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- PDB-6oml: Human BMP chimera BV261 -

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Basic information

Entry
Database: PDB / ID: 6oml
TitleHuman BMP chimera BV261
ComponentsBone morphogenetic protein 2 and Bone morphogenetic protein 6
KeywordsCYTOKINE / BMP / bone morphogenetic protein
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSeeherman, H. / Juo, Z.S.
CitationJournal: Sci Transl Med / Year: 2019
Title: A BMP/activin A chimera is superior to native BMPs and induces bone repair in nonhuman primates when delivered in a composite matrix.
Authors: Seeherman, H.J. / Berasi, S.P. / Brown, C.T. / Martinez, R.X. / Juo, Z.S. / Jelinsky, S. / Cain, M.J. / Grode, J. / Tumelty, K.E. / Bohner, M. / Grinberg, O. / Orr, N. / Shoseyov, O. / ...Authors: Seeherman, H.J. / Berasi, S.P. / Brown, C.T. / Martinez, R.X. / Juo, Z.S. / Jelinsky, S. / Cain, M.J. / Grode, J. / Tumelty, K.E. / Bohner, M. / Grinberg, O. / Orr, N. / Shoseyov, O. / Eyckmans, J. / Chen, C. / Morales, P.R. / Wilson, C.G. / Vanderploeg, E.J. / Wozney, J.M.
History
DepositionApr 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Bone morphogenetic protein 2 and Bone morphogenetic protein 6
Y: Bone morphogenetic protein 2 and Bone morphogenetic protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9954
Polymers23,7012
Non-polymers1,2942
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint2 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.779, 67.779, 148.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Bone morphogenetic protein 2 and Bone morphogenetic protein 6


Mass: 11850.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2, BMP2A / Production host: Cricetulus griseus (Chinese hamster)
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.38 Å3/Da / Density % sol: 63.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM Ammonium Sulfate, 100mM Bis-Tris pH 6.5, 30% Pentaerythritol Ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→49.98 Å / Num. obs: 10061 / % possible obs: 99.97 % / Redundancy: 4 % / Biso Wilson estimate: 61.18 Å2 / Net I/σ(I): 2
Reflection shellResolution: 2.7→49.98 Å / Num. unique obs: 10061

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.98 Å / Cor.coef. Fo:Fc: 0.9154 / Cor.coef. Fo:Fc free: 0.8682 / SU R Cruickshank DPI: 0.447 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.578 / SU Rfree Blow DPI: 0.32 / SU Rfree Cruickshank DPI: 0.306
RfactorNum. reflection% reflectionSelection details
Rfree0.2654 485 4.82 %RANDOM
Rwork0.1987 ---
obs0.2017 10061 99.97 %-
Displacement parametersBiso mean: 48.01 Å2
Baniso -1Baniso -2Baniso -3
1--6.3962 Å20 Å20 Å2
2---6.3962 Å20 Å2
3---12.7923 Å2
Refine analyzeLuzzati coordinate error obs: 0.305 Å
Refinement stepCycle: 1 / Resolution: 2.7→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 0 91 1745
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011816HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.292496HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d571SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes254HARMONIC5
X-RAY DIFFRACTIONt_it1816HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion23.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion246SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1991SEMIHARMONIC4
LS refinement shellResolution: 2.7→3.02 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3002 140 5.05 %
Rwork0.2047 2633 -
all0.209 2773 -
obs--99.97 %

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