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- PDB-4ntc: Crystal structure of GliT -

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Basic information

Entry
Database: PDB / ID: 4ntc
TitleCrystal structure of GliT
ComponentsGliT
KeywordsOXIDOREDUCTASE / disulfide bond / epipolythiodioxopiperazine / gliotoxin / natural sulfur products
Function / homology
Function and homology information


gliotoxin biosynthetic process / Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor / mycotoxin biosynthetic process / cellular response to mycotoxin / thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / flavin adenine dinucleotide binding
Similarity search - Function
: / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase gliT / Thioredoxin reductase gliT
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsScharf, D.H. / Groll, M. / Habel, A. / Heinekamp, T. / Hertweck, C. / Brakhage, A.A. / Huber, E.M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Flavoenzyme-Catalyzed Formation of Disulfide Bonds in Natural Products
Authors: Scharf, D.H. / Groll, M. / Habel, A. / Heinekamp, T. / Hertweck, C. / Brakhage, A.A. / Huber, E.M.
History
DepositionDec 2, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GliT
B: GliT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8244
Polymers72,2532
Non-polymers1,5712
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-38 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.790, 118.180, 69.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.901316, 0.404283, 0.155524), (0.419479, 0.904181, 0.080631), (-0.108021, 0.137913, -0.984539)-72.73806, 19.84907, -66.40308

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Components

#1: Protein GliT


Mass: 36126.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: deltaakuB / Gene: gliT / Plasmid: pET43.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5MBU7, UniProt: E9RAH5*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M tri-Na citrate, 20% PEG3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2012
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 54166 / Num. obs: 51186 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.3 / % possible all: 97.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FBS

3fbs


Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.258 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.627 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22272 2559 5 %RANDOM
Rwork0.1839 ---
all0.189 51186 --
obs0.18583 48627 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.882 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å2-0 Å2-0 Å2
2---1.82 Å2-0 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4831 0 106 267 5204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195046
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.9826881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0395638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36824.155219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68315784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1641534
X-RAY DIFFRACTIONr_chiral_restr0.0720.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213834
X-RAY DIFFRACTIONr_rigid_bond_restr3.07635046
X-RAY DIFFRACTIONr_sphericity_free21.331573
X-RAY DIFFRACTIONr_sphericity_bonded13.65955137
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 188 -
Rwork0.24 3561 -
obs--97.83 %
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)
10.3654-0.08670.06160.06330.00220.18230.0238-0.06-0.02520.0216-0.00760.0113-0.0079-0.0161-0.01610.0221-0.02010.00340.05480.00720.0047-40.561715.5189-16.0854
20.2077-0.05570.00390.0483-0.00610.13790.0410.0469-0.0282-0.0152-0.0279-0.0106-0.01620.0043-0.01310.0110.0126-0.00150.0434-0.00150.0159-37.268414.7984-44.8327
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 325
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B12 - 325
4X-RAY DIFFRACTION2B401

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