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- PDB-5ixb: Structure of human Melanoma Inhibitory Activity (MIA) Protein in ... -

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Basic information

Entry
Database: PDB / ID: 5ixb
TitleStructure of human Melanoma Inhibitory Activity (MIA) Protein in complex with Pyrimidin-2-amine
ComponentsMelanoma-derived growth regulatory protein
KeywordsCELL ADHESION / all beta / SH3 domain-like fold / extracellular
Function / homology
Function and homology information


extracellular matrix organization / growth factor activity / extracellular space
Similarity search - Function
Melanoma-derived growth regulatory protein / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / PYRIMIDIN-2-AMINE / Melanoma-derived growth regulatory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.39 Å
AuthorsYip, K.T. / Gasper, R. / Zhong, X.Y. / Seibel, N. / Puetz, S. / Autzen, J. / Scherkenbeck, J. / Hofmann, E. / Stoll, R.
CitationJournal: Sci Rep / Year: 2016
Title: Small Molecules Antagonise the MIA-Fibronectin Interaction in Malignant Melanoma.
Authors: Yip, K.T. / Zhong, X.Y. / Seibel, N. / Putz, S. / Autzen, J. / Gasper, R. / Hofmann, E. / Scherkenbeck, J. / Stoll, R.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Melanoma-derived growth regulatory protein
B: Melanoma-derived growth regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8256
Polymers24,5162
Non-polymers3084
Water4,774265
1
A: Melanoma-derived growth regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4123
Polymers12,2581
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Melanoma-derived growth regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4123
Polymers12,2581
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.440, 47.480, 87.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 3 and (name O or name...
21(chain B and ((resid 3 and (name O or name...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMET(chain A and ((resid 3 and (name O or name...AA34
12GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
13GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
14GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
15GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
16GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
17GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
18GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
19GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
110GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
111GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
112GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
113GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
114GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
115GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
116GLNGLN(chain A and ((resid 3 and (name O or name...AA3 - 1074 - 108
21METMET(chain B and ((resid 3 and (name O or name...BB34
22GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
23GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
24GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
25GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
26GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
27GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
28GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
29GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
210GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
211GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
212GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
213GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
214GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
215GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108
216GLNGLN(chain B and ((resid 3 and (name O or name...BB3 - 1074 - 108

NCS oper: (Code: given
Matrix: (0.000825, 0.999995, 0.003006), (0.999999, -0.000827, 0.000635), (0.000638, 0.003005, -0.999995)
Vector: 11.7372, -11.8566, 65.672699)

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Components

#1: Protein Melanoma-derived growth regulatory protein / Melanoma inhibitory activity protein


Mass: 12258.138 Da / Num. of mol.: 2 / Fragment: UNP residues 25-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIA / Plasmid: pQE-40 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q16674
#2: Chemical ChemComp-LGA / PYRIMIDIN-2-AMINE


Mass: 95.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5N3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 100 mM Tris/HCl, pH 8.2, 20% MPD, 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97962 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2013
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97962 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 40375 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 15.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 28.53
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.39-1.430.2496.66196.2
1.43-1.470.2218.44198.8
1.47-1.510.19511.351100
1.51-1.550.15914.821100
1.55-1.610.12917.451100
1.61-1.660.10421.121100
1.66-1.720.09123.691100
1.72-1.790.07828.561100
1.79-1.870.0731.781100
1.87-1.970.06335.261100
1.97-2.070.0638.241100
2.07-2.20.05643.341100
2.2-2.350.05443.71100
2.35-2.540.05243.971100
2.54-2.780.0546.21100
2.78-3.110.04948.771100
3.11-3.590.04848.71100
3.59-4.40.04649.461100
4.4-6.220.04650.231100
6.220.04846.981100

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.436
Highest resolutionLowest resolution
Rotation19.14 Å1.95 Å
Translation19.14 Å1.95 Å

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Processing

Software
NameVersionClassification
PHENIX1.10-2155refinement
XSCALEVERSION July 4, 2012 BUILT=20130617data scaling
MOLREPVers 11.2.05; 31.07.2013phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I1J

1i1j


Resolution: 1.39→43.745 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 14.75
RfactorNum. reflection% reflection
Rfree0.1598 2019 10 %
Rwork0.1323 --
obs0.1337 40373 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.31 Å2 / Biso mean: 24.1098 Å2 / Biso min: 7.98 Å2
Refinement stepCycle: final / Resolution: 1.39→43.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 38 265 1983
Biso mean--37.1 30.62 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011860
X-RAY DIFFRACTIONf_angle_d1.1052516
X-RAY DIFFRACTIONf_chiral_restr0.091250
X-RAY DIFFRACTIONf_plane_restr0.008332
X-RAY DIFFRACTIONf_dihedral_angle_d14.265718
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1438X-RAY DIFFRACTIONPOSITIONAL0.236
12B1438X-RAY DIFFRACTIONPOSITIONAL0.236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.39-1.42470.17461350.13532565270096
1.4247-1.46320.18211410.11912690283199
1.4632-1.50630.16161430.108227022845100
1.5063-1.55490.17381430.110427182861100
1.5549-1.61050.16591420.106327062848100
1.6105-1.6750.171450.105127442889100
1.675-1.75120.16691430.112727322875100
1.7512-1.84360.15191440.110227212865100
1.8436-1.95910.1581440.118327392883100
1.9591-2.11030.15751440.116527482892100
2.1103-2.32270.13151450.11927592904100
2.3227-2.65870.16971470.137227752922100
2.6587-3.34950.17021480.147928122960100
3.3495-43.76670.15641550.152729433098100

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