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- PDB-6kzf: Racemic X-ray Structure of Calcicludine -

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Basic information

Entry
Database: PDB / ID: 6kzf
TitleRacemic X-ray Structure of Calcicludine
Components
  • D-calcicludine
  • Kunitz-type serine protease inhibitor homolog calcicludine
KeywordsTOXIN / calcicludine / racemic crystal / L-type Ca2+ channels
Function / homology
Function and homology information


calcium channel regulator activity / serine-type endopeptidase inhibitor activity / toxin activity / extracellular space
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
polypeptide(D) / polypeptide(D) (> 10) / Kunitz-type serine protease inhibitor homolog calcicludine
Similarity search - Component
Biological speciesDendroaspis angusticeps (eastern green mamba)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsQu, Q. / Gao, S. / Liu, L.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Synthesis of Disulfide Surrogate Peptides Incorporating Large-Span Surrogate Bridges Through a Native-Chemical-Ligation-Assisted Diaminodiacid Strategy
Authors: Qu, Q. / Gao, S. / Wu, F. / Zhang, M.G. / Li, Y. / Zhang, L.H. / Bierer, D. / Tian, C.L. / Zheng, J.S. / Liu, L.
History
DepositionSep 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kunitz-type serine protease inhibitor homolog calcicludine
B: D-calcicludine


Theoretical massNumber of molelcules
Total (without water)13,9692
Polymers13,9692
Non-polymers00
Water1,09961
1
A: Kunitz-type serine protease inhibitor homolog calcicludine


Theoretical massNumber of molelcules
Total (without water)6,9801
Polymers6,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-calcicludine


Theoretical massNumber of molelcules
Total (without water)6,9891
Polymers6,9891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.600, 94.600, 38.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Kunitz-type serine protease inhibitor homolog calcicludine / CAC / L-type calcium channel blocker


Mass: 6980.236 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Dendroaspis angusticeps (eastern green mamba)
References: UniProt: P81658
#2: Protein D-calcicludine


Mass: 6989.211 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Dendroaspis angusticeps (eastern green mamba)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. obs: 5969 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 36.27 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 14.6
Reflection shellResolution: 2.52→2.56 Å / Rmerge(I) obs: 0.996 / Num. unique obs: 312

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Processing

Software
NameClassification
PHENIXrefinement
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YV7

5yv7


Resolution: 2.52→35.71 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.2821 584 -
Rwork0.2389 --
obs-5865 97.9 %
Refinement stepCycle: LAST / Resolution: 2.52→35.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms982 0 0 61 1043
LS refinement shellResolution: 2.52→2.56 Å /
Num. reflection% reflection
obs312 100 %

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