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- PDB-1zkz: Crystal Structure of BMP9 -

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Basic information

Entry
Database: PDB / ID: 1zkz
TitleCrystal Structure of BMP9
ComponentsGrowth/differentiation factor 2
KeywordsHORMONE/GROWTH FACTOR / glycoprotein / growth factor / cytokine / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


positive regulation of epithelial cell differentiation / positive regulation of cartilage development / positive regulation of endothelial cell differentiation / positive regulation of bicellular tight junction assembly / cellular response to BMP stimulus / Signaling by BMP / activin receptor signaling pathway / positive regulation of BMP signaling pathway / cartilage development / blood vessel morphogenesis ...positive regulation of epithelial cell differentiation / positive regulation of cartilage development / positive regulation of endothelial cell differentiation / positive regulation of bicellular tight junction assembly / cellular response to BMP stimulus / Signaling by BMP / activin receptor signaling pathway / positive regulation of BMP signaling pathway / cartilage development / blood vessel morphogenesis / negative regulation of endothelial cell migration / branching involved in blood vessel morphogenesis / positive regulation of Notch signaling pathway / negative regulation of DNA replication / negative regulation of endothelial cell proliferation / positive regulation of SMAD protein signal transduction / negative regulation of blood vessel endothelial cell migration / vasculogenesis / BMP signaling pathway / positive regulation of endothelial cell proliferation / ossification / negative regulation of angiogenesis / protein serine/threonine kinase activator activity / cytokine activity / positive regulation of interleukin-8 production / growth factor activity / negative regulation of cell growth / osteoblast differentiation / positive regulation of angiogenesis / angiogenesis / intracellular iron ion homeostasis / transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region
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
Growth/differentiation factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsBrown, M.A. / Zhao, Q. / Baker, K.A. / Naik, C. / Chen, C. / Pukac, L. / Singh, M. / Tsareva, T. / Parice, Y. / Mahoney, A. ...Brown, M.A. / Zhao, Q. / Baker, K.A. / Naik, C. / Chen, C. / Pukac, L. / Singh, M. / Tsareva, T. / Parice, Y. / Mahoney, A. / Roschke, V. / Sanyal, I. / Choe, S.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of BMP-9 and functional interactions with pro-region and receptors
Authors: Brown, M.A. / Zhao, Q. / Baker, K.A. / Naik, C. / Chen, C. / Pukac, L. / Singh, M. / Tsareva, T. / Parice, Y. / Mahoney, A. / Roschke, V. / Sanyal, I. / Choe, S.
History
DepositionMay 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth/differentiation factor 2


Theoretical massNumber of molelcules
Total (without water)12,1031
Polymers12,1031
Non-polymers00
Water72140
1
A: Growth/differentiation factor 2

A: Growth/differentiation factor 2


Theoretical massNumber of molelcules
Total (without water)24,2062
Polymers24,2062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+1/2,y,-z-1/41
Buried area2650 Å2
ΔGint-19 kcal/mol
Surface area11790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.234, 71.234, 144.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThe biological assembly is a homodimer.

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Components

#1: Protein Growth/differentiation factor 2 / GDF-2 / Bone morphogenetic protein 9 / BMP-9


Mass: 12102.971 Da / Num. of mol.: 1 / Fragment: Growth/differentiation factor 2, residues 320-429
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GDF2, BMP9 / Plasmid: pC4 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-DG44 / Tissue (production host): ovary cells / References: UniProt: Q9UK05
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.8 Å3/Da / Density % sol: 67.6 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1-1.2 M Sodium Chloride, 7-10 mM Hexadecyltrimethylammonium Bromide 10 mM Magnesium Chloride, pH 7.5, temperature 296K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2004
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→23.8 Å / Num. all: 8346 / Num. obs: 8142 / Redundancy: 13.5 % / Rmerge(I) obs: 0.077
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID
2.32-2.411.30.3571
2.4-2.512.70.3281
2.5-2.6113.70.271
2.61-2.7514.10.1921
2.75-2.9214.30.1451
2.92-3.1514.20.0991
3.15-3.4714.20.0821
3.47-3.9713.90.081
3.97-513.50.071
5-5012.60.0451

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Phasing

Phasing MR
Highest resolutionLowest resolution
Translation2.5 Å25.152 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.6data extraction
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BMP

3bmp


Resolution: 2.33→23.8 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.904 / Cross valid method: THROUGHOUT / ESU R: 0.801 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27181 392 4.7 %RANDOM
Rwork0.23074 ---
obs0.23254 7954 99.52 %-
all-8346 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.434 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.33→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms831 0 0 40 871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022857
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.9621165
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2345106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91124.06232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33815143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.867152
X-RAY DIFFRACTIONr_chiral_restr0.1030.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02638
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.2329
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2565
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3660.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4651.5534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.4032866
X-RAY DIFFRACTIONr_scbond_it3.063323
X-RAY DIFFRACTIONr_scangle_it4.4394.5299
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.387 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 25 -
Rwork0.239 574 -
obs--96.77 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
14.596913.2237-31.0303745
212.260312.9723-10.0131
321.595517.8092-9.55
46.90161.7012-35.5279
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 344 - 34
2X-RAY DIFFRACTION2AA35 - 5435 - 54
3X-RAY DIFFRACTION3AA55 - 7855 - 78
4X-RAY DIFFRACTION4AA79 - 10879 - 108

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