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- PDB-6bsm: BMP1 complexed with a reverse hydroxamate - compound 4 -

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Basic information

Entry
Database: PDB / ID: 6bsm
TitleBMP1 complexed with a reverse hydroxamate - compound 4
ComponentsBone morphogenetic protein 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / endopeptidase / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


procollagen C-endopeptidase / Anchoring fibril formation / Crosslinking of collagen fibrils / positive regulation of cartilage development / HDL assembly / Collagen biosynthesis and modifying enzymes / dorsal/ventral pattern formation / collagen fibril organization / cartilage condensation / Degradation of the extracellular matrix ...procollagen C-endopeptidase / Anchoring fibril formation / Crosslinking of collagen fibrils / positive regulation of cartilage development / HDL assembly / Collagen biosynthesis and modifying enzymes / dorsal/ventral pattern formation / collagen fibril organization / cartilage condensation / Degradation of the extracellular matrix / ossification / skeletal system development / cytokine activity / growth factor activity / protein processing / metalloendopeptidase activity / metallopeptidase activity / peptidase activity / vesicle / cell differentiation / serine-type endopeptidase activity / calcium ion binding / Golgi apparatus / proteolysis / extracellular space / zinc ion binding / extracellular region / identical protein binding
Similarity search - Function
Bone morphogenetic protein 1/tolloid-like protein / Tolloid/BMP1 peptidase domain / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / : / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. ...Bone morphogenetic protein 1/tolloid-like protein / Tolloid/BMP1 peptidase domain / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / : / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Calcium-binding EGF domain / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / Metallopeptidase, catalytic domain superfamily / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-E7D / Bone morphogenetic protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsGampe, R. / Shewchuk, L.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Reverse Hydroxamate Inhibitors of Bone Morphogenetic Protein 1.
Authors: Kallander, L.S. / Washburn, D. / Hilfiker, M.A. / Eidam, H.S. / Lawhorn, B.G. / Prendergast, J. / Fox, R. / Dowdell, S. / Manns, S. / Hoang, T. / Zhao, S. / Ye, G. / Hammond, M. / Holt, D.A. ...Authors: Kallander, L.S. / Washburn, D. / Hilfiker, M.A. / Eidam, H.S. / Lawhorn, B.G. / Prendergast, J. / Fox, R. / Dowdell, S. / Manns, S. / Hoang, T. / Zhao, S. / Ye, G. / Hammond, M. / Holt, D.A. / Roethke, T. / Hong, X. / Reid, R.A. / Gampe, R. / Zhang, H. / Diaz, E. / Rendina, A.R. / Quinn, A.M. / Willette, B.
History
DepositionDec 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone morphogenetic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4634
Polymers22,9251
Non-polymers5383
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.789, 101.789, 101.789
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Bone morphogenetic protein 1 / / BMP-1 / Mammalian tolloid protein / mTld / Procollagen C-proteinase / PCP


Mass: 22925.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP1, PCOLC / Production host: Escherichia coli (E. coli) / References: UniProt: P13497, procollagen C-endopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-E7D / N-({[(2R)-2-{[hydroxy(hydroxymethyl)amino]methyl}heptanoyl]amino}methyl)-7-methoxy-1-benzofuran-2-carboxamide


Mass: 407.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N3O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.83 Å3/Da / Density % sol: 67.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 5% PEG3350, 200 mM KSCN, 10mM spermadine

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 15311 / % possible obs: 100 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.068 / Χ2: 1.036 / Net I/σ(I): 12.8 / Num. measured all: 140111
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.33-2.419.30.57615021.0111100
2.41-2.519.30.44514961.031100
2.51-2.629.30.31215401.0481100
2.62-2.769.20.25215031.0871100
2.76-2.949.30.16815171.043199.9
2.94-3.169.20.11215101.0481100
3.16-3.489.30.07215251.0141100
3.48-3.9890.06215391.0371100
3.98-5.028.90.05215541.0281100
5.02-108.70.04416251.017199.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→45.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.667 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.181
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 475 3.1 %RANDOM
Rwork0.1923 ---
obs0.1933 14815 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 114.57 Å2 / Biso mean: 57.112 Å2 / Biso min: 27.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.33→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 31 107 1737
Biso mean--52.32 50.02 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191692
X-RAY DIFFRACTIONr_bond_other_d0.0020.021497
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9512293
X-RAY DIFFRACTIONr_angle_other_deg0.96333458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0065203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.20422.17685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79915261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9141517
X-RAY DIFFRACTIONr_chiral_restr0.0710.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02387
LS refinement shellResolution: 2.33→2.391 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 46 -
Rwork0.272 1051 -
all-1097 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 14.013 Å / Origin y: -8.607 Å / Origin z: -15.631 Å
111213212223313233
T0.0308 Å20.0079 Å20.0219 Å2-0.0533 Å20.042 Å2--0.0613 Å2
L2.2941 °2-0.6158 °2-0.0946 °2-0.81 °20.0372 °2--0.0047 °2
S0.1022 Å °0.0537 Å °0.0734 Å °0.0561 Å °-0.1001 Å °-0.0944 Å °-0.0033 Å °-0.0082 Å °-0.0021 Å °

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