[English] 日本語
Yorodumi
- PDB-2os5: Macrophage migration inhibitory factor from Ancylostoma ceylanicum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2os5
TitleMacrophage migration inhibitory factor from Ancylostoma ceylanicum
ComponentsAceMIF
KeywordsCYTOKINE / macrophage migration inhibitory factor / nematode / hookworm
Function / homology
Function and homology information


phenylpyruvate tautomerase activity / cytokine receptor binding / cytokine activity / extracellular space / metal ion binding
Similarity search - Function
Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesAncylostoma ceylanicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsCho, Y. / Lolis, E.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and functional characterization of a secreted hookworm Macrophage Migration Inhibitory Factor (MIF) that interacts with the human MIF receptor CD74.
Authors: Cho, Y. / Jones, B.F. / Vermeire, J.J. / Leng, L. / DiFedele, L. / Harrison, L.M. / Xiong, H. / Kwong, Y.K. / Chen, Y. / Bucala, R. / Lolis, E. / Cappello, M.
History
DepositionFeb 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence This sequence is unavailable in uniprot database at the time of processing.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AceMIF
B: AceMIF
C: AceMIF
D: AceMIF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9498
Polymers52,5654
Non-polymers3844
Water5,008278
1
A: AceMIF
hetero molecules

A: AceMIF
hetero molecules

A: AceMIF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0009
Polymers39,4233
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8020 Å2
ΔGint-84 kcal/mol
Surface area14090 Å2
MethodPISA
2
B: AceMIF
C: AceMIF
D: AceMIF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6165
Polymers39,4233
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-32 kcal/mol
Surface area14310 Å2
MethodPISA
3
A: AceMIF
B: AceMIF
C: AceMIF
D: AceMIF
hetero molecules

A: AceMIF
B: AceMIF
C: AceMIF
D: AceMIF
hetero molecules

A: AceMIF
B: AceMIF
C: AceMIF
D: AceMIF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,84724
Polymers157,69412
Non-polymers1,15312
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area42980 Å2
ΔGint-296 kcal/mol
Surface area43730 Å2
MethodPISA
4
A: AceMIF
B: AceMIF
C: AceMIF
D: AceMIF
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)317,69348
Polymers315,38824
Non-polymers2,30624
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)115.340, 115.340, 199.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-204-

SO4

21A-382-

HOH

-
Components

#1: Protein
AceMIF


Mass: 13141.149 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancylostoma ceylanicum (invertebrata) / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / References: UniProt: A4GRE3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.0 M ammonium sulfate, 0.1 M sodium citrate, 0.2 M potassium sodium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONNSLS X29A11.1
SYNCHROTRONNSLS X29A20.9565,0.9791,0.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 17, 2005
ADSC QUANTUM 3152CCDJun 17, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.95651
30.97911
40.97931
ReflectionResolution: 1.6→100 Å / Num. obs: 88266 / % possible obs: 90.05 % / Redundancy: 14.5 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 3.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→100 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.071
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20016 4639 5 %RANDOM
Rwork0.19506 ---
obs0.19532 88266 90.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.194 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 20 278 3946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9695052
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2045468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28624.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91615656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7141528
X-RAY DIFFRACTIONr_chiral_restr0.090.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022740
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21748
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22599
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.293
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6061.52368
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21723864
X-RAY DIFFRACTIONr_scbond_it2.58331352
X-RAY DIFFRACTIONr_scangle_it4.2624.51188
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 205 -
Rwork0.262 3878 -
obs--54.43 %

+
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://pdbjlvh1.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