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- PDB-7zjf: R399E, a mutated form of GDF5, for disease modification of osteoa... -

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Basic information

Entry
Database: PDB / ID: 7zjf
TitleR399E, a mutated form of GDF5, for disease modification of osteoarthritis
ComponentsGrowth/differentiation factor 5
KeywordsSIGNALING PROTEIN / GROWTH FACTOR / GROWTH DIFFERENTIATION FACTOR / BONE MORPHOGENETIC
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 / BMP signaling pathway / chondrocyte differentiation / 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 cytokine
Similarity search - Domain/homology
Growth/differentiation factor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsGigout, A. / Wekmann, D. / Menges, S. / Brenneis, C. / Henson, F. / Cowan, K.J. / Musil, D. / Thudium, C. / Guehring, H. / Michaelis, M. / Kleinschmidt-Doerr, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Arthritis Rheumatol / Year: 2023
Title: R399E, A Mutated Form of Growth and Differentiation Factor 5, for Disease Modification of Osteoarthritis.
Authors: Gigout, A. / Werkmann, D. / Menges, S. / Brenneis, C. / Henson, F. / Cowan, K.J. / Musil, D. / Thudium, C.S. / Guhring, H. / Michaelis, M. / Kleinschmidt-Doerr, K.
History
DepositionApr 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth/differentiation factor 5
B: Growth/differentiation factor 5


Theoretical massNumber of molelcules
Total (without water)27,1412
Polymers27,1412
Non-polymers00
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-32 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.426, 84.732, 98.448
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Growth/differentiation factor 5 / GDF-5 / Bone morphogenetic protein 14 / BMP-14 / Cartilage-derived morphogenetic protein 1 / CDMP-1 ...GDF-5 / Bone morphogenetic protein 14 / BMP-14 / Cartilage-derived morphogenetic protein 1 / CDMP-1 / Lipopolysaccharide-associated protein 4 / LAP-4 / LPS-associated protein 4 / Radotermin


Mass: 13570.558 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF5, BMP14, CDMP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P43026
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.15 / Details: 01 M Hepes, 32% PEG 400, 230 mM MgCl2, pH 8.15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.3→49.22 Å / Num. obs: 75754 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rpim(I) all: 0.023 / Rrim(I) all: 0.069 / Net I/σ(I): 11.6
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 6.1 % / Num. unique obs: 11997 / CC1/2: 0.516 / Rpim(I) all: 0.436 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (3-FEB-2022)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bhk

2bhk


Resolution: 1.3→49.22 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.052 / SU Rfree Blow DPI: 0.052 / SU Rfree Cruickshank DPI: 0.048
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 3788 5 %RANDOM
Rwork0.207 ---
obs0.2077 75747 99.9 %-
Displacement parametersBiso max: 77.6 Å2 / Biso mean: 31.25 Å2 / Biso min: 17.19 Å2
Baniso -1Baniso -2Baniso -3
1--10.9187 Å20 Å20 Å2
2--4.7559 Å20 Å2
3---6.1628 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 1.3→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 0 306 2022
Biso mean---44.28 -
Num. residues----217
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d638SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes318HARMONIC5
X-RAY DIFFRACTIONt_it1862HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion247SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1977SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1862HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2552HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion4.07
X-RAY DIFFRACTIONt_other_torsion15.56
LS refinement shellResolution: 1.3→1.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.5472 76 5.02 %
Rwork0.5098 1439 -
all0.5115 1515 -
obs--95.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05980.0201-0.1271.05351.24983.03560.01960.00440.0578-0.032-0.0033-0.0014-0.30020.0419-0.01640.0368-0.0057-0.0112-0.0414-0.0118-0.0512-14.55520.276415.3652
20.2027-0.274-0.56680.62580.51781.0823-0.0386-0.02390.04770.003-0.00450.01020.05250.03970.04310.007-0.0036-0.0069-0.0093-0.007-0.0266-12.6233-12.0693.3723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A397 - 501
2X-RAY DIFFRACTION2{ B|* }B383 - 501

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