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- PDB-5xs1: Solution structure of Crustacean Hyperglycemic Hormone-like (CHH-... -

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Basic information

Entry
Database: PDB / ID: 5xs1
TitleSolution structure of Crustacean Hyperglycemic Hormone-like (CHH-L) from the Scylla Olivacea
ComponentsHyperglycemic hormone-like peptide
KeywordsHORMONE / Crustacean Hyperglycemic Hormone / neuropeptide
Function / homology
Function and homology information


neuropeptide hormone activity / neuropeptide signaling pathway / circadian rhythm / extracellular region
Similarity search - Function
Crustacean neurohormone H / Crustacean neurohormone H / Hyperglycemic hormone type 1 / Hyperglycemic hormone / Crustacean neurohormone, conserved site / Crustacean CHH/MIH/GIH neurohormone family / Crustacean CHH/MIH/GIH neurohormone superfamily / Crustacean CHH/MIH/GIH neurohormone family / Arthropod CHH/MIH/GIH neurohormones family signature.
Similarity search - Domain/homology
Hyperglycemic hormone-like peptide
Similarity search - Component
Biological speciesScylla olivacea (orange mud crab)
MethodSOLUTION NMR / distance geometry
AuthorsChen, Y.R. / Lyu, P.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Taiwan
CitationJournal: To Be Published
Title: Solution structure of Crustacean Hyperglycemic Hormone-like (CHH-L) from the Scylla Olivacea
Authors: Chen, Y.R. / Lyu, P.C.
History
DepositionJun 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hyperglycemic hormone-like peptide


Theoretical massNumber of molelcules
Total (without water)8,5121
Polymers8,5121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5070 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hyperglycemic hormone-like peptide


Mass: 8511.561 Da / Num. of mol.: 1 / Fragment: UNP residues 67-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scylla olivacea (orange mud crab) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A5A599
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic33D (H)CCH-TOCSY
131isotropic33D (H)CCH-COSY
141isotropic33D 1H-15N NOESY
151isotropic13D HNCA
1121isotropic13D HN(CO)CA
1111isotropic13D HNCO
1101isotropic13D HN(CA)CO
191isotropic13D HN(CA)CB
181isotropic13D CBCA(CO)NH
171isotropic23D H(CCO)NH
161isotropic23D HBHA(CO)NH
1131isotropic33D CC(CO)NH
1141isotropic33D 1H-15N TOCSY

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Sample preparation

DetailsType: solution / Contents: 0.9 mM [U-13C; U-15N] CHH-L, 90% H2O/10% D2O / Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.9 mM / Component: CHH-L / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: citrate phosphate 10 mM; sodium chloride 100 mM; potassium chloride 10 mM; L-Glu 50 mM; sodium azide 0.02%
Ionic strength: 0.13 M / Label: condition_1 / pH: 3 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Uniform NMR SystemVarianUniform NMR System7001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE8503

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
MOLMOLKoradi, Billeter and Wuthrichstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxchemical shift calculation
RefinementMethod: distance geometry / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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