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- PDB-4lkb: Crystal structure of a putative 4-Oxalocrotonate Tautomerase from... -

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Basic information

Entry
Database: PDB / ID: 4lkb
TitleCrystal structure of a putative 4-Oxalocrotonate Tautomerase from Nostoc sp. PCC 7120
Componentshypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
KeywordsISOMERASE / PSI-BIOLOGY / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI Biology / New York Structural Genomics Research Consortium / NYSGRC / 026795 / Dimer of trimer / alpha/beta / Putative Tautomerase
Function / homologyTautomerase, MSAD family / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / Alr4568 protein
Function and homology information
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsKumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Al Obaidi, N. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a putative 4-Oxalocrotonate Tautomerase from Nostoc sp. PCC 7120
Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S.
History
DepositionJul 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
F: hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
B: hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
C: hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
D: hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
E: hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
A: hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,33315
Polymers107,4856
Non-polymers8499
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17720 Å2
ΔGint-121 kcal/mol
Surface area27160 Å2
MethodPISA
2
F: hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
D: hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
E: hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,40310
Polymers53,7423
Non-polymers6617
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-69 kcal/mol
Surface area14160 Å2
MethodPISA
3
B: hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
C: hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
A: hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9305
Polymers53,7423
Non-polymers1882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-33 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.022, 132.926, 133.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsDimer of trimers

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Components

#1: Protein
hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase


Mass: 17914.096 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / Gene: alr4568 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q8YNJ7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Lithium Sulfate, 0.1M bis-tris, 25% PEG 3350., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2013 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. all: 52878 / Num. obs: 52878 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.2
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2 / Num. unique all: 4339 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.16→47.85 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.178 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.195 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22095 2690 5.1 %RANDOM
Rwork0.17552 ---
all0.209 50187 --
obs0.1778 50187 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2---0.34 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.16→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6039 0 49 260 6348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196202
X-RAY DIFFRACTIONr_bond_other_d0.0010.026119
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9948350
X-RAY DIFFRACTIONr_angle_other_deg0.881314138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21924.305295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.192151157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0571536
X-RAY DIFFRACTIONr_chiral_restr0.1130.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021368
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.162→2.218 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 213 -
Rwork0.182 3656 -
obs--99.13 %

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