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- PDB-3rf5: Ancylostoma ceylanicum mif in complex with n-(2,3,4,5,6-pentafluo... -

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Basic information

Entry
Database: PDB / ID: 3rf5
TitleAncylostoma ceylanicum mif in complex with n-(2,3,4,5,6-pentafluoro-benzyl)-4-sulfamoyl-benzamide
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE/ISOMERASE INHIBITOR / PROTEIN-SMALL MOLECULE COMPLEX / ISOMERASE / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


phenylpyruvate tautomerase activity / cytokine receptor binding / cytokine activity / extracellular space / metal ion binding
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
ACETATE ION / 2-[(furan-2-ylmethyl)amino]benzoic acid / IMIDAZOLE / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesAncylostoma ceylanicum (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCho, Y. / Lolis, E.
CitationJournal: Chem.Biol. / Year: 2011
Title: Drug Repositioning and Pharmacophore Identification in the Discovery of Hookworm MIF Inhibitors.
Authors: Cho, Y. / Vermeire, J.J. / Merkel, J.S. / Leng, L. / Du, X. / Bucala, R. / Cappello, M. / Lolis, E.
History
DepositionApr 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,88620
Polymers38,3333
Non-polymers1,55317
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-55 kcal/mol
Surface area13030 Å2
MethodPISA
2
A: Macrophage migration inhibitory factor
hetero molecules

A: Macrophage migration inhibitory factor
hetero molecules

B: Macrophage migration inhibitory factor
hetero molecules

B: Macrophage migration inhibitory factor
hetero molecules

C: Macrophage migration inhibitory factor
hetero molecules

C: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,77240
Polymers76,6666
Non-polymers3,10634
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
crystal symmetry operation2_545-y,x-y-1,z+1/31
crystal symmetry operation4_545y,x-1,-z1
crystal symmetry operation3_554-x+y,-x,z-1/31
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area5130 Å2
ΔGint-353 kcal/mol
Surface area38030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.160, 86.160, 114.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-121-

ZN

21C-118-

ZN

31C-180-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Macrophage migration inhibitory factor


Mass: 12777.654 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 2-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancylostoma ceylanicum (invertebrata) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4GRE3

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Non-polymers , 5 types, 279 molecules

#2: Chemical ChemComp-FUZ / 2-[(furan-2-ylmethyl)amino]benzoic acid


Mass: 217.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H11NO3
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growpH: 8
Details: 0.1 M IMIDAZOLE, 0.16-0.24 M ZINC ACETATE, 15-25% PEG3000 , PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 3, 2009 / Details: MIRRORS
RadiationMonochromator: RIGAKU VARIMAX HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→35.5 Å / Num. all: 29384 / Num. obs: 29381 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.4 % / Biso Wilson estimate: 25.47 Å2 / Rsym value: 0.087 / Net I/σ(I): 8.1
Reflection shellResolution: 2.1→2.1 Å / Redundancy: 10.2 % / Rsym value: 0.447 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0091refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JQS

3jqs
PDB Unreleased entry


Resolution: 2.1→35.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.507 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1490 5.1 %RANDOM
Rwork0.164 ---
obs0.166 27851 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å20 Å2
2--0.27 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 86 262 3031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222826
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.9873806
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48724.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00715476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.151521
X-RAY DIFFRACTIONr_chiral_restr0.1760.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212120
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_it1.0281.51749
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6622851
X-RAY DIFFRACTIONr_scbond_it3.2623991
X-RAY DIFFRACTIONr_scangle_it5.0754.5861
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 111 -
Rwork0.192 2021 -
obs--100 %

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