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- PDB-6lnh: Crystal structure of IDO from Bacillus thuringiensis -

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Basic information

Entry
Database: PDB / ID: 6lnh
TitleCrystal structure of IDO from Bacillus thuringiensis
ComponentsL-isoleucine-4-hydroxylase
KeywordsOXIDOREDUCTASE / synthesis
Function / homologyL-isoleucine 4-hydroxylase / 2OG-Fe dioxygenase / 2OG-Fe dioxygenase / L-ascorbic acid binding / dioxygenase activity / ferrous iron binding / : / : / L-isoleucine-4-hydroxylase
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.34 Å
AuthorsFeng, Y. / Huang, J.W. / Liu, W.D. / Chen, C.C. / Guo, R.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal structure of IDO from Bacillus thuringiensis
Authors: Feng, Y. / Huang, J.W. / Liu, W.D. / Chen, C.C. / Guo, R.T.
History
DepositionDec 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 25, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_audit_support / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / refine / refine_hist / refine_ls_restr_ncs / reflns / reflns_shell / struct_conn / struct_ncs_dom / struct_ncs_dom_lim / struct_site / struct_site_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly_prop.value / _refine.B_iso_mean / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_restr_ncs.pdbx_rms / _refine_ls_restr_ncs.pdbx_type / _refine_ls_restr_ncs.rms_dev_position / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_number_measured_all / _struct_ncs_dom.details
Description: Ligand geometry
Details: The position of four Fe atoms and the surrounding water molecules around Fe are moved a little bit to be more realistic.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-isoleucine-4-hydroxylase
B: L-isoleucine-4-hydroxylase
C: L-isoleucine-4-hydroxylase
D: L-isoleucine-4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,48815
Polymers114,8604
Non-polymers1,62811
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-266 kcal/mol
Surface area40680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.425, 120.965, 81.715
Angle α, β, γ (deg.)90.000, 108.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESID 16 THROUGH 63 OR RESID 66 THROUGH 89 OR RESID 107 THROUGH 249))
21(CHAIN B AND (RESID 16 THROUGH 63 OR RESID 66 THROUGH 89 OR RESID 107 THROUGH 249))
31(CHAIN C AND (RESID 16 THROUGH 89 OR RESID 107 THROUGH 249))
41(CHAIN D AND (RESID 16 THROUGH 63 OR RESID 66 THROUGH 249))

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Components

#1: Protein
L-isoleucine-4-hydroxylase / L-isoleucine dioxygenase / IDO


Mass: 28715.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: ido / Plasmid: pRSF-DuetI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E2GIN1, L-isoleucine 4-hydroxylase
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Hg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.05 % / Mosaicity: 0.516 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG 3350, 0.1 M Bis-Tris, pH 5.6, Tacsimate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 16, 2018
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→25 Å / Num. obs: 52010 / % possible obs: 97.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 10.9
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 3 % / Rmerge(I) obs: 0.375 / Num. unique obs: 4513 / % possible all: 85.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SIR / Resolution: 2.34→24.86 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1998 3.85 %
Rwork0.228 49935 -
obs0.23 51933 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 291.55 Å2 / Biso mean: 56.46 Å2 / Biso min: 27.24 Å2
Refinement stepCycle: final / Resolution: 2.34→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7268 0 11 113 7392
Biso mean--117.42 48.29 -
Num. residues----887
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2580X-RAY DIFFRACTIONPOSITIONAL0
12B2580X-RAY DIFFRACTIONPOSITIONAL0
13C2580X-RAY DIFFRACTIONPOSITIONAL0
14D2580X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.34-2.420.3291670.30394186435383
2.42-2.520.32311940.29524859505395
2.52-2.640.30522030.28485068527199
2.64-2.770.30092040.276150795283100
2.77-2.950.32442040.260551165320100
2.95-3.170.28062040.261150815285100
3.17-3.490.28862040.236951185322100
3.49-40.26612060.222351195325100
4-5.030.21292040.18451315335100
5.03-24.860.24532080.210151785386100

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