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- PDB-2bhk: Crystal structure of human growth and differentiation factor 5 (GDF5) -

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Basic information

Entry
Database: PDB / ID: 2bhk
TitleCrystal structure of human growth and differentiation factor 5 (GDF5)
ComponentsGROWTH DIFFERENTIATION FACTOR 5
KeywordsGROWTH FACTOR / GROWTH DIFFERENTIATION FACTOR / BONE MORPHOGENETIC FACTOR / HORMONE-RECEPTOR INTERACTION / CYSTINE KNOT / PREFORMED RECEPTOR DIMER / CYTOKINE / DWARFISM / GLYCOPROTEIN
Function / homology
Function and homology information


ossification involved in bone remodeling / forelimb morphogenesis / BMP binding / chondroblast differentiation / hindlimb morphogenesis / negative regulation of mesenchymal cell apoptotic process / positive regulation of chondrocyte differentiation / mesenchymal cell apoptotic process / positive regulation of BMP signaling pathway / negative regulation of chondrocyte differentiation ...ossification involved in bone remodeling / forelimb morphogenesis / BMP binding / chondroblast differentiation / hindlimb morphogenesis / negative regulation of mesenchymal cell apoptotic process / positive regulation of chondrocyte differentiation / mesenchymal cell apoptotic process / positive regulation of BMP signaling pathway / negative regulation of chondrocyte differentiation / embryonic limb morphogenesis / Molecules associated with elastic fibres / positive regulation of SMAD protein signal transduction / regulation of multicellular organism growth / chondrocyte differentiation / BMP signaling pathway / response to mechanical stimulus / positive regulation of neuron differentiation / transforming growth factor beta receptor signaling pathway / cytokine activity / growth factor activity / negative regulation of epithelial cell proliferation / cell-cell signaling / negative regulation of neuron apoptotic process / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B ...TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Growth/differentiation factor 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchreuder, H. / Liesum, A. / Pohl, J. / Kruse, M. / Koyama, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: Crystal Structure of Recombinant Human Growth Differentiation Factor 5. Evidence for Interaction of the Type I and Type II Receptor Binding Sites.
Authors: Schreuder, H. / Liesum, A. / Pohl, J. / Kruse, M. / Koyama, M.
History
DepositionJan 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: GROWTH DIFFERENTIATION FACTOR 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8996
Polymers13,5991
Non-polymers3005
Water1,29772
1
A: GROWTH DIFFERENTIATION FACTOR 5
hetero molecules

A: GROWTH DIFFERENTIATION FACTOR 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,79812
Polymers27,1972
Non-polymers60110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)98.200, 98.200, 43.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein GROWTH DIFFERENTIATION FACTOR 5 / / GDF-5 / CARTILAGE-DERIVED MORPHOGENETIC PROTEIN 1 / CDMP-1


Mass: 13598.638 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: INTERCHAIN DISULFIDE LINK BETWEEN TWO CRYSTALLOGRAPHICALLY RELATED MONOMERS
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PUC18 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P43026
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: POSSIBLE INVOLVEMENT IN BONE FORMATION

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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: 5.1 Å3/Da / Density % sol: 75 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: 100 MM SODIUM ACETATE, PH 5.0 30% ISOPROPANOL 14 MG/ML PROTEIN HANGING DROP

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 26, 1997 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→60 Å / Num. obs: 9310 / % possible obs: 95.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMP

1bmp


Resolution: 2.4→8 Å / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22 939 10.4 %RANDOM
Rwork0.168 ---
obs0.168 9058 96 %-
Displacement parametersBiso mean: 35.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms834 0 20 72 926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
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
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8 /
Rfactor% reflection
Rfree0.31 9.7 %
Rwork0.267 -
obs-98.7 %

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