[English] 日本語
Yorodumi
- PDB-5ixb: Structure of human Melanoma Inhibitory Activity (MIA) Protein in ... -

+
Open data


ID or keywords:

Loading...

-
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 / :
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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 (eV)
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more