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- PDB-3b64: Macrophage Migration Inhibitory Factor (MIF) From /Leishmania Major -

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Basic information

Entry
Database: PDB / ID: 3b64
TitleMacrophage Migration Inhibitory Factor (MIF) From /Leishmania Major
ComponentsMacrophage migration inhibitory factor-like protein
KeywordsCYTOKINE / LEISHMANIA / MACROPHAGE MIGRATION INHIBITORY FACTOR / MIF / Lm1740MIF / LmMIF / UNKNOWN FUNCTION
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
ISOPROPYL ALCOHOL / L-dopachrome isomerase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.03 Å
AuthorsZierow, S. / Cho, Y. / Lolis, E.
CitationJournal: J.Immunol. / Year: 2008
Title: A leishmania ortholog of macrophage migration inhibitory factor modulates host macrophage responses.
Authors: Kamir, D. / Zierow, S. / Leng, L. / Cho, Y. / Diaz, Y. / Griffith, J. / McDonald, C. / Merk, M. / Mitchell, R.A. / Trent, J. / Chen, Y. / Kwong, Y.K. / Xiong, H. / Vermeire, J. / Cappello, M. ...Authors: Kamir, D. / Zierow, S. / Leng, L. / Cho, Y. / Diaz, Y. / Griffith, J. / McDonald, C. / Merk, M. / Mitchell, R.A. / Trent, J. / Chen, Y. / Kwong, Y.K. / Xiong, H. / Vermeire, J. / Cappello, M. / McMahon-Pratt, D. / Walker, J. / Bernhagen, J. / Lolis, E. / Bucala, R.
History
DepositionOct 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4552
Polymers12,3951
Non-polymers601
Water2,162120
1
A: Macrophage migration inhibitory factor-like protein
hetero molecules

A: Macrophage migration inhibitory factor-like protein
hetero molecules

A: Macrophage migration inhibitory factor-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3666
Polymers37,1853
Non-polymers1803
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.321, 52.321, 96.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Macrophage migration inhibitory factor-like protein


Mass: 12395.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Plasmid: pCRT7/CT-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q4Q413
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES-Na, 20% (v/v) iso-Propano polyethylene glycol 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.95 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.03→50 Å / Num. all: 46731 / Num. obs: 46731 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 22
Reflection shellResolution: 1.03→1.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 6.8 / % possible all: 71.6

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
CBASSdata collection
HKL-2000data reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.03→10 Å / Num. parameters: 9061 / Num. restraintsaints: 11105 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1568 2334 5.3 %RANDOM
Rwork0.1386 ---
obs0.1386 44388 100 %-
all-44388 --
Refine analyzeNum. disordered residues: 13 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 985
Refinement stepCycle: LAST / Resolution: 1.03→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 0 124 1004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0266
X-RAY DIFFRACTIONs_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.034
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.032
X-RAY DIFFRACTIONs_approx_iso_adps0.093

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