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- PDB-6cuq: Crystal structure of Macrophage migration inhibitory factor-like ... -

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Basic information

Entry
Database: PDB / ID: 6cuq
TitleCrystal structure of Macrophage migration inhibitory factor-like protein (EhMIF) from Entamoeba histolytica
ComponentsMacrophage migration inhibitory factor-like protein
KeywordsCYTOKINE / SSGCID / Structural genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyMacrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily / Macrophage migration inhibitory factor-like protein
Function and homology information
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Macrophage migration inhibitory factor-like protein (EhMIF) from Entamoeba histolytica
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMar 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage migration inhibitory factor-like protein
B: Macrophage migration inhibitory factor-like protein
C: Macrophage migration inhibitory factor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0984
Polymers40,0363
Non-polymers621
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-38 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.610, 100.060, 98.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 70 or (resid 71...
21(chain B and (resid 0 through 37 or (resid 38...
31(chain C and (resid 0 through 37 or (resid 38...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISGLYGLY(chain A and (resid 0 through 70 or (resid 71...AA0 - 708 - 78
12LYSLYSLYSLYS(chain A and (resid 0 through 70 or (resid 71...AA7179
13HISHISPHEPHE(chain A and (resid 0 through 70 or (resid 71...AA0 - 1138 - 121
14HISHISPHEPHE(chain A and (resid 0 through 70 or (resid 71...AA0 - 1138 - 121
15HISHISPHEPHE(chain A and (resid 0 through 70 or (resid 71...AA0 - 1138 - 121
16HISHISPHEPHE(chain A and (resid 0 through 70 or (resid 71...AA0 - 1138 - 121
21HISHISSERSER(chain B and (resid 0 through 37 or (resid 38...BB0 - 378 - 45
22TYRTYRTYRTYR(chain B and (resid 0 through 37 or (resid 38...BB3846
23HISHISPHEPHE(chain B and (resid 0 through 37 or (resid 38...BB-3 - 1135 - 121
24HISHISPHEPHE(chain B and (resid 0 through 37 or (resid 38...BB-3 - 1135 - 121
25HISHISPHEPHE(chain B and (resid 0 through 37 or (resid 38...BB-3 - 1135 - 121
31HISHISSERSER(chain C and (resid 0 through 37 or (resid 38...CC0 - 378 - 45
32TYRTYRTYRTYR(chain C and (resid 0 through 37 or (resid 38...CC3846
33HISHISPHEPHE(chain C and (resid 0 through 37 or (resid 38...CC-1 - 1137 - 121

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Components

#1: Protein Macrophage migration inhibitory factor-like protein


Mass: 13345.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_092370 / Plasmid: EnhiA.00834.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: C4LV00
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytics MCSG1 screen, condition G9: 20% PEG 3350, 200mM sodium formate: EnhiA.00834.a.B1.PS38385 at 22.83mg/ml: cryo: 20% EG: tray 297191g9: puck gmt2-2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→38.376 Å / Num. obs: 14405 / % possible obs: 99.9 % / Redundancy: 7.349 % / Biso Wilson estimate: 66.67 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.035 / Χ2: 1.019 / Net I/σ(I): 32.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.45-2.517.4980.5474.210480.9540.58799.9
2.51-2.587.5150.4015.4810150.980.43199.7
2.58-2.667.4870.2927.329990.9860.314100
2.66-2.747.5430.2528.449560.990.27100
2.74-2.837.4350.19110.539390.9920.205100
2.83-2.937.4940.13314.459170.9960.143100
2.93-3.047.4330.09918.478780.9970.10699.9
3.04-3.167.4410.06526.288580.9990.07100
3.16-3.37.3960.05232.467960.9990.056100
3.3-3.467.4010.04238.867880.9990.045100
3.46-3.657.3970.03149.8274410.033100
3.65-3.877.3680.02853.957030.9990.031100
3.87-4.147.2860.02660.316680.9990.028100
4.14-4.477.2340.02465.6762810.025100
4.47-4.97.2060.02368.8357310.025100
4.9-5.487.1960.02370.452110.025100
5.48-6.337.0740.02270.0747510.024100
6.33-7.756.9680.02172.5640110.02299.8
7.75-10.966.6030.0273.8931510.02299.7
10.96-38.3765.4750.02370.091830.9990.02694.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3063)refinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3t5s, selected by MorDa

3t5s


Resolution: 2.45→38.376 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.19
RfactorNum. reflection% reflection
Rfree0.2253 1443 10.04 %
Rwork0.1775 --
obs0.1822 14378 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 160.94 Å2 / Biso mean: 83.7065 Å2 / Biso min: 38.72 Å2
Refinement stepCycle: final / Resolution: 2.45→38.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 4 19 2594
Biso mean--92.35 66.39 -
Num. residues----346
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1530X-RAY DIFFRACTION8.116TORSIONAL
12B1530X-RAY DIFFRACTION8.116TORSIONAL
13C1530X-RAY DIFFRACTION8.116TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4501-2.53760.30441400.2521268140899
2.5376-2.63920.3131270.250412791406100
2.6392-2.75930.2991250.241713031428100
2.7593-2.90470.31041690.240312411410100
2.9047-3.08660.31941600.252912661426100
3.0866-3.32480.28791580.22512751433100
3.3248-3.65920.25411340.195112951429100
3.6592-4.18810.25321410.162913171458100
4.1881-5.27440.16631500.133213071457100
5.2744-38.38070.1731390.1561384152399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.16480.70440.82253.687-0.72544.228-0.4931-0.04251.0090.1683-0.0621-0.0279-1.03190.88790.4430.7031-0.1584-0.20870.56510.00450.7009-20.365415.2704-14.8696
23.32980.00960.76282.2478-0.00486.5895-0.05630.1924-0.19430.3020.0623-0.41420.70991.261-0.00460.54010.18760.0180.63540.04360.4623-19.6587-4.0004-18.2444
34.1618-1.07621.23473.71110.0274.6805-0.20130.96470.5738-0.491-0.0372-0.6635-0.18481.49010.20210.5782-0.13840.03320.99240.19310.626-18.10548.3565-33.4845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 113)A0 - 113
2X-RAY DIFFRACTION2(chain 'B' and resid -3 through 113)B-3 - 113
3X-RAY DIFFRACTION3(chain 'C' and resid -1 through 113)C-1 - 113

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