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- PDB-3uc7: Trp-cage cyclo-TC1 - monoclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 3uc7
TitleTrp-cage cyclo-TC1 - monoclinic crystal form
ComponentsCyclo-TC1
KeywordsDE NOVO PROTEIN / mini-protein / Trp-cage / cyclic peptide / multimer / protein-protein interaction
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 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
Revision 1.5Oct 30, 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: Cyclo-TC1
B: Cyclo-TC1
C: Cyclo-TC1
D: Cyclo-TC1
E: Cyclo-TC1
F: Cyclo-TC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9368
Polymers12,8656
Non-polymers712
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-43 kcal/mol
Surface area6080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.697, 48.748, 35.259
Angle α, β, γ (deg.)90.000, 116.910, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide
Cyclo-TC1


Mass: 2144.240 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: solid-phase synthesis and cyclization
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 28.42 %
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: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.82 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 3, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82 Å / Relative weight: 1
ReflectionResolution: 0.99→50 Å / Num. all: 39329 / Num. obs: 39329 / % possible obs: 81.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Rmerge(I) obs: 0.089 / Χ2: 1.13 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
0.99-1.033.714980.928131.1
1.03-1.07521491.007144.60.783
1.07-1.116.131551.022165.60.714
1.11-1.177.639881.033182.60.519
1.17-1.259.445471.077194.30.489
1.25-1.3412.147141.145197.90.387
1.34-1.4814.747421.179198.40.295
1.48-1.6915.247981.069199.10.159
1.69-2.1315.248321.166199.60.09
2.13-5013.349061.23199.60.068

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2LL5

2ll5


Resolution: 1.1→35.39 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.2024 / WRfactor Rwork: 0.1564 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.7959 / SU B: 1.834 / SU ML: 0.038 / SU R Cruickshank DPI: 0.0368 / SU Rfree: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.037 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 1695 5.1 %RANDOM
Rwork0.1491 ---
obs0.1514 33543 94.81 %-
all-33543 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 47.19 Å2 / Biso mean: 18.274 Å2 / Biso min: 8.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20.13 Å2
2---0.58 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.1→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 2 107 1015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.021973
X-RAY DIFFRACTIONr_bond_other_d0.0030.02701
X-RAY DIFFRACTIONr_angle_refined_deg2.4021.9851335
X-RAY DIFFRACTIONr_angle_other_deg1.18631687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7755128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.40822.63238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6961596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.126158
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0231141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02189
X-RAY DIFFRACTIONr_mcbond_it4.6524660
X-RAY DIFFRACTIONr_mcbond_other3.1834272
X-RAY DIFFRACTIONr_mcangle_it6.0961032
X-RAY DIFFRACTIONr_scbond_it6.736313
X-RAY DIFFRACTIONr_scangle_it7.79710303
X-RAY DIFFRACTIONr_rigid_bond_restr2.10911674
X-RAY DIFFRACTIONr_sphericity_free18.6435113
X-RAY DIFFRACTIONr_sphericity_bonded9.73951637
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 88 -
Rwork0.245 1838 -
all-1926 -
obs--73.62 %

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