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- PDB-1huw: THE CRYSTAL STRUCTURE OF AFFINITY-MATURED HUMAN GROWTH HORMONE AT... -

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Basic information

Entry
Database: PDB / ID: 1huw
TitleTHE CRYSTAL STRUCTURE OF AFFINITY-MATURED HUMAN GROWTH HORMONE AT 2 ANGSTROMS RESOLUTION
ComponentsHUMAN GROWTH HORMONE
KeywordsHORMONE
Function / homology
Function and homology information


growth hormone activity / growth hormone receptor complex / prolactin receptor binding / bone maturation / animal organ development / positive regulation of multicellular organism growth / positive regulation of D-glucose transmembrane transport / cell surface receptor signaling pathway via STAT / growth hormone receptor binding / positive regulation of insulin-like growth factor receptor signaling pathway ...growth hormone activity / growth hormone receptor complex / prolactin receptor binding / bone maturation / animal organ development / positive regulation of multicellular organism growth / positive regulation of D-glucose transmembrane transport / cell surface receptor signaling pathway via STAT / growth hormone receptor binding / positive regulation of insulin-like growth factor receptor signaling pathway / growth hormone receptor signaling pathway / Prolactin receptor signaling / positive regulation of MAP kinase activity / growth hormone receptor signaling pathway via JAK-STAT / Synthesis, secretion, and deacylation of Ghrelin / cell surface receptor signaling pathway via JAK-STAT / Growth hormone receptor signaling / endosome lumen / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / response to nutrient levels / hormone activity / cytokine-mediated signaling pathway / response to estradiol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Somatotropin / Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsUltsch, M.H. / Somers, W.S. / Kossiakoff, A.A. / De Vos, A.M.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: The crystal structure of affinity-matured human growth hormone at 2 A resolution.
Authors: Ultsch, M.H. / Somers, W. / Kossiakoff, A.A. / de Vos, A.M.
#1: Journal: To be Published
Title: Affinity Maturation of Human Growth Hormone by Monovalent Phage Display
Authors: Lowman, H.B. / Wells, J.A.
History
DepositionSep 22, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / 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.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN GROWTH HORMONE


Theoretical massNumber of molelcules
Total (without water)21,9871
Polymers21,9871
Non-polymers00
Water1,38777
1
A: HUMAN GROWTH HORMONE

A: HUMAN GROWTH HORMONE


Theoretical massNumber of molelcules
Total (without water)43,9732
Polymers43,9732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Unit cell
Length a, b, c (Å)80.450, 59.340, 50.870
Angle α, β, γ (deg.)90.00, 128.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HUMAN GROWTH HORMONE


Mass: 21986.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01241
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %(w/v)PEG80001reservoir
20.2 Mmagnesium acetate1reservoir
30.1 Msodium cacodylate1reservoir
46 mg/mlprotein1drop
5120 mM1dropNaCl
620 mMsodium cacoylate1drop
75.0 mMEDTA1drop
81 mMphenylmethylsulfonyl fluoride1drop
910 %(w/v)PEG80001drop
100.2 Mmagnesium acetate1drop
110.1 Msodium cacodylate1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / Num. obs: 6630 / % possible obs: 97.3 % / Num. measured all: 16335 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.48 Å / % possible obs: 94.1 % / Num. unique obs: 626 / Num. measured obs: 1167 / Rmerge(I) obs: 0.144

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→8 Å / Rfactor Rwork: 0.185 / Rfactor obs: 0.185 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 0 77 1438
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / Num. reflection all: 12423 / Num. reflection obs: 11341 / σ(F): 2 / Rfactor all: 0.199 / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.63
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / Num. reflection Rfree: 4151 / Rfactor obs: 0.298

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