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- PDB-1bmo: BM-40, FS/EC DOMAIN PAIR -

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Basic information

Entry
Database: PDB / ID: 1bmo
TitleBM-40, FS/EC DOMAIN PAIR
ComponentsBM-40
KeywordsEXTRACELLULAR MODULE / GLYCOPROTEIN / ANTI-ADHESIVE PROTEIN
Function / homology
Function and homology information


Scavenging by Class H Receptors / platelet alpha granule membrane / platelet alpha granule / anatomical structure development / extracellular matrix binding / regulation of cell morphogenesis / negative regulation of endothelial cell proliferation / basement membrane / ECM proteoglycans / Nuclear signaling by ERBB4 ...Scavenging by Class H Receptors / platelet alpha granule membrane / platelet alpha granule / anatomical structure development / extracellular matrix binding / regulation of cell morphogenesis / negative regulation of endothelial cell proliferation / basement membrane / ECM proteoglycans / Nuclear signaling by ERBB4 / endocytic vesicle lumen / collagen binding / negative regulation of angiogenesis / positive regulation of endothelial cell migration / platelet alpha granule lumen / nuclear matrix / Platelet degranulation / collagen-containing extracellular matrix / intracellular membrane-bounded organelle / calcium ion binding / cell surface / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
SPARC / Osteonectin-like, conserved site / SPARC/Testican, calcium-binding domain / Osteonectin domain signature 1. / Osteonectin domain signature 2. / Secreted protein acidic and rich in cysteine Ca binding region / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like ...SPARC / Osteonectin-like, conserved site / SPARC/Testican, calcium-binding domain / Osteonectin domain signature 1. / Osteonectin domain signature 2. / Secreted protein acidic and rich in cysteine Ca binding region / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand domain pair / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT, 2-FOLD NCS AVERAGING / Resolution: 3.1 Å
AuthorsHohenester, E. / Maurer, P. / Timpl, R.
Citation
Journal: EMBO J. / Year: 1997
Title: Crystal structure of a pair of follistatin-like and EF-hand calcium-binding domains in BM-40.
Authors: Hohenester, E. / Maurer, P. / Timpl, R.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Structure of a Novel Extracellular Ca(2+)-Binding Module in Bm-40
Authors: Hohenester, E. / Maurer, P. / Hohenadl, C. / Timpl, R. / Jansonius, J.N. / Engel, J.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: The C-Terminal Portion of Bm-40 (Sparc/Osteonectin) is an Autonomously Folding and Crystallisable Domain that Binds Calcium and Collagen Iv
Authors: Maurer, P. / Hohenadl, C. / Hohenester, E. / Gohring, W. / Timpl, R. / Engel, J.
#3: Journal: Faseb J. / Year: 1994
Title: The Biology of Sparc, a Protein that Modulates Cell-Matrix Interactions
Authors: Lane, T.F. / Sage, E.H.
History
DepositionMar 25, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / software / struct_asym / struct_conn / struct_conn_type / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.2Aug 9, 2023Group: Advisory / Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _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: BM-40
B: BM-40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2338
Polymers54,2242
Non-polymers1,0096
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.770, 56.350, 111.600
Angle α, β, γ (deg.)90.00, 104.38, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.1305, -0.1035, 0.986), (-0.1127, -0.9896, -0.089), (0.985, -0.0995, -0.1408)15.833, 40.835, -13.868
2given(0.1016, -0.0417, 0.994), (-0.0718, -0.9968, -0.0345), (0.9922, -0.0679, -0.1042)14.97, 38.195, -15.646

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Components

#1: Protein BM-40 / SPARC / OSTEONECTIN / BASEMENT MEMBRANE PROTEIN BM-40


Mass: 27111.934 Da / Num. of mol.: 2 / Fragment: FS/EC DOMAIN PAIR, RESIDUES 53 - 286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: 293 / Organ: KIDNEY / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P09486
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 65 %
Description: THE R-FACTOR AFTER RIGID-BODY REFINEMENT OF THE TWO EC DOMAINS WAS 0.46 (8-3.1 A)
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOUR DIFFUSION AT 20 DEG C: 10 MG/ML PROTEIN IN 10 MM TRIS PH 7.5 + 2 MM CACL2; 0.1 M HEPES PH 7.5, 0.15 M NA-ACETATE, 15% PEG4K, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-5 mg/mlprotein1drop
25 mMTris1drop
31 mM1dropCaCl2
47 %(w/v)PEG40001drop
50.075 Msodium acetate1drop
60.05 MNa HEPES1drop
714 %(w/v)PEG40001reservoir
80.15 Msodium acetate1reservoir
90.1 MNa HEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→25 Å / Num. obs: 14328 / % possible obs: 90.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 6.5
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2.7 / % possible all: 85.1
Reflection
*PLUS
Num. measured all: 47563
Reflection shell
*PLUS
% possible obs: 85.1 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4PROGRAMS SCALAdata reduction
Agrovatadata reduction
TRUNCATEdata reduction
MAMAmodel building
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
TRUNCATEdata scaling
SCALAdata scaling
MAMAphasing
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, 2-FOLD NCS AVERAGING
Starting model: BM-40 EC DOMAIN (PDB ENTRY 1SRA)

1sra


Resolution: 3.1→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01
Isotropic thermal model: RESTRAINED INDIVIDUAL WIT NCS RESTRAINTS
Cross valid method: FREE R-FACTOR / σ(F): 0
Details: A BULK SOLVENT CORRECTION WAS USED (R=0.25, K=0.33, B=50A**2)
RfactorNum. reflection% reflectionSelection details
Rfree0.322 678 5.1 %RANDOM
Rwork0.262 ---
obs0.262 13378 90.4 %-
Displacement parametersBiso mean: 28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-8 Å
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3794 0 60 0 3854
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51
X-RAY DIFFRACTIONx_mcangle_it2.52
X-RAY DIFFRACTIONx_scbond_it1.52
X-RAY DIFFRACTIONx_scangle_it2.53
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11X-RAY DIFFRACTION3.60.03410200
22X-RAY DIFFRACTION4.80.03510200
LS refinement shellResolution: 3.1→3.23 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.534 83 5.3 %
Rwork0.386 1485 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3_MOD.CHOTOPH3.CHO

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