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- PDB-2x4k: Crystal structure of SAR1376, a putative 4-oxalocrotonate tautome... -

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Basic information

Entry
Database: PDB / ID: 2x4k
TitleCrystal structure of SAR1376, a putative 4-oxalocrotonate tautomerase from the methicillin-resistant Staphylococcus aureus (MRSA)
Components4-OXALOCROTONATE TAUTOMERASE
KeywordsISOMERASE
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups / : / isomerase activity
Similarity search - Function
4-oxalocrotonate tautomerase, Pseudomonas-type / 4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Tautomerase / Probable tautomerase SAR1376
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.1 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionFeb 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,52010
Polymers13,9442
Non-polymers5768
Water1,24369
1
A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,56030
Polymers41,8326
Non-polymers1,72824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area17840 Å2
ΔGint-158.9 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.190, 50.190, 150.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1062-

PO4

21A-1063-

ZN

31B-1063-

PO4

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Components

#1: Protein 4-OXALOCROTONATE TAUTOMERASE /


Mass: 6971.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: 252 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q33C63, UniProt: Q6GH41*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 1.98 Å3/Da / Density % sol: 37.83 % / Description: OFFLINE FUJI PLATE
Crystal growpH: 5
Details: 1.49M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 5.0, 0.1M ZINC SULFATE, 25% ETHYLENE GLYCOL. CRYSTAL WAS CRYOPROTECTED DIRECTLY IN THIS SOLUTION WITH AMMONIUM SULPHATE CONCENTRATION OF 1.6M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.6
DetectorType: FUJIFILM / Detector: IMAGE PLATE / Date: Nov 16, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6 Å / Relative weight: 1
ReflectionResolution: 1.1→28.4 Å / Num. obs: 19685 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.7
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.35 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALEPACKdata scaling
SHELXCDESOLVE RESOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.1→28.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.975 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19533 2291 5 %RANDOM
Rwork0.18763 ---
obs0.188 43774 98.73 %-
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: 9.348 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.1→28.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 19 69 1042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221032
X-RAY DIFFRACTIONr_bond_other_d0.0010.02683
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9841406
X-RAY DIFFRACTIONr_angle_other_deg0.85231704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3215140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1225.77845
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57415204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.653156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02171
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_it0.891.5649
X-RAY DIFFRACTIONr_mcbond_other0.1911.5260
X-RAY DIFFRACTIONr_mcangle_it1.54221064
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0823383
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3074.5334
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.67831715
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 185 -
Rwork0.198 3113 -
obs--98.3 %
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)
1-0.01030.17070.18691.48891.84452.79330.0225-0.01450.0078-0.0651-0.08130.0196-0.0625-0.13340.05870.03060.0061-0.00290.03-0.00250.005916.32717.23213.024
20.7031-0.53490.16020.3327-0.10130.97610.04880.06720.036-0.0212-0.0618-0.01520.0051-0.02570.0130.02680.00420.00020.02770.00180.00569.5726.40616.006
30.1085-0.63790.07392.11270.070.65590.08680.0244-0.0101-0.28-0.06640.11060.05030.0234-0.02040.03620.0094-0.01590.0278-0.00610.005817.8758.2749.538
40.7753-0.1323-0.1160.20790.33140.830.0009-0.0146-0.04260.0138-0.00810.01010.0455-0.01540.00720.0252-0.0005-0.00080.01810.00420.00559.88417.63223.593
55.43823.32324.14473.17312.67393.71970.021-0.20140.02690.2021-0.16990.15450.1896-0.12430.14880.0511-0.00260.03590.0282-0.00490.019411.37212.02622.191
62.62611.486-0.4163.1502-3.85054.7502-0.0194-0.26870.17340.29790.02350.1057-0.4217-0.1509-0.00410.05050.0258-0.00230.0495-0.03110.010127.30728.84528.993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 13
2X-RAY DIFFRACTION2A14 - 39
3X-RAY DIFFRACTION3A40 - 61
4X-RAY DIFFRACTION4B2 - 36
5X-RAY DIFFRACTION5B37 - 46
6X-RAY DIFFRACTION6B47 - 61

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