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- PDB-6cdx: High-resolution crystal structure of fluoropropylated cystine kno... -

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Basic information

Entry
Database: PDB / ID: 6cdx
TitleHigh-resolution crystal structure of fluoropropylated cystine knot, binding to alpha-5 beta-6 integrin
Componentscystine knot (fluoropropylated)
KeywordsPROTEIN BINDING / Cysteine / Disulfides / alpha-5 beta-6 integrin binding epitope / Cancer Imaging
Function / homologyProteinase inhibitor I7, squash / Squash family serine protease inhibitor / Squash family of serine protease inhibitors signature. / Proteinase/amylase inhibitor domain superfamily / negative regulation of serine-type endopeptidase activity / serine-type endopeptidase inhibitor activity / extracellular region / Trypsin inhibitor 1
Function and homology information
Biological speciesMomordica cochinchinensis (spiny bitter cucumber)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsKimura, R. / Nix, J. / Bongura, C. / Chakraborti, S. / Gambhir, S. / Filipp, F.V.
Funding support Germany, United States, 3items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchDJUSA Germany
National Institutes of Health/National Cancer Institute (NIH/NCI)CA154887 United States
The University Grants Committee, Research Grants Council (RGC)CRN-17-427258 United States
CitationJournal: Nat Commun / Year: 2019
Title: Evaluation of integrin alpha v beta6cystine knot PET tracers to detect cancer and idiopathic pulmonary fibrosis.
Authors: Kimura, R.H. / Wang, L. / Shen, B. / Huo, L. / Tummers, W. / Filipp, F.V. / Guo, H.H. / Haywood, T. / Abou-Elkacem, L. / Baratto, L. / Habte, F. / Devulapally, R. / Witney, T.H. / Cheng, Y. ...Authors: Kimura, R.H. / Wang, L. / Shen, B. / Huo, L. / Tummers, W. / Filipp, F.V. / Guo, H.H. / Haywood, T. / Abou-Elkacem, L. / Baratto, L. / Habte, F. / Devulapally, R. / Witney, T.H. / Cheng, Y. / Tikole, S. / Chakraborti, S. / Nix, J. / Bonagura, C.A. / Hatami, N. / Mooney, J.J. / Desai, T. / Turner, S. / Gaster, R.S. / Otte, A. / Visser, B.C. / Poultsides, G.A. / Norton, J. / Park, W. / Stolowitz, M. / Lau, K. / Yang, E. / Natarajan, A. / Ilovich, O. / Srinivas, S. / Srinivasan, A. / Paulmurugan, R. / Willmann, J. / Chin, F.T. / Cheng, Z. / Iagaru, A. / Li, F. / Gambhir, S.S.
History
DepositionFeb 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 23, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: cystine knot (fluoropropylated)
B: cystine knot (fluoropropylated)


Theoretical massNumber of molelcules
Total (without water)7,8332
Polymers7,8332
Non-polymers00
Water93752
1
A: cystine knot (fluoropropylated)


Theoretical massNumber of molelcules
Total (without water)3,9161
Polymers3,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cystine knot (fluoropropylated)


Theoretical massNumber of molelcules
Total (without water)3,9161
Polymers3,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)16.950, 44.250, 66.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide cystine knot (fluoropropylated) / Trypsin inhibitor 1 / MCoTI-I / Trypsin inhibitor I


Mass: 3916.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Momordica cochinchinensis (spiny bitter cucumber)
Production host: Escherichia coli (E. coli) / References: UniProt: P82408
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.59 Å3/Da / Density % sol: 22.63 %
Crystal growTemperature: 298 K / Method: evaporation / Details: Isopropanol

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 26, 2016
RadiationMonochromator: Rosenbaum-Rock Si(111) sagittally focused / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→36.82 Å / Num. obs: 27921 / % possible obs: 94.1 % / Redundancy: 29 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 32.3
Reflection shellHighest resolution: 1 Å / Num. unique obs: 999

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2N8C & 2N8B
Resolution: 1→36.82 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 0.457 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.036
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 1341 5 %RANDOM
Rwork0.2029 ---
obs0.204 25665 96.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 41.53 Å2 / Biso mean: 10.152 Å2 / Biso min: 3.54 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms529 0 0 52 581
Biso mean---16.36 -
Num. residues----73
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.019534
X-RAY DIFFRACTIONr_bond_other_d0.0080.02494
X-RAY DIFFRACTIONr_angle_refined_deg3.3661.983716
X-RAY DIFFRACTIONr_angle_other_deg1.70331128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.462570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.8352024
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7981586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6861510
X-RAY DIFFRACTIONr_chiral_restr0.5310.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02620
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02134
LS refinement shellResolution: 1→1.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 77 -
Rwork0.359 1388 -
all-1465 -
obs--73.88 %

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