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- PDB-7rj9: Crystal structure of the Vitronectin hemopexin-like domain bindin... -

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Basic information

Entry
Database: PDB / ID: 7rj9
TitleCrystal structure of the Vitronectin hemopexin-like domain binding Calcium
ComponentsVitronectin
KeywordsCELL ADHESION / Integrin ligand / homopexin-like domain / beta-propeller / serum protein / complement pathway inhibitor
Function / homology
Function and homology information


smooth muscle cell-matrix adhesion / rough endoplasmic reticulum lumen / peptidase inhibitor complex / alphav-beta3 integrin-vitronectin complex / scavenger receptor activity / negative regulation of endopeptidase activity / protein complex involved in cell-matrix adhesion / negative regulation of blood coagulation / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway ...smooth muscle cell-matrix adhesion / rough endoplasmic reticulum lumen / peptidase inhibitor complex / alphav-beta3 integrin-vitronectin complex / scavenger receptor activity / negative regulation of endopeptidase activity / protein complex involved in cell-matrix adhesion / negative regulation of blood coagulation / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / Molecules associated with elastic fibres / extracellular matrix structural constituent / cell adhesion mediated by integrin / polysaccharide binding / Syndecan interactions / positive regulation of wound healing / positive regulation of smooth muscle cell migration / endodermal cell differentiation / oligodendrocyte differentiation / basement membrane / protein polymerization / ECM proteoglycans / Integrin cell surface interactions / negative regulation of fibrinolysis / regulation of cell adhesion / collagen binding / extracellular matrix organization / cell-matrix adhesion / Regulation of Complement cascade / liver regeneration / positive regulation of receptor-mediated endocytosis / Golgi lumen / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / integrin binding / positive regulation of protein binding / heparin binding / collagen-containing extracellular matrix / blood microparticle / cell adhesion / immune response / intracellular membrane-bounded organelle / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain ...Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAleshin, A.E. / Marassi, F.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: To Be Published
Title: Crystal structure of the Vitronectin hemopexin-like domain binding Calcium
Authors: Aleshin, A.E. / Marassi, F.M.
History
DepositionJul 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitronectin
B: Vitronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1659
Polymers46,8722
Non-polymers2937
Water6,197344
1
A: Vitronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5354
Polymers23,4361
Non-polymers993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vitronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6315
Polymers23,4361
Non-polymers1954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.832, 125.575, 40.883
Angle α, β, γ (deg.)90.000, 119.250, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 153 - 473 / Label seq-ID: 1 - 203

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Vitronectin / VN / S-protein / Serum-spreading factor / V75


Mass: 23436.197 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 154-285, 324-354, 435-474 / Mutation: C180S, C215S, delta 286-323, delta 355-434
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VTN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04004

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Non-polymers , 5 types, 351 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 UL PROTEIN SOLUTION + 1 UL PRECIPITATE SOLUTION contaning 0.09 M IMIDAZOLE/MES, PH 6.5, 27 mM SODIUM NITRATE, 27 mM SODIUM PHOSPHATE, 27 mM AMMONIUM SULFATE, 11.25% V/V MPD, 11.25% W/V ...Details: 1 UL PROTEIN SOLUTION + 1 UL PRECIPITATE SOLUTION contaning 0.09 M IMIDAZOLE/MES, PH 6.5, 27 mM SODIUM NITRATE, 27 mM SODIUM PHOSPHATE, 27 mM AMMONIUM SULFATE, 11.25% V/V MPD, 11.25% W/V PEG1000, 11.25% W/V PEG3350, 3% W/V D- (+)-TREHALOSE. Crystals were soaked with the well solution containing 100 mM CaCl2 and missing SODIUM PHOSPHATE, AMMONIUM SULFATE, and IMIDAZOLE/MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→35.69 Å / Num. obs: 38571 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.6
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.593 / Num. unique obs: 1742

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O5E

6o5e


Resolution: 1.7→35.69 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.513 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 2261 5.9 %RANDOM
Rwork0.1705 ---
obs0.173 36276 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.83 Å2 / Biso mean: 23.966 Å2 / Biso min: 9.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-0.36 Å2
2--0.49 Å20 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 1.7→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 11 344 3493
Biso mean--18.77 35.67 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123334
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172924
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.6534530
X-RAY DIFFRACTIONr_angle_other_deg1.371.5866765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5985396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.98220.849212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08615500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4371531
X-RAY DIFFRACTIONr_chiral_restr0.0780.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02848
Refine LS restraints NCS

Ens-ID: 1 / Number: 5476 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 176 -
Rwork0.265 2342 -
all-2518 -
obs--87.86 %

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