protein-protein interaction
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.33 Å
AuthorsScian, M. / Le Trong, I. / Stenkamp, R.E. / Andersen, N.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction.
Authors: Scian, M. / Lin, J.C. / Le Trong, I. / Makhatadze, G.I. / Stenkamp, R.E. / Andersen, N.H.
History
DepositionOct 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Aug 15, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 13, 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

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Assembly

Deposited unit
A: cyclo-TC1
B: cyclo-TC1
C: cyclo-TC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5554
Polymers6,4333
Non-polymers1221
Water1,838102
1
A: cyclo-TC1
B: cyclo-TC1
C: cyclo-TC1
hetero molecules

A: cyclo-TC1
B: cyclo-TC1
C: cyclo-TC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1108
Polymers12,8656
Non-polymers2442
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Unit cell
Length a, b, c (Å)36.848, 36.848, 66.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein/peptide cyclo-TC1


Mass: 2144.240 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: solid-phase synthesis and cyclization
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.75 Å3/Da / Density % sol: 29.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 2.5
Details: 0.2 M Tris-HCl, 0.2 M magnesium chloride, 2.0 M sodium chloride, pH 2.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 31, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. all: 9797 / Num. obs: 9797 / % possible obs: 86.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.032 / Χ2: 1.112 / Net I/σ(I): 55.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.32-1.372.50.0963301.106129.9
1.37-1.425.40.0927271.251166
1.42-1.499.70.07310141.089191.8
1.49-1.5710.90.05510381.168194.1
1.57-1.66110.04910661.055195.3
1.66-1.7911.10.04410890.948196.3
1.79-1.9711.10.0410931.127197.4
1.97-2.2611.10.04311141.2197.5
2.26-2.84110.03611551.18198.2
2.84-509.60.02511711.074192.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UC7

3uc7


Resolution: 1.33→36.85 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2509 / WRfactor Rwork: 0.1694 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8821 / SU B: 1.947 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0745 / SU Rfree: 0.0706 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.075 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1977 469 4.8 %RANDOM
Rwork0.1355 ---
obs0.1382 9316 87.5 %-
all-9785 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.03 Å2 / Biso mean: 15.3019 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.33→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms453 0 8 102 563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021510
X-RAY DIFFRACTIONr_bond_other_d0.0010.02375
X-RAY DIFFRACTIONr_angle_refined_deg2.0612.017695
X-RAY DIFFRACTIONr_angle_other_deg1.1533900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.241562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.4952220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6811552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.735155
X-RAY DIFFRACTIONr_chiral_restr0.1230.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0296
X-RAY DIFFRACTIONr_mcbond_it3.1294340
X-RAY DIFFRACTIONr_mcbond_other2.2814134
X-RAY DIFFRACTIONr_mcangle_it4.1476529
X-RAY DIFFRACTIONr_scbond_it5.1756170
X-RAY DIFFRACTIONr_scangle_it6.34510165
X-RAY DIFFRACTIONr_rigid_bond_restr2.5793885
X-RAY DIFFRACTIONr_sphericity_free11.3063104
X-RAY DIFFRACTIONr_sphericity_bonded4.5863870
LS refinement shellResolution: 1.33→1.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.012 16 -
Rwork0.788 238 -
all-254 -
obs--31.55 %

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