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- PDB-2mbk: The Clip-segment of the von Willebrand domain 1 of the BMP modula... -

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Basic information

Entry
Database: PDB / ID: 2mbk
TitleThe Clip-segment of the von Willebrand domain 1 of the BMP modulator protein Crossveinless 2 is preformed
ComponentsCrossveinless 2
KeywordsSIGNALING PROTEIN / von Willebrand type C domain / BMP modulator / Crossveinless 2 / BMPER
Function / homology
Function and homology information


otic placode formation / neural crest formation / regulation of BMP signaling pathway / dorsal/ventral pattern formation / extracellular matrix binding / blood vessel development / hemopoiesis / regulation of angiogenesis / extracellular matrix / extracellular space
Similarity search - Function
Defensin A-like - #20 / Defensin A-like / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily ...Defensin A-like - #20 / Defensin A-like / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Other non-globular / Special
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsMueller, T.D. / Fiebig, J.E. / Weidauer, S.E. / Qiu, L. / Bauer, M. / Schmieder, P. / Beerbaum, M. / Zhang, J. / Oschkinat, H. / Sebald, W.
CitationJournal: Molecules / Year: 2013
Title: The Clip-Segment of the von Willebrand Domain 1 of the BMP Modulator Protein Crossveinless 2 Is Preformed.
Authors: Fiebig, J.E. / Weidauer, S.E. / Qiu, L.Y. / Bauer, M. / Schmieder, P. / Beerbaum, M. / Zhang, J.L. / Oschkinat, H. / Sebald, W. / Mueller, T.D.
History
DepositionAug 2, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Crossveinless 2


Theoretical massNumber of molelcules
Total (without water)7,3361
Polymers7,3361
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Crossveinless 2


Mass: 7336.424 Da / Num. of mol.: 1 / Fragment: UNP residues 28-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: bmper, cvl2, id:ibd5071 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5D734

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-1H TOCSY
1232D DQF-COSY
1332D 1H-1H NOESY
1423D 1H-15N NOESY
1523D 1H-15N TOCSY
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D HNCO
1913D HN(CA)CO
11013D HBHA(CO)NH
11113D H(CCO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-99% 13C; U-99% 15N] CV2 VWC1, 20 mM sodium phosphate, 20 mM sodium chloride, 5 % [U-2H] D2O, 0.2 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21.5 mM [U-99% 15N] CV2 VWC1, 20 mM sodium phosphate, 20 mM sodium chloride, 5 % [U-2H] D2O, 0.2 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
32 mM CV2 VWC1, 20 mM sodium phosphate, 20 mM sodium chloride, 5 % [U-2H] D2O, 0.2 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMCV2 VWC1-1[U-99% 13C; U-99% 15N]1
20 mMsodium phosphate-21
20 mMsodium chloride-31
5 %D2O-4[U-2H]1
0.2 %sodium azide-51
1.5 mMCV2 VWC1-6[U-99% 15N]2
20 mMsodium phosphate-72
20 mMsodium chloride-82
5 %D2O-9[U-2H]2
0.2 %sodium azide-102
2 mMCV2 VWC1-113
20 mMsodium phosphate-123
20 mMsodium chloride-133
5 %D2O-14[U-2H]3
0.2 %sodium azide-153
Sample conditionsIonic strength: 0.04 / pH: 6.6 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
AURELIA3.85Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerdata analysis
AURELIA3.85Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerchemical shift assignment
X-PLOR NIH2.29Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.29Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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