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- PDB-6akz: Crystal structure of GlcNAc Inducible Gene 2, GIG2 (DUF1479) from... -

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Basic information

Entry
Database: PDB / ID: 6akz
TitleCrystal structure of GlcNAc Inducible Gene 2, GIG2 (DUF1479) from Candida albicans
ComponentsGlcNAc Inducible Gene 2, GIG2
KeywordsOXIDOREDUCTASE / GIG / candida
Function / homologyGig2-like / Gig2-like / Isopenicillin N synthase-like superfamily / metal ion binding / : / DUF1479 domain protein
Function and homology information
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsGautam, G. / Rani, P. / Dutta, A. / Gourinath, S.
Citation
Journal: Int.J.Biol.Macromol. / Year: 2020
Title: Crystal structure of Gig2 protein from Candida albicans provides a structural insight into DUF1479 family oxygenases.
Authors: Rani, P. / Gautam, G. / Anwar, T. / Gourinath, S. / Datta, A.
#1: Journal: Journal of Proteins & Proteomics / Year: 2017
Title: CLONING, EXPRESSION, PURIFICATION AND CRYSTALLIZATION OF A NOVEL GLCNAC METABOLIC PROTEIN, GIG2 (DUF1479) FROM PATHOGENIC FUNGUS CANDIDA ALBICANS
Authors: Rani, P. / Gautam, G. / Rao, H.K. / Ghosh, S. / Gourinath, S. / Dhar, S.K. / Dutta, A.
History
DepositionSep 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 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 / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GlcNAc Inducible Gene 2, GIG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9492
Polymers54,8931
Non-polymers561
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.652, 54.545, 74.850
Angle α, β, γ (deg.)90.00, 105.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GlcNAc Inducible Gene 2, GIG2


Mass: 54892.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: orf19.4783, CAALFM_C109240CA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D8PEJ2
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 6000, 0.1M Tris pH 8.0, 0.1M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.69→72.09 Å / Num. obs: 52149 / % possible obs: 99 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.4
Reflection shellResolution: 1.69→1.75 Å / Rmerge(I) obs: 1.001 / Num. unique obs: 4894

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CSG

2csg


Resolution: 1.69→72.09 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.766 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21623 2581 5 %RANDOM
Rwork0.18054 ---
obs0.18223 49560 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.728 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å2-0.79 Å2
2---1.45 Å20 Å2
3---1.41 Å2
Refinement stepCycle: 1 / Resolution: 1.69→72.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3641 0 1 236 3878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193732
X-RAY DIFFRACTIONr_bond_other_d0.0020.023474
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.955049
X-RAY DIFFRACTIONr_angle_other_deg1.0738021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91324.699183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04215649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7071518
X-RAY DIFFRACTIONr_chiral_restr0.1310.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214197
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02865
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_it2.0652.0721800
X-RAY DIFFRACTIONr_mcbond_other2.0552.0711799
X-RAY DIFFRACTIONr_mcangle_it2.8533.0942243
X-RAY DIFFRACTIONr_mcangle_other2.8553.0962244
X-RAY DIFFRACTIONr_scbond_it3.2092.3911932
X-RAY DIFFRACTIONr_scbond_other3.2082.3871930
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8993.4642806
X-RAY DIFFRACTIONr_long_range_B_refined6.21217.3364454
X-RAY DIFFRACTIONr_long_range_B_other6.18317.1874375
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.695→1.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 184 -
Rwork0.297 3376 -
obs--91.89 %

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