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- PDB-4ttn: Quasi-racemic structure of [G6A]kalata B1 -

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Basic information

Entry
Database: PDB / ID: 4ttn
TitleQuasi-racemic structure of [G6A]kalata B1
Components
  • D-kalata B1
  • Kalata-B1
KeywordsPLANT PROTEIN / cyclic peptide / disulfide bonds
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium
Similarity search - Function
Cyclotide, moebius, conserved site / Cyclotides Moebius subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family
Similarity search - Domain/homology
polypeptide(D) / polypeptide(D) (> 10) / Kalata-B1
Similarity search - Component
Biological speciesOldenlandia affinis (plant)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2507 Å
AuthorsWang, C.K. / King, G.J. / Craik, D.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Racemic and Quasi-Racemic X-ray Structures of Cyclic Disulfide-Rich Peptide Drug Scaffolds.
Authors: Wang, C.K. / King, G.J. / Northfield, S.E. / Ojeda, P.G. / Craik, D.J.
History
DepositionJun 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_validate_symm_contact / refine_hist / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kalata-B1
B: D-kalata B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9673
Polymers5,8492
Non-polymers1181
Water1,11762
1
A: Kalata-B1


Theoretical massNumber of molelcules
Total (without water)2,9311
Polymers2,9311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-kalata B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0362
Polymers2,9171
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.186, 25.923, 37.713
Angle α, β, γ (deg.)93.80, 106.59, 99.91
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein/peptide Kalata-B1


Mass: 2931.371 Da / Num. of mol.: 1 / Mutation: G6A / Source method: obtained synthetically / Source: (synth.) Oldenlandia affinis (plant) / References: UniProt: P56254
#2: Polypeptide(D) D-kalata B1


Mass: 2917.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.73 Å3/Da / Density % sol: 29.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14% w/v (+/-)-2-methyl-2,4-pentanediol, 4% v/v 1,3-Propanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.25→25.35 Å / Num. obs: 20418 / % possible obs: 93.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 47.33 Å2 / Net I/σ(I): 16.95
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.138 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 1.2507→25.345 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 2000 9.8 %
Rwork0.2116 --
obs0.2133 20417 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 1.2507→25.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms395 0 105 62 562
Biso mean--10.56 23.51 -
Num. residues----47
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007451
X-RAY DIFFRACTIONf_angle_d1.302620
X-RAY DIFFRACTIONf_dihedral_angle_d12.432160
X-RAY DIFFRACTIONf_chiral_restr0.05678
X-RAY DIFFRACTIONf_plane_restr0.00979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2507-1.2820.22741310.25571212X-RAY DIFFRACTION87
1.282-1.31660.27321410.23221301X-RAY DIFFRACTION91
1.3166-1.35540.23981420.22561308X-RAY DIFFRACTION92
1.3554-1.39910.29451410.21211287X-RAY DIFFRACTION92
1.3991-1.44910.26341410.22121296X-RAY DIFFRACTION93
1.4491-1.50710.22081420.2021308X-RAY DIFFRACTION94
1.5071-1.57570.18811430.18771322X-RAY DIFFRACTION93
1.5757-1.65880.2081410.19751299X-RAY DIFFRACTION95
1.6588-1.76270.21381470.20011356X-RAY DIFFRACTION95
1.7627-1.89870.21631440.19851327X-RAY DIFFRACTION95
1.8987-2.08970.26711470.20091342X-RAY DIFFRACTION96
2.0897-2.39190.23081460.20921357X-RAY DIFFRACTION96
2.3919-3.01280.23431460.22061338X-RAY DIFFRACTION96
3.0128-25.35040.21451480.22061364X-RAY DIFFRACTION97

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