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- PDB-3t5s: Structure of macrophage migration inhibitory factor from Giardia ... -

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Basic information

Entry
Database: PDB / ID: 3t5s
TitleStructure of macrophage migration inhibitory factor from Giardia lamblia
ComponentsMacrophage migration inhibitory factor
KeywordsIMMUNE SYSTEM / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / cytokine activity / extracellular space
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
L-dopachrome isomerase
Similarity search - Component
Biological speciesGiardia lamblia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J.Struct.Funct.Genom. / Year: 2013
Title: Crystal structure of a macrophage migration inhibitory factor from Giardia lamblia.
Authors: Buchko, G.W. / Abendroth, J. / Robinson, H. / Zhang, Y. / Hewitt, S.N. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8013
Polymers14,6701
Non-polymers1322
Water18010
1
A: Macrophage migration inhibitory factor
hetero molecules

A: Macrophage migration inhibitory factor
hetero molecules

A: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4049
Polymers44,0093
Non-polymers3956
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area5180 Å2
ΔGint-87 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.550, 95.550, 95.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-123-

HOH

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Components

#1: Protein Macrophage migration inhibitory factor / GILAA.00834.A


Mass: 14669.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia (eukaryote) / Strain: ATCC 50803 / Gene: GL50803_12091 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8BFP4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: EMERALD BIOSYSTEMS PRECIPITANT SYNERGY 15: 2 M LITHIUM SULFATE, 5% ISOPROPANOL, 0.1 M ACETATE PH 4.5, 0.1 M MGSO4; GILAA.00834.A.A1 AT 4 MG/ML, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.54
SYNCHROTRONAPS 23-ID-D20.97934
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDApr 15, 2011
MARMOSAIC 300 mm CCD2CCDJun 30, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Cryogenically cooled double crystal monochromator with horizontal focusing sagittal bend second mono crystalSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
20.979341
ReflectionResolution: 2.3→50 Å / Num. all: 6597 / Num. obs: 6594 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 70.32 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 33.86
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 4.4 / Num. unique all: 494 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→39.01 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 14.714 / SU ML: 0.169 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.268 298 4.5 %RANDOM
Rwork0.221 ---
all0.223 6597 --
obs0.223 6569 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.32 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms685 0 6 10 701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02702
X-RAY DIFFRACTIONr_bond_other_d0.0010.02430
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.951956
X-RAY DIFFRACTIONr_angle_other_deg0.90631051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.439595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.84723.7524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0661591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.817152
X-RAY DIFFRACTIONr_chiral_restr0.0840.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02148
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 23 -
Rwork0.444 422 -
obs-494 99.55 %
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)
12.4171-0.83122.21661.68730.42193.45560.1466-0.1233-0.2733-0.0027-0.03810.33460.5771-0.0966-0.10860.4194-0.0114-0.06660.21520.02230.3814-23.41120.15812.695
22.8110.29432.29523.3745-1.84327.03670.49450.1615-0.7132-0.0370.00110.11531.30750.1204-0.49560.677-0.0092-0.11940.10170.00960.4333-20.55911.85213.779
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 66
2X-RAY DIFFRACTION2A72 - 101

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