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- PDB-4ttm: Racemic structure of kalata B1 (kB1) -

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Basic information

Entry
Database: PDB / ID: 4ttm
TitleRacemic structure of kalata B1 (kB1)
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)
MethodX-RAY DIFFRACTION / Resolution: 1.9001 Å
AuthorsWang, C.K. / King, G.J. / Craik, D.J.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)LP110200213 Australia
National Health and Medical Research Council (NHMRC, Australia)546578 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1026501 Australia
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 / Source and taxonomy
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Jul 20, 2016Group: Data collection
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Dec 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
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_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


Theoretical massNumber of molelcules
Total (without water)5,8352
Polymers5,8352
Non-polymers00
Water1,02757
1
A: Kalata-B1


Theoretical massNumber of molelcules
Total (without water)2,9171
Polymers2,9171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-kalata B1


Theoretical massNumber of molelcules
Total (without water)2,9171
Polymers2,9171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.279, 25.960, 37.887
Angle α, β, γ (deg.)93.75, 106.73, 99.92
Int Tables number2
Space group name H-MP-1

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Components

#1: Protein/peptide Kalata-B1


Mass: 2917.345 Da / Num. of mol.: 1 / 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.) Oldenlandia affinis (plant)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.79 Å3/Da / Density % sol: 31.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14% w/v (+/-)-2-methyl-2,4-pentanediol, 4% v/v 1,3-Propanediol or 14% w/v (+/-)-2-methyl-2,4-pentanediol, 5% w/v polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→25.38 Å / Num. obs: 7049 / % possible obs: 94 % / Redundancy: 3.94 % / Biso Wilson estimate: 49.42 Å2 / Net I/σ(I): 7.8
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 3.88 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.409 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 1.9001→22.051 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2784 591 9.99 %
Rwork0.2202 --
obs0.2259 5913 94.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 1.9001→22.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms394 0 89 57 540
Biso mean--8.05 25.24 -
Num. residues----47
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007435
X-RAY DIFFRACTIONf_angle_d1.199596
X-RAY DIFFRACTIONf_dihedral_angle_d7.336152
X-RAY DIFFRACTIONf_chiral_restr0.07374
X-RAY DIFFRACTIONf_plane_restr0.00778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-2.09110.33111410.22341274X-RAY DIFFRACTION92
2.0911-2.39340.30831480.22621330X-RAY DIFFRACTION94
2.3934-3.01420.29211480.22191338X-RAY DIFFRACTION95
3.0142-22.05290.23751540.21531380X-RAY DIFFRACTION98

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