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- PDB-2xcz: Crystal Structure of macrophage migration inhibitory factor homol... -

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Basic information

Entry
Database: PDB / ID: 2xcz
TitleCrystal Structure of macrophage migration inhibitory factor homologue from Prochlorococcus marinus
ComponentsPOSSIBLE ATLS1-LIKE LIGHT-INDUCIBLE PROTEIN
KeywordsIMMUNE SYSTEM / CYTOKINE / TAUTOMERASE / CYANOBACTERIUM
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
DI(HYDROXYETHYL)ETHER / L-dopachrome isomerase
Similarity search - Component
Biological speciesPROCHLOROCOCCUS MARINUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsWasiel, A.A. / Rozeboom, H.J. / Hauke, D. / Baas, B.J. / Zandvoort, E. / Quax, W.J. / Thunnissen, A.M.W.H. / Poelarends, G.J.
CitationJournal: Biochemistry / Year: 2010
Title: Structural and Functional Characterization of a Macrophage Migration Inhibitory Factor Homologue from the Marine Cyanobacterium Prochlorococcus Marinus.
Authors: Wasiel, A.A. / Rozeboom, H.J. / Hauke, D. / Baas, B.J. / Zandvoort, E. / Quax, W.J. / Thunnissen, A.M.W.H. / Poelarends, G.J.
History
DepositionApr 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: POSSIBLE ATLS1-LIKE LIGHT-INDUCIBLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4862
Polymers12,3801
Non-polymers1061
Water2,054114
1
A: POSSIBLE ATLS1-LIKE LIGHT-INDUCIBLE PROTEIN
hetero molecules

A: POSSIBLE ATLS1-LIKE LIGHT-INDUCIBLE PROTEIN
hetero molecules

A: POSSIBLE ATLS1-LIKE LIGHT-INDUCIBLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4586
Polymers37,1403
Non-polymers3183
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area7150 Å2
ΔGint-29.9 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.450, 52.450, 63.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

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Components

#1: Protein POSSIBLE ATLS1-LIKE LIGHT-INDUCIBLE PROTEIN / MACROPHAGE MIGRATION INHIBITORY FACTOR / MIF


Mass: 12380.046 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROCHLOROCOCCUS MARINUS (bacteria) / Strain: MIT 9313 / Plasmid: PET20B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7V867
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.94 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 42% PEG300, 0.2 M SODIUM CHLORIDE, 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP,TEMPERATURE 298 K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE DIP2030H / Detector: IMAGE PLATE / Date: Jan 26, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→26.2 Å / Num. obs: 12309 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.3
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.4 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1GIF, 1GCZ, 1FIM, 1UIZ.

1gif

1gcz

1fim

1uiz


Resolution: 1.64→26.22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.02 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21277 590 4.8 %RANDOM
Rwork0.16377 ---
obs0.16604 11702 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.213 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.64→26.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms858 0 7 114 979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022892
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9751213
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5245117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.74725.83336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32115146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.735153
X-RAY DIFFRACTIONr_chiral_restr0.0850.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021666
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5631.5571
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1492922
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0863321
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6074.5289
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
LS refinement shellResolution: 1.639→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 51 -
Rwork0.232 828 -
obs--96.7 %

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