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- PDB-1vrz: Helix turn helix motif -

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Basic information

Entry
Database: PDB / ID: 1vrz
TitleHelix turn helix motif
ComponentsDE NOVO DESIGNED 21 RESIDUE PEPTIDE
KeywordsDE NOVO PROTEIN / HTH / HELIX-TURN-HELIX MOTIF
Function / homologyACETATE ION
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.05 Å
AuthorsRudresh / Ramakumar, S. / Ramagopal, U.A. / Inai, Y. / Sahal, D.
CitationJournal: Structure / Year: 2004
Title: De Novo Design and Characterization of a Helical Hairpin Eicosapeptide; Emergence of an Anion Receptor in the Linker Region.
Authors: Rudresh / Ramakumar, S. / Ramagopal, U.A. / Inai, Y. / Goel, S. / Sahal, D. / Chauhan, V.S.
History
DepositionOct 14, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionNov 1, 2005ID: 1Q4F
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: DE NOVO DESIGNED 21 RESIDUE PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,2002
Polymers2,1411
Non-polymers591
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.651, 20.987, 14.449
Angle α, β, γ (deg.)90.00, 94.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide DE NOVO DESIGNED 21 RESIDUE PEPTIDE


Mass: 2141.365 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE IS CHEMICALY SYNTHEISED BY SOLID PHASE MANUAL PEPTIDE SYNTHESIS USING FMOC CHEMISTRY.
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.65 Å3/Da / Density % sol: 25.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: ACETIC ACID AND ETHANOL (1:1 V/V) MIXTURE, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.987
DetectorDetector: CCD / Date: Aug 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.05→12.71 Å / Num. all: 7388 / Num. obs: 6913 / % possible obs: 93.6 % / Observed criterion σ(F): 4 / Biso Wilson estimate: 5.71 Å2 / Net I/σ(I): 15.5
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 6 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 20 / Num. unique all: 623 / % possible all: 99.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHELXSphasing
SHELXL-97refinement
HKL-2000data reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.05→12.71 Å / Num. parameters: 1532 / Num. restraintsaints: 1 / σ(F): 4 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflection
Rwork0.1254 --
all0.1311 7382 -
obs0.1254 6913 93.57 %
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 122 / Occupancy sum non hydrogen: 172
Refinement stepCycle: LAST / Resolution: 1.05→12.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms286 0 4 13 303
LS refinement shellResolution: 1.05→1.1 Å /
RfactorNum. reflection
Rwork0.119 758

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