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- PDB-1bzg: THE SOLUTION STRUCTURE OF HUMAN PARATHYROID HORMONE-RELATED PROTE... -

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Entry
Database: PDB / ID: 1bzg
TitleTHE SOLUTION STRUCTURE OF HUMAN PARATHYROID HORMONE-RELATED PROTEIN (1-34) IN NEAR-PHYSIOLOGICAL SOLUTION, NMR, 30 STRUCTURES
ComponentsPARATHYROID HORMONE-RELATED PROTEIN
KeywordsHORMONE / HUMAN PEPTIDE HORMONE / STIMULATING INTRACELLULAR CAMP FORMATION / SERUM CALCIUM LEVEL / HUMORAL HYPERCALCEMIA OF MALIGNANCY / SOLUTION STRUCTURE / PTHRP / PTH
Function / homology
Function and homology information


negative regulation of chondrocyte development / regulation of chondrocyte differentiation / cAMP metabolic process / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / peptide hormone receptor binding / bone mineralization / epidermis development / skeletal system development ...negative regulation of chondrocyte development / regulation of chondrocyte differentiation / cAMP metabolic process / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / peptide hormone receptor binding / bone mineralization / epidermis development / skeletal system development / female pregnancy / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / cell-cell signaling / regulation of gene expression / G alpha (s) signalling events / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Golgi apparatus / extracellular space / extracellular region / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Parathyroid hormone-related protein / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone
Similarity search - Domain/homology
Parathyroid hormone-related protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsWeidler, M. / Marx, U.C. / Seidel, G. / Roesch, P.
CitationJournal: FEBS Lett. / Year: 1999
Title: The structure of human parathyroid hormone-related protein(1-34) in near-physiological solution.
Authors: Weidler, M. / Marx, U.C. / Seidel, G. / Schafer, W. / Hoffmann, E. / Esswein, A. / Rosch, P.
History
DepositionOct 28, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PARATHYROID HORMONE-RELATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)4,0281
Polymers4,0281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
RepresentativeModel #1

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Components

#1: Protein/peptide PARATHYROID HORMONE-RELATED PROTEIN


Mass: 4027.636 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P12272

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121CLEAN-TOCSY
131NOESY

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Sample preparation

DetailsContents: H2O/D2O (9:1)
Sample conditionsIonic strength: 550mM / pH: 5.1 / Pressure: 10E+5PA atm / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
X-PLOR3phasing
NMR software
NameVersionDeveloperClassification
X-PLOR V3.840V3.840BRUNGERrefinement
NDEE2structure solution
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: STRATEGY USED FOR NMR STRUCTURE CALCULATION: EXPERIMENTAL RESTRAINTS FOR THE STRUCTURE CALCULATIONS INITIALLY, FREQUENCY DEGENERATED NOESY CROSS-PEAKS WERE INCORPORATED INTO THE STRUCTURE ...Details: STRATEGY USED FOR NMR STRUCTURE CALCULATION: EXPERIMENTAL RESTRAINTS FOR THE STRUCTURE CALCULATIONS INITIALLY, FREQUENCY DEGENERATED NOESY CROSS-PEAKS WERE INCORPORATED INTO THE STRUCTURE CALCULATION AS 'AMBIGUOUS'. SUBSEQUENTLY, THE PROTON- PROTON DISTANCES IN THE CALCULATED STRUCTURES WERE DETERMINED USING THE PROGRAM BACKCALC_DB 2.0 (SOFTWARE SYMBIOSE, INC., BAYREUTH, GERMANY) AND COMPARED WITH THE COMBINATIONS OF DISTANCES POSSIBLE FOR EACH FREQUENCY DEGENERATED NOESY CROSS-PEAK. IF ONLY ONE OF THE POSSIBLE DISTANCE COMBINATIONS WAS FULFILLED IN MORE THAN 50% OF THE CALCULATED STRUCTURES, THE DISTANCE INFORMATION WAS USED IN FURTHER STRUCTURE CALCULATIONS. THIS PROCEDURE WAS REPEATED SEVERAL TIMES, LEADING TO A TOTAL OF 424 INTRARESIDUAL AND 337 INTERRESIDUAL NOE CONNECTIVITIES. STRUCTURES CALCULATIONS WERE PERFORMED USING A MODIFIED AB INITIO SIMULATED ANNEALING PROTOCOL (NILGES, UNPUBLISHED) WITH X-PLOR V3.840. THE CALCULATION STRATEGY INCLUDES FLOATING ASSIGNMENT OF PROCHIRAL GROUPS AND A REDUCED PRESENTATION FOR NON-BONDED INTERACTIONS FOR PART OF THE CALCULATION TO INCREASE EFFICIENCY. A MORE DETAILED DESCRIPTION OF THE PROTOCOL IS GIVEN IN KHARRAT ET AL. (EMBO J. 14 (1995) 3572-84). STRUCTURE PARAMETERS WERE EXTRACTED FROM THE STANDARD FILES PARALLHDG.PRO AND TOPALLHDG.PRO OF X-PLOR V3.840. IN EACH ROUND OF THE STRUCTURE CALCULATION 100 STRUCTURES WERE CALCULATED. OF THE 100 STRUCTURES RESULTING FROM THE FINAL ROUND OF STRUCTURE CALCULATION, THOSE 30 STRUCTURES THAT SHOWED THE LOWEST TOTAL ENERGY VALUES WERE SELECTED FOR FURTHER CHARACTERIZATION.
NMR ensembleConformer selection criteria: ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Conformers calculated total number: 100 / Conformers submitted total number: 30

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