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- PDB-3c6v: Crystal structure of AU4130/APC7354, a probable enzyme from the t... -

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Basic information

Entry
Database: PDB / ID: 3c6v
TitleCrystal structure of AU4130/APC7354, a probable enzyme from the thermophilic fungus Aspergillus fumigatus
ComponentsProbable tautomerase/dehalogenase AU4130
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Aspergillus fumigatus trimeric thermophilic probable tautomerase/dehalogenase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / Tautomerase_3 domain-containing protein
Function and homology information
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSinger, A.U. / Binkowski, T.A. / Skarina, T. / Kagan, O. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of AU4130/APC7354, a probable enzyme from the thermophilic fungus Aspergillus fumigatus.
Authors: Singer, A.U. / Binkowski, T.A. / Skarina, T. / Kagan, O. / Edwards, A.M. / Joachimiak, A. / Savchenko, A.
History
DepositionFeb 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable tautomerase/dehalogenase AU4130
B: Probable tautomerase/dehalogenase AU4130
C: Probable tautomerase/dehalogenase AU4130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4036
Polymers56,2483
Non-polymers1553
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.136, 66.913, 128.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable tautomerase/dehalogenase AU4130


Mass: 18749.434 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Species: Aspergillus fumigatus / Strain: Af293 / CBS 101355 / FGSC A1100 / Gene: AU04310, AFUA_3G03220 / Plasmid: p15Tvlic / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WF74
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2 M Ammonium sulfate, 100 mM Tris-HCl pH 8.5, 0.3M NDSB 221, 2mM L-Cysteine. Cryoprotected with Paratone-N oil, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2006 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 43671 / Num. obs: 43671 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 59.7
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 7.7 / Num. unique all: 4491 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→44.32 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.64 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.131 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19689 2072 5.1 %RANDOM
Rwork0.15734 ---
all0.15932 ---
obs0.15932 38840 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.682 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---0.28 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3529 0 7 567 4103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223681
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9385018
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9785438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71823.457188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50615574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9121525
X-RAY DIFFRACTIONr_chiral_restr0.1180.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022930
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21891
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22486
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2441
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8381.52184
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53823546
X-RAY DIFFRACTIONr_scbond_it2.85931570
X-RAY DIFFRACTIONr_scangle_it4.4274.51469
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 145 -
Rwork0.153 2809 -
obs-2954 99.43 %
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)
10.63690.04340.2120.4012-0.02060.183-0.011-0.04190.03190.0425-0.01010.0281-0.0081-0.02450.0211-0.01080.0097-0.0026-0.0035-0.0021-0.033725.45964.35358.206
20.28150.0620.23270.8230.31770.5149-0.01990.0136-0.0004-0.06750.0103-0.0862-0.0250.07170.0096-0.0242-0.00950.0196-0.01340.0038-0.01742.2659.93444.16
30.39960.1268-0.20810.3186-0.12510.6421-0.03750.0262-0.0162-0.06170.02490.03810.0653-0.01890.01260.0035-0.0184-0.003-0.01930.0048-0.034421.59854.36638.756
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 14019 - 161
2X-RAY DIFFRACTION2BB-6 - 14015 - 161
3X-RAY DIFFRACTION3CC-2 - 14019 - 161

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