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- PDB-5awl: CRYSTAL STRUCTURE OF A MUTANT OF CHIGNOLIN, CLN025 -

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Basic information

Entry
Database: PDB / ID: 5awl
TitleCRYSTAL STRUCTURE OF A MUTANT OF CHIGNOLIN, CLN025
ComponentsA mutant of Chignolin, CLN025
KeywordsDE NOVO PROTEIN / BETA-HAIRPIN / MINI-PROTEIN / MINIATURE PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 1.11 Å
AuthorsAkiba, T. / Ishimura, M. / Odahara, T. / Harata, K. / Honda, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
New Energy and Industrial Technology Development Organization (NEDO) Japan
Citation
#1: Journal: Structure / Year: 2004
Title: 10 residue folded peptide designed by segment statistics.
Authors: Honda, S. / Yamasaki, K. / Sawada, Y. / Morii, H.
History
DepositionJul 5, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Other
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entity_src_syn / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A mutant of Chignolin, CLN025


Theoretical massNumber of molelcules
Total (without water)1,2941
Polymers1,2941
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1210 Å2
Unit cell
Length a, b, c (Å)19.246, 33.597, 11.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-105-

HOH

21A-112-

HOH

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Components

#1: Protein/peptide A mutant of Chignolin, CLN025


Mass: 1294.322 Da / Num. of mol.: 1 / Mutation: G1Y G10Y / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 1.4 Å3/Da / Density % sol: 14.1 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5
Details: using 2 uL drop of protein at 5 mg/mL in a solution of 35.7 mM sodium citrate-citric acid buffer (pH 5.0) containing 14.5% saturated ammonium sulfate against a crystallization well solution ...Details: using 2 uL drop of protein at 5 mg/mL in a solution of 35.7 mM sodium citrate-citric acid buffer (pH 5.0) containing 14.5% saturated ammonium sulfate against a crystallization well solution of 71.4 mM sodium citrate-citric acid buffer (pH 5.0) containing 29% saturated ammonium sulfate.
PH range: 5

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Dec 9, 2005 / Details: OSMIC CONFOCAL MAX-FLUX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.11→16.8 Å / Num. obs: 3094 / % possible obs: 95.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 26.4
Reflection shellResolution: 1.11→1.71 Å / Redundancy: 4 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 5 / % possible all: 88.9

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Processing

Software
NameVersionClassification
SAINTdata processing
SnB2.2phasing
CNSrefinement
SMART6000data reduction
SAINTPLUSdata scaling
SHELXL-97refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.11→16.8 Å / Num. parameters: 940 / Num. restraintsaints: 1193 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1188 287 10.2 %RANDOM
obs0.088 3080 95.7 %-
all-3087 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 73 / Occupancy sum non hydrogen: 103.5
Refinement stepCycle: LAST / Resolution: 1.11→16.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms93 0 0 12 105
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0215
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.193
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0.11

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