[English] 日本語
Yorodumi
- PDB-5bsi: Crystal structure of Y36A mutant of human macrophage migration in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bsi
TitleCrystal structure of Y36A mutant of human macrophage migration inhibitory factor
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / surface / mutation
Function / homology
Function and homology information


positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of arachidonate secretion / cytokine receptor binding / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of arachidonate secretion / cytokine receptor binding / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / carboxylic acid metabolic process / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / negative regulation of protein metabolic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of macrophage activation / chemoattractant activity / protein homotrimerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of cAMP/PKA signal transduction / negative regulation of cellular senescence / positive regulation of phosphorylation / positive regulation of B cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / positive regulation of cytokine production / cytokine activity / Cell surface interactions at the vascular wall / DNA damage response, signal transduction by p53 class mediator / positive regulation of fibroblast proliferation / positive regulation of tumor necrosis factor production / cellular senescence / protease binding / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPantouris, G. / Lolis, E.
CitationJournal: Chem.Biol. / Year: 2015
Title: An Analysis of MIF Structural Features that Control Functional Activation of CD74.
Authors: Pantouris, G. / Syed, M.A. / Fan, C. / Rajasekaran, D. / Cho, T.Y. / Rosenberg, E.M. / Bucala, R. / Bhandari, V. / Lolis, E.J.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
D: Macrophage migration inhibitory factor
E: Macrophage migration inhibitory factor
F: Macrophage migration inhibitory factor
G: Macrophage migration inhibitory factor
J: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,42522
Polymers98,1048
Non-polymers1,32114
Water10,377576
1
A: Macrophage migration inhibitory factor
B: Macrophage migration inhibitory factor
C: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3539
Polymers36,7893
Non-polymers5646
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-77 kcal/mol
Surface area13000 Å2
MethodPISA
2
D: Macrophage migration inhibitory factor
E: Macrophage migration inhibitory factor
F: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3539
Polymers36,7893
Non-polymers5646
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-76 kcal/mol
Surface area12970 Å2
MethodPISA
3
G: Macrophage migration inhibitory factor
hetero molecules

G: Macrophage migration inhibitory factor
hetero molecules

G: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0776
Polymers36,7893
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_435-y-1,x-y-2,z1
crystal symmetry operation3_645-x+y+1,-x-1,z1
Buried area6870 Å2
ΔGint-74 kcal/mol
Surface area13400 Å2
MethodPISA
4
J: Macrophage migration inhibitory factor
hetero molecules

J: Macrophage migration inhibitory factor
hetero molecules

J: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0776
Polymers36,7893
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6880 Å2
ΔGint-71 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.771, 177.771, 217.783
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27J
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213J
114C
214D
115C
215E
116C
216F
117C
217G
118C
218J
119D
219E
120D
220F
121D
221G
122D
222J
123E
223F
124E
224G
125E
225J
126F
226G
127F
227J
128G
228J

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 114 / Label seq-ID: 1 - 114

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27JH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213JH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218JH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222JH
123EE
223FF
124EE
224GG
125EE
225JH
126FF
226GG
127FF
227JH
128GG
228JH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

-
Components

#1: Protein
Macrophage migration inhibitory factor / MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / ...MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / Phenylpyruvate tautomerase


Mass: 12262.959 Da / Num. of mol.: 8 / Mutation: Y36A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIF, GLIF, MMIF / Production host: Escherichia coli (E. coli)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 6.75 Å3/Da / Density % sol: 81.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 M ammonium sulfate, 3% 2-propanol, 0.1 M Tris-HCl, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 173102 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 6.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.609 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DJH

3djh


Resolution: 2→44.45 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.221 8507 5 %RANDOM
Rwork0.208 ---
obs0.208 163006 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6831 0 76 576 7483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0197048
X-RAY DIFFRACTIONr_bond_other_d00.026631
X-RAY DIFFRACTIONr_angle_refined_deg1.951.9669591
X-RAY DIFFRACTIONr_angle_other_deg3.633.00215217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4535904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.07524.564287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.319151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7181534
X-RAY DIFFRACTIONr_chiral_restr0.1330.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218122
X-RAY DIFFRACTIONr_gen_planes_other0.0220.021604
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_it2.2712.6593640
X-RAY DIFFRACTIONr_mcbond_other2.2712.6583639
X-RAY DIFFRACTIONr_mcangle_it2.4833.9614536
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A128520.07
12B128520.07
21A128020.08
22C128020.08
31A128280.08
32D128280.08
41A126980.08
42E126980.08
51A127440.07
52F127440.07
61A129020.07
62G129020.07
71A126540.08
72J126540.08
81B127300.08
82C127300.08
91B127760.08
92D127760.08
101B127280.07
102E127280.07
111B126520.08
112F126520.08
121B128000.08
122G128000.08
131B126200.08
132J126200.08
141C126520.09
142D126520.09
151C125780.09
152E125780.09
161C129080.07
162F129080.07
171C127220.09
172G127220.09
181C128340.07
182J128340.07
191D127320.08
192E127320.08
201D126900.08
202F126900.08
211D128260.08
212G128260.08
221D126540.09
222J126540.09
231E125960.07
232F125960.07
241E127240.07
242G127240.07
251E125820.08
252J125820.08
261F126740.08
262G126740.08
271F128120.08
272J128120.08
281G127120.08
282J127120.08
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 610 -
Rwork0.23 11903 -
obs--97.78 %

+
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