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- PDB-1waq: Crystal structure of human Growth and Differentiation Factor 5 (GDF-5) -

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Basic information

Entry
Database: PDB / ID: 1waq
TitleCrystal structure of human Growth and Differentiation Factor 5 (GDF-5)
ComponentsGROWTH/DIFFERENTIATION FACTOR 5
KeywordsGROWTH FACTOR / TGF-BETA SUPERFAMILY / CYTOKINE
Function / homology
Function and homology information


ossification involved in bone remodeling / forelimb morphogenesis / chondroblast differentiation / BMP binding / 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 / chondroblast differentiation / BMP binding / 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 / response to mechanical stimulus / BMP signaling pathway / 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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain ...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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
Growth/differentiation factor 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsMueller, T.D. / Nickel, J. / Sebald, W.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: A Single Residue of Gdf-5 Defines Binding Specificity to Bmp Receptor Ib.
Authors: Nickel, J. / Kotzsch, A. / Sebald, W. / Mueller, T.D.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Molecular Recognition of Bmp-2 and Bmp Receptor Ia
Authors: Keller, S. / Nickel, J. / Sebald, W. / Mueller, T.D.
History
DepositionOct 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GROWTH/DIFFERENTIATION FACTOR 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7604
Polymers13,4051
Non-polymers3553
Water41423
1
A: GROWTH/DIFFERENTIATION FACTOR 5
hetero molecules

A: GROWTH/DIFFERENTIATION FACTOR 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5208
Polymers26,8112
Non-polymers7096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_679x-y+1,-y+2,-z+13/31
MethodPQS
Unit cell
Length a, b, c (Å)97.771, 97.771, 43.325
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: 13405.481 Da / Num. of mol.: 1 / Fragment: RESIDUES 387-501 (RESIDUES 6-120 OF MATURE GDF-5)
Source method: isolated from a genetically manipulated source
Details: DIMERIC CONNECTED THROUGH INTERMOLECULAR DISULFIDE BOND BETWEEN CYS 84
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: FIBROBLAST / Plasmid: RBSIIN25X/O / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P43026
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOULD BE INVOLVED IN BONE FORMATION. HOMODIMER; DISULFIDE-LINKED (BY SIMILARITY). DEFECTS IN GDF5 ...COULD BE INVOLVED IN BONE FORMATION. HOMODIMER; DISULFIDE-LINKED (BY SIMILARITY). DEFECTS IN GDF5 ARE THE CAUSE OF CHONDRODYSPLASIA GREBE.
Has protein modificationY
Sequence detailsRESIDUES 6 TO 120 OF MATURE GDF-5 WERE EXPRESSED WITH AN N- TERMINAL EXTENSION MET-LYS FROM THE ...RESIDUES 6 TO 120 OF MATURE GDF-5 WERE EXPRESSED WITH AN N- TERMINAL EXTENSION MET-LYS FROM THE EXPRESSION VECTOR

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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: 4.4 Å3/Da / Density % sol: 72 %
Crystal growDetails: 25% 2-METHLY-2,4-PENTANEDIOL, 0.1M SODIUM CITRATE PH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9183
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 16, 2002 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 2.28→84.52 Å / Num. obs: 11084 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.7
Reflection shellResolution: 2.28→2.39 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.4 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMP

1bmp


Resolution: 2.28→17 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.508 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 6 TO 16 OF THE MATURE PART OF GDF-5 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.237 546 5 %RANDOM
Rwork0.222 ---
obs0.223 10300 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.28→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms825 0 24 23 872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021877
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9711197
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4575103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02659
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.3337
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.552
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.344
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.58
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.0141.5525
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it11.0612858
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it14.1253352
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it17.9544.5339
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.34 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 35
Rwork0.289 645
Refinement TLS params.Method: refined / Origin x: 96.007 Å / Origin y: 92.403 Å / Origin z: 88.654 Å
111213212223313233
T0.1577 Å20.0177 Å2-0.024 Å2-0.0609 Å20.0226 Å2--0.0145 Å2
L1.5191 °24.9477 °2-0.8447 °2-21.7989 °2-2.1301 °2--1.1117 °2
S-0.1208 Å °0.0873 Å °0.1941 Å °-1.2863 Å °0.1412 Å °0.7956 Å °0.0089 Å °-0.01 Å °-0.0204 Å °

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