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- PDB-1hfo: The Structure of the Macrophage Migration Inhibitory Factor from ... -

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Basic information

Entry
Database: PDB / ID: 1hfo
TitleThe Structure of the Macrophage Migration Inhibitory Factor from Trichinella Spiralis.
ComponentsMIGRATION INHIBITORY FACTOR
KeywordsTAUTOMERASE
Function / homology
Function and homology information


dopachrome isomerase activity / 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
Macrophage migration inhibitory factor homolog / Macrophage migration inhibitory factor homolog
Similarity search - Component
Biological speciesTRICHINELLA SPIRALIS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRoe, S.M. / Meyer, D.J.
CitationJournal: Biochem.J. / Year: 2001
Title: Macrophage Migration Inhibitory Factor of the Parasitic Nematode Trichinella Spiralis
Authors: Tan, T.H. / Edgerton, S.A. / Kumari, R. / Mcalister, M.S. / Rowe, S.M. / Nagl, S. / Pearl, L.H. / Selkirk, M.E. / Bianco, A.E. / Totty, N.F. / Engwerda, C. / Gray, C.A. / Meyer, D.J.
History
DepositionDec 7, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MIGRATION INHIBITORY FACTOR
B: MIGRATION INHIBITORY FACTOR
C: MIGRATION INHIBITORY FACTOR
D: MIGRATION INHIBITORY FACTOR
E: MIGRATION INHIBITORY FACTOR
F: MIGRATION INHIBITORY FACTOR


Theoretical massNumber of molelcules
Total (without water)73,0606
Polymers73,0606
Non-polymers00
Water18,5911032
1
A: MIGRATION INHIBITORY FACTOR
B: MIGRATION INHIBITORY FACTOR
C: MIGRATION INHIBITORY FACTOR


Theoretical massNumber of molelcules
Total (without water)36,5303
Polymers36,5303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-44.8 kcal/mol
Surface area15970 Å2
MethodPQS
2
D: MIGRATION INHIBITORY FACTOR
E: MIGRATION INHIBITORY FACTOR
F: MIGRATION INHIBITORY FACTOR


Theoretical massNumber of molelcules
Total (without water)36,5303
Polymers36,5303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-47.1 kcal/mol
Surface area15350 Å2
MethodPQS
Unit cell
Length a, b, c (Å)110.128, 88.344, 86.355
Angle α, β, γ (deg.)90.00, 131.13, 90.00
Int Tables number5
Space group name H-MC121
DetailsBIOLOGICAL_UNIT: HOMOTRIMER

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Components

#1: Protein
MIGRATION INHIBITORY FACTOR


Mass: 12176.610 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHINELLA SPIRALIS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): JM109 / References: UniProt: Q9Y063, UniProt: P81529*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1032 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMASS SPEC ANALYSIS AND THE CRYSTAL STRUCTURE (AT 1.65A) UNAMBIGUOSLY IDENTIFY RESIDUE 85 AS A THR.

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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 Å3/Da / Density % sol: 40.5 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: CRYSTALS GROWN BY HANGING DROP METHOD. WELL CONTAINED 400-600 AMMONIUM ACETATE, 30-36% PEG4K, 100MM SODIUM ACETATE PH4.6. DROP CONTAINED 1:1 MIX OF WELL AND 16.5MG/ML TSMIF IN MINIMAL BUFFER., pH 4.60
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116.5 mg/mlprotein11
2400-600 mMammonium acetate11
330-36 %PEG400011
4100 mMsodium acetate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.65→28 Å / Num. obs: 72915 / % possible obs: 97.6 % / Redundancy: 2.3 % / Biso Wilson estimate: 26.9 Å2 / Rsym value: 0.057 / Net I/σ(I): 3.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.281 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 28 Å / Num. measured all: 163895 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 97.6 % / Num. unique obs: 7060 / Num. measured obs: 16174 / Rmerge(I) obs: 0.281

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MIF

1mif


Resolution: 1.65→28.33 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1356759.35 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: NCS USED INITIALLY, BUT REMOVED IN FINAL STAGES. THERE IS A LARGE AREA OF UNMODELLED ELECTRON DENSITY AT THE N-TERMINUS OF EACH CHAIN. IT IS UNKNOWN WHAT THIS MAY BE, AND IS ASSUMED TO HAVE ...Details: NCS USED INITIALLY, BUT REMOVED IN FINAL STAGES. THERE IS A LARGE AREA OF UNMODELLED ELECTRON DENSITY AT THE N-TERMINUS OF EACH CHAIN. IT IS UNKNOWN WHAT THIS MAY BE, AND IS ASSUMED TO HAVE COPURIFIED WITH THE PROTEIN. IT SITS AT THE SITE OF TAUTOMERASE ACTIVITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 3687 5.1 %RANDOM
Rwork0.225 ---
obs0.225 72854 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.3598 Å2 / ksol: 0.309311 e/Å3
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.19 Å20 Å2-1.43 Å2
2--0.37 Å20 Å2
3---2.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.65→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5134 0 0 1032 6166
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.121.5
X-RAY DIFFRACTIONc_mcangle_it2.742
X-RAY DIFFRACTIONc_scbond_it3.792
X-RAY DIFFRACTIONc_scangle_it5.12.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 607 5.1 %
Rwork0.31 11346 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rwork: 0.31

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