[English] 日本語
Yorodumi
- PDB-6ice: Crystal structure of Hamster MIF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ice
TitleCrystal structure of Hamster MIF
ComponentsMacrophage migration inhibitory factor
KeywordsCYTOKINE / TAUTOMERASE
Function / homology
Function and homology information


Macrophage migration inhibitory factor, conserved site / Macrophage migration inhibitory factor family signature. / 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 speciesMesocricetus auratus (golden hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSundaram, R. / Vasudevan, D.
CitationJournal: Sci Rep / Year: 2019
Title: Macrophage migration inhibitory factor of Syrian golden hamster shares structural and functional similarity with human counterpart and promotes pancreatic cancer.
Authors: Suresh, V. / Sundaram, R. / Dash, P. / Sabat, S.C. / Mohapatra, D. / Mohanty, S. / Vasudevan, D. / Senapati, S.
History
DepositionSep 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Macrophage migration inhibitory factor
B: Macrophage migration inhibitory factor
C: Macrophage migration inhibitory factor


Theoretical massNumber of molelcules
Total (without water)40,3693
Polymers40,3693
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Elution volume matched trimer size
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-37 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.877, 55.846, 112.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA1 - 1132 - 114
21PHEPHEBB1 - 1132 - 114
12PHEPHEAA1 - 1132 - 114
22PHEPHECC1 - 1132 - 114
13ALAALABB1 - 1142 - 115
23ALAALACC1 - 1142 - 115

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Macrophage migration inhibitory factor


Mass: 13456.253 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Cell: Stellate cell / Gene: mif, Mif / Organ: Pancreas / Plasmid: pET22B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140EDM8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.14 Å3/Da / Density % sol: 42.46 % / Description: Thin, plate-like
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 200 mM Succinic Acid (pH 7.0), 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.8→56.08 Å / Num. obs: 31590 / % possible obs: 98.5 % / Redundancy: 7.6 % / Biso Wilson estimate: 6.78 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.059 / Rrim(I) all: 0.119 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.525 / Num. unique obs: 1840 / CC1/2: 0.868 / Rpim(I) all: 0.297 / Rrim(I) all: 0.605 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MFF

1mff


Resolution: 1.8→38.85 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.296 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21284 1557 4.9 %RANDOM
Rwork0.1756 ---
obs0.17751 29978 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.8→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 0 0 196 2785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192660
X-RAY DIFFRACTIONr_bond_other_d0.0020.022414
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.9593628
X-RAY DIFFRACTIONr_angle_other_deg1.04435617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6395347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56124.34106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15915413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7371512
X-RAY DIFFRACTIONr_chiral_restr0.1250.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212993
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02515
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4021.4071379
X-RAY DIFFRACTIONr_mcbond_other1.3921.4051378
X-RAY DIFFRACTIONr_mcangle_it1.9342.0971720
X-RAY DIFFRACTIONr_mcangle_other1.9362.0981721
X-RAY DIFFRACTIONr_scbond_it2.5791.691281
X-RAY DIFFRACTIONr_scbond_other2.5791.691281
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8712.4231905
X-RAY DIFFRACTIONr_long_range_B_refined4.80817.9813000
X-RAY DIFFRACTIONr_long_range_B_other4.67917.6922951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A65580.1
12B65580.1
21A66280.09
22C66280.09
31B66040.11
32C66040.11
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 111 -
Rwork0.259 2183 -
obs--99.22 %

+
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