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- PDB-6btp: BMP1 complexed with a hydroxamate -

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Basic information

Entry
Database: PDB / ID: 6btp
TitleBMP1 complexed with a hydroxamate
ComponentsBone morphogenetic protein 1
KeywordsHYDROLASE / endopeptidase
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 / metalloendopeptidase activity / protein processing / 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. / Spermadhesin, CUB domain superfamily ...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 / Metallopeptidase, catalytic domain superfamily / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / 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-E8J / THIOCYANATE ION / Bone morphogenetic protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 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 7, 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
B: Bone morphogenetic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,71210
Polymers45,8502
Non-polymers8628
Water6,485360
1
A: Bone morphogenetic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5475
Polymers22,9251
Non-polymers6224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bone morphogenetic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1655
Polymers22,9251
Non-polymers2404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.331, 124.366, 43.642
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 Bone morphogenetic protein 1 / BMP-1 / Mammalian tolloid protein / mTld / Procollagen C-proteinase / PCP


Mass: 22925.027 Da / Num. of mol.: 2 / Fragment: residues 121-321
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-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-E8J / (1R,3S,4S)-2-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]heptanoyl}-N-(3-methoxypyrazin-2-yl)-2-azabicyclo[2.2.1]heptane-3-carboxamide


Mass: 433.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H31N5O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 8-12% PEG 3350 150-200mM KSCN 10mM spermidine

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Nov 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.927→124.366 Å / Num. all: 36873 / Num. obs: 36873 / % possible obs: 97 % / Redundancy: 7.3 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.126 / Rsym value: 0.108 / Net I/av σ(I): 7.1 / Net I/σ(I): 17.1 / Num. measured all: 267447
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.93-2.037.40.6061.351680.2560.7040.60694.7
2.03-2.157.30.385249370.1640.4490.38595.4
2.15-2.37.30.2862.746920.1230.3360.28695.9
2.3-2.497.30.2323.444170.0980.2690.23297.4
2.49-2.727.30.1624.840700.0690.1890.16296.7
2.72-3.057.30.1087.237580.0460.1240.10898.8
3.05-3.527.30.05812.633350.0250.0680.05898.4
3.52-4.317.10.03619.228900.0160.0430.03699.1
4.31-6.0970.03223.222740.0140.0380.03299.5
6.09-106.30.02723.213320.0130.0330.02798.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALAdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→73.09 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.644 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.149
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 1844 5 %RANDOM
Rwork0.2026 ---
obs0.2041 34958 96.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.65 Å2 / Biso mean: 26.822 Å2 / Biso min: 7.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0 Å2
2---0.39 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 1.93→73.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 46 360 3590
Biso mean--34.34 29.43 -
Num. residues----401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193351
X-RAY DIFFRACTIONr_bond_other_d0.0020.022982
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.934544
X-RAY DIFFRACTIONr_angle_other_deg0.92636905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9265408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.11722.425167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83915529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8241532
X-RAY DIFFRACTIONr_chiral_restr0.0670.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213770
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02754
LS refinement shellResolution: 1.927→1.977 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 128 -
Rwork0.26 2498 -
all-2626 -
obs--94.46 %
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)
10.4966-0.55530.03924.4591-0.2250.1253-0.06-0.06780.1423-0.24810.0676-0.71140.02-0.0958-0.00750.03320.00060.02470.08170.01570.136415.97316.5210.078
20.6148-0.1631-0.31710.3870.24680.52970.03070.01550.0303-0.0174-0.0006-0.0116-0.05280.0176-0.03010.0215-0.0058-0.00960.06060.01260.0138-15.4669.931-7.044
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 200
2X-RAY DIFFRACTION2B1 - 200

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