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- PDB-1sra: STRUCTURE OF A NOVEL EXTRACELLULAR CA2+-BINDING MODULE IN BM-40(S... -

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Basic information

Entry
Database: PDB / ID: 1sra
TitleSTRUCTURE OF A NOVEL EXTRACELLULAR CA2+-BINDING MODULE IN BM-40(SLASH)SPARC(SLASH)OSTEONECTIN
ComponentsSPARC
KeywordsCALCIUM-BINDING PROTEIN / EXTRACELLULAR MATRIX PROTEIN
Function / homology
Function and homology information


semicircular canal morphogenesis / Scavenging by Class H Receptors / platelet alpha granule / platelet alpha granule membrane / regulation of cell morphogenesis / extracellular matrix binding / regulation of synapse organization / negative regulation of endothelial cell proliferation / basement membrane / ECM proteoglycans ...semicircular canal morphogenesis / Scavenging by Class H Receptors / platelet alpha granule / platelet alpha granule membrane / regulation of cell morphogenesis / extracellular matrix binding / regulation of synapse organization / negative regulation of endothelial cell proliferation / basement membrane / ECM proteoglycans / Nuclear signaling by ERBB4 / collagen binding / endocytic vesicle lumen / positive regulation of endothelial cell migration / platelet alpha granule lumen / negative regulation of angiogenesis / nuclear matrix / Platelet degranulation / : / 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 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsHohenester, E. / Maurer, P. / Hohenadl, C. / Timpl, R. / Jansonius, J.N. / Engel, J.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: The C-Terminal Portion of Bm-40 (Sparc(Slash)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.
#2: 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
DepositionAug 21, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_auth_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_asym_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 / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPARC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0614
Polymers17,9401
Non-polymers1203
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.700, 55.200, 75.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 225

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Components

#1: Protein SPARC / BM-40 / OSTEONECTIN


Mass: 17940.428 Da / Num. of mol.: 1 / Fragment: CARBOXY-TERMINAL DOMAIN (RESIDUES 136 - 286)
Source method: isolated from a genetically manipulated source
Details: CRYSTALLIZED FROM 0.7 M K, NA-TARTRATE, PH 7.5 + 2 MM CACL2
Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN BM-40 / Organ: KIDNEY / Plasmid: BLUESCRIPT, PCIS
Cell line (production host): HUMAN EMBRYONIC KIDNEY CELLS (293, ATCC CRL 1573)
Gene (production host): HUMAN BM-40 / Production host: Homo sapiens (human) / References: UniProt: P09486
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsCA 303 IS A NONIDENTIFIED METAL ION WHICH HAS BEEN MODELED AS CA+2 WITH UNIT OCCUPANCY.
Source detailsMOLECULE_NAME: SPARC. FRAGMENT 136 - 286 PRODUCED BY PCR.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.26 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Density % sol: 61 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.7 MK, Na tartrate1drop
22 mM1reservoirCaCl2

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.02
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 5, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 15597 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.063
Reflection
*PLUS
Num. measured all: 56738 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Redundancy: 3.6 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.249 -10 %
Rwork0.196 --
obs0.196 13737 87.1 %
Displacement parametersBiso mean: 24.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 3 112 1377
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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