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- PDB-1lxi: Refinement of BMP7 crystal structure -

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Basic information

Entry
Database: PDB / ID: 1lxi
TitleRefinement of BMP7 crystal structure
ComponentsBONE MORPHOGENETIC PROTEIN 7
KeywordsHORMONE/GROWTH FACTOR / Cystine-knot growth factor / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


negative regulation of prostatic bud formation / negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis / negative regulation of glomerular mesangial cell proliferation / mesenchymal cell apoptotic process involved in nephron morphogenesis / positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of hyaluranon cable assembly / chorio-allantoic fusion / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / embryonic skeletal joint morphogenesis ...negative regulation of prostatic bud formation / negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis / negative regulation of glomerular mesangial cell proliferation / mesenchymal cell apoptotic process involved in nephron morphogenesis / positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of hyaluranon cable assembly / chorio-allantoic fusion / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / embryonic skeletal joint morphogenesis / neural fold elevation formation / negative regulation of striated muscle cell apoptotic process / metanephric mesenchymal cell proliferation involved in metanephros development / mesenchyme development / positive regulation of epithelial cell differentiation / ameloblast differentiation / embryonic camera-type eye morphogenesis / monocyte aggregation / allantois development / mesonephros development / regulation of removal of superoxide radicals / hindbrain development / mesenchymal cell differentiation / pericardium morphogenesis / BMP receptor binding / endocardial cushion formation / pharyngeal system development / heart trabecula morphogenesis / cellular response to BMP stimulus / branching involved in salivary gland morphogenesis / embryonic pattern specification / metanephros development / negative regulation of mitotic nuclear division / positive regulation of heterotypic cell-cell adhesion / cartilage development / embryonic limb morphogenesis / negative regulation of non-canonical NF-kappaB signal transduction / response to vitamin D / positive regulation of dendrite development / cardiac muscle tissue development / ureteric bud development / Molecules associated with elastic fibres / regulation of branching involved in prostate gland morphogenesis / negative regulation of neuron differentiation / branching morphogenesis of an epithelial tube / cardiac septum morphogenesis / odontogenesis of dentin-containing tooth / dendrite development / negative regulation of cell cycle / mesoderm formation / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / negative regulation of Notch signaling pathway / positive regulation of bone mineralization / positive regulation of osteoblast differentiation / BMP signaling pathway / positive regulation of epithelial to mesenchymal transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / neuron projection morphogenesis / positive regulation of brown fat cell differentiation / positive regulation of neuron differentiation / axon guidance / protein serine/threonine kinase activator activity / cytokine activity / skeletal system development / growth factor activity / response to peptide hormone / negative regulation of neurogenesis / osteoblast differentiation / response to estradiol / heparin binding / cellular response to hypoxia / vesicle / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / 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 / 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
Bone morphogenetic protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGreenwald, J. / Groppe, J. / Kwiatkowski, W. / Choe, S.
CitationJournal: Mol.Cell / Year: 2003
Title: The BMP7/ActRII Extracellular Domain Complex Provides New Insights into the Cooperative Nature of Receptor Assembly
Authors: Greenwald, J. / Groppe, J. / Gray, P. / Wiater, E. / Kwiatkowski, W. / Vale, W. / Choe, S.
History
DepositionJun 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: BONE MORPHOGENETIC PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9212
Polymers15,7001
Non-polymers2211
Water1,27971
1
A: BONE MORPHOGENETIC PROTEIN 7
hetero molecules

A: BONE MORPHOGENETIC PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8424
Polymers31,3992
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area3170 Å2
ΔGint-15 kcal/mol
Surface area12180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.294, 101.294, 41.812
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe second part of the biological assembly is generated by the two fold axis: x-y+1,-y+2,1/3-z

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Components

#1: Protein BONE MORPHOGENETIC PROTEIN 7 / BMP7 / Osteogenic protein 1 / OP-1


Mass: 15699.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: DHFR- / Gene: BMP7 / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P18075
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.94 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% MPD, 0.1M Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 23 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
220 %MPD1reservoir
3100 mMsodium acetate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 2000 / Details: mirror
RadiationMonochromator: Si 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 15770 / Num. obs: 15770 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.054 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.08 Å / Rsym value: 0.333 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 100 Å / % possible obs: 93.3 % / Num. measured all: 67831 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.333

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
REFMAC5refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BMP

1bmp


Resolution: 2→23.96 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.128 / SU ML: 0.119 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.127 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24449 795 5.1 %RANDOM
Rwork0.22788 ---
all0.22873 14892 --
obs0.22873 14892 92.61 %-
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: 35.983 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0.64 Å20 Å2
2---1.29 Å20 Å2
3---1.93 Å2
Refinement stepCycle: LAST / Resolution: 2→23.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 14 71 913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.021872
X-RAY DIFFRACTIONr_bond_other_d0.0010.02742
X-RAY DIFFRACTIONr_angle_refined_deg2.4621.9491198
X-RAY DIFFRACTIONr_angle_other_deg1.42431729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1573107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.50515139
X-RAY DIFFRACTIONr_chiral_restr0.1560.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02967
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02173
X-RAY DIFFRACTIONr_nbd_refined0.3060.3175
X-RAY DIFFRACTIONr_nbd_other0.2320.3650
X-RAY DIFFRACTIONr_nbtor_other0.3890.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4090.568
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.120.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3090.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6670.510
X-RAY DIFFRACTIONr_mcbond_it1.6181.5528
X-RAY DIFFRACTIONr_mcangle_it2.882859
X-RAY DIFFRACTIONr_scbond_it4.0933344
X-RAY DIFFRACTIONr_scangle_it6.5264.5339
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 66
Rwork0.265 1160
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.03
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.462

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