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- PDB-6btq: BMP1 complexed with a hydroxamate - compound 2 -

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Basic information

Entry
Database: PDB / ID: 6btq
TitleBMP1 complexed with a hydroxamate - compound 2
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-E8S / THIOCYANATE ION / Bone morphogenetic protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)47,22515
Polymers45,9922
Non-polymers1,23313
Water7,566420
1
A: Bone morphogenetic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7967
Polymers22,9961
Non-polymers8006
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bone morphogenetic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4298
Polymers22,9961
Non-polymers4337
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.740, 90.682, 124.013
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 22996.105 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

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Non-polymers , 5 types, 433 molecules

#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.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-E8S / N~2~-[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-N~2~-[(4-methoxyphenyl)sulfonyl]-3-thiophen-2-yl-D-alaninamide


Mass: 490.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N2O7S2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 54 %
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: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 50881 / % possible obs: 99.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.066 / Χ2: 1 / Net I/σ(I): 8.9 / Num. measured all: 245458
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.75-1.814.80.5249920.955199.4
1.81-1.894.80.36850091.016199.5
1.89-1.974.80.26750071.025199.5
1.97-2.074.80.19750171.012199.5
2.07-2.24.90.13450680.999199.9
2.2-2.384.90.10250480.987199.9
2.38-2.614.90.07951090.9991100
2.61-2.994.90.06851271.0071100
2.99-3.774.70.05751871.003199.8
3.77-104.70.0453170.995198

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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: 1.75→37.61 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.043 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.102
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 2580 5.1 %RANDOM
Rwork0.1833 ---
obs0.1845 48243 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 59.69 Å2 / Biso mean: 26.366 Å2 / Biso min: 15.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2--1.25 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 1.75→37.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3200 0 65 420 3685
Biso mean--31.15 35.51 -
Num. residues----404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193450
X-RAY DIFFRACTIONr_bond_other_d0.0020.023099
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9314682
X-RAY DIFFRACTIONr_angle_other_deg0.94237163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8795426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.78621.921177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60415549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5731539
X-RAY DIFFRACTIONr_chiral_restr0.0710.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213893
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02801
LS refinement shellResolution: 1.743→1.789 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 176 -
Rwork0.254 3321 -
all-3497 -
obs--94.36 %
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)
10.5524-0.1-0.08780.30070.04280.7022-0.0133-0.0463-0.06810.0127-0.0278-0.0282-0.1172-0.03230.04110.0573-0.0067-0.01540.01480.01230.018420.45515.78116.368
20.4424-0.50520.06730.9432-0.14630.4566-0.074-0.07150.05610.0070.102-0.05350.0014-0.0286-0.0280.02850.0039-0.01180.0244-0.00550.010215.234-15.8210.321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 201
2X-RAY DIFFRACTION2B-1 - 201

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