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- PDB-1et1: CRYSTAL STRUCTURE OF HUMAN PARATHYROID HORMONE 1-34 AT 0.9 A RESO... -

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Basic information

Entry
Database: PDB / ID: 1et1
TitleCRYSTAL STRUCTURE OF HUMAN PARATHYROID HORMONE 1-34 AT 0.9 A RESOLUTION
ComponentsPARATHYROID HORMONE
KeywordsHORMONE/GROWTH FACTOR / HELICAL DIMER / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


macromolecule biosynthetic process / parathyroid hormone receptor binding / type 1 parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / response to parathyroid hormone / positive regulation of cell proliferation in bone marrow / hormone-mediated apoptotic signaling pathway / magnesium ion homeostasis ...macromolecule biosynthetic process / parathyroid hormone receptor binding / type 1 parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / response to parathyroid hormone / positive regulation of cell proliferation in bone marrow / hormone-mediated apoptotic signaling pathway / magnesium ion homeostasis / positive regulation of signal transduction / response to fibroblast growth factor / cAMP metabolic process / phosphate ion homeostasis / Class B/2 (Secretin family receptors) / negative regulation of chondrocyte differentiation / response to vitamin D / positive regulation of inositol phosphate biosynthetic process / peptide hormone receptor binding / bone mineralization / positive regulation of glycogen biosynthetic process / bone resorption / response to cadmium ion / positive regulation of bone mineralization / Rho protein signal transduction / homeostasis of number of cells within a tissue / skeletal system development / positive regulation of D-glucose import / hormone activity / response to lead ion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / cell-cell signaling / regulation of gene expression / response to ethanol / G alpha (s) signalling events / transcription by RNA polymerase II / G protein-coupled receptor signaling pathway / receptor ligand activity / response to xenobiotic stimulus / negative regulation of gene expression / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Parathyroid hormone / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.9 Å
AuthorsJin, L. / Briggs, S.L. / Chandrasekhar, S. / Chirgadze, N.Y. / Clawson, D.K. / Schevitz, R.W. / Smiley, D.L. / Tashjian, A.H. / Zhang, F.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Crystal structure of human parathyroid hormone 1-34 at 0.9-A resolution.
Authors: Jin, L. / Briggs, S.L. / Chandrasekhar, S. / Chirgadze, N.Y. / Clawson, D.K. / Schevitz, R.W. / Smiley, D.L. / Tashjian, A.H. / Zhang, F.
History
DepositionApr 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PARATHYROID HORMONE
B: PARATHYROID HORMONE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2984
Polymers8,2522
Non-polymers462
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-24 kcal/mol
Surface area6420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.177, 30.177, 110.435
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biological functional unit is a monomer of hPTH (1-34).

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Components

#1: Protein/peptide PARATHYROID HORMONE


Mass: 4125.778 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01270
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.76 Å3/Da / Density % sol: 30.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2.5 M ammonium sulfate, 5% isopropanol and 0.1 M sodium acetate buffer, pH 4.5., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 %glycerol1drop
32.5 Mammonium sulfate1reservoir
45 %isopropanol1reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.9→13.5 Å / Num. all: 37771 / Num. obs: 37771 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 4.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 8.2
Reflection shellResolution: 0.9→0.93 Å / Rmerge(I) obs: 0.163 / Num. unique all: 3148 / % possible all: 75.5
Reflection
*PLUS
Num. measured all: 111749
Reflection shell
*PLUS
% possible obs: 75.5 %

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Processing

Software
NameClassification
SOLVEphasing
SHELXL-97refinement
MAR345data collection
HKL-2000data scaling
RefinementResolution: 0.9→13.5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Used conjugate-gradient algorithm with riding hydrogens with anisotropic B factor refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.14 1881 -5% of randomly selected data.
Rwork0.137 ---
obs0.137 37765 90.5 %-
all-41735 --
Refinement stepCycle: LAST / Resolution: 0.9→13.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms658 0 2 104 764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2.259
X-RAY DIFFRACTIONx_torsion_deg16.628
X-RAY DIFFRACTIONx_torsion_impr_deg1.795
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_deg
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg16.628

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