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- PDB-3bxd: Crystal structure of Mouse Myo-inositol oxygenase (re-refined) -

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Basic information

Entry
Database: PDB / ID: 3bxd
TitleCrystal structure of Mouse Myo-inositol oxygenase (re-refined)
ComponentsINOSITOL OXYGENASE
KeywordsOXIDOREDUCTASE / PROTEIN-SUBSTRATE COMPLEX / HD DOMAIN FOLD / DIIRON
Function / homology
Function and homology information


inositol oxygenase / inositol oxygenase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol catabolic process / aldo-keto reductase (NADPH) activity / oxidoreductase activity, acting on NAD(P)H / inclusion body / ferric iron binding / NADP binding / oxidoreductase activity / cytoplasm
Similarity search - Function
Inositol oxygenase / Myo-inositol oxygenase / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase, conserved site
Similarity search - Domain/homology
: / FORMIC ACID / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / HYDROXIDE ION / Inositol oxygenase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHallberg, B.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Crystal structure of a substrate complex of myo-inositol oxygenase, a di-iron oxygenase with a key role in inositol metabolism.
Authors: Brown, P.M. / Caradoc-Davies, T.T. / Dickson, J.M. / Cooper, G.J. / Loomes, K.M. / Baker, E.N.
History
DepositionJan 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 12, 2011Group: Other
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0 THIS ENTRY 3BXD REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R2HUOSF. IN PDB ENTRY ... THIS ENTRY 3BXD REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R2HUOSF. IN PDB ENTRY 3BXD INFORMATION IN REMARK 200 SERIES IS BASED ON THE EXPERIMENT DESCRIBED IN PDB ENTRY 2HUO. ORIGINAL DATA DETERMINED BY AUTHOR J.WANG

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INOSITOL OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8716
Polymers33,5161
Non-polymers3555
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.600, 77.200, 85.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein INOSITOL OXYGENASE / / E.C.1.13.99.1 / Myo-inositol oxygenase / Aldehyde reductase-like 6 / Renal-specific oxidoreductase


Mass: 33515.891 Da / Num. of mol.: 1 / Fragment: Mus musculus Myo-inositol oxygenase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Miox, Aldrl6, Rsor / Plasmid: PPRO EX HTB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PRP / References: UniProt: Q9QXN5, inositol oxygenase

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Non-polymers , 5 types, 109 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#4: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL / Inositol


Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Comment: neurotransmitter, hormone*YM
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.19 Å3/Da / Density % sol: 43.92 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2HUO

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementStarting model: 2HUO

2huo


Resolution: 2→42.7 Å / σ(F): 0 / Stereochemistry target values: ML
Details: THIS ENTRY REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R2HUOSF
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1057 5.14 %The same R-free set as 2HUO
Rwork0.21 ---
all0.212 20586 --
obs0.212 20574 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 14.35 Å2 / Biso mean: 56.54 Å2 / Biso min: 126.06 Å2
Baniso -1Baniso -2Baniso -3
1--12.48 Å2-0 Å2-0 Å2
2---9.755 Å20 Å2
3----19.716 Å2
Refinement stepCycle: LAST / Resolution: 2→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 18 104 2241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054171
X-RAY DIFFRACTIONf_angle_d0.7567479
X-RAY DIFFRACTIONf_chiral_restr0.053306
X-RAY DIFFRACTIONf_plane_restr0.003648
X-RAY DIFFRACTIONf_dihedral_angle_d15.5211000
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.0910.311390.30423882527
2.091-2.2010.311450.2823702515
2.201-2.3390.3271040.25524422546
2.339-2.520.2861360.24224072543
2.52-2.7730.2781370.22124052542
2.773-3.1740.3011290.2224512580
3.174-3.9990.2151350.16424602595
3.999-42.710.2041320.17225942726
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)
11.9341-0.5678-0.85420.63382.40622.82630.0809-0.05360.2138-0.51650.00760.0143-0.3121-0.0435-0.05631.48110.3087-0.29560.4015-0.07370.492937.563320.670842.7932
20.0745-0.7218-0.82846.7662-2.9011-1.541-0.0973-0.7116-0.20451.98730.2326-0.3426-0.2461-0.043-0.00390.53620.0514-0.30380.37950.0508-0.154635.56485.649730.5804
31.3258-0.6708-0.09333.5-0.8126-0.1729-0.00610.064-0.29050.56730.0471.5146-0.0685-0.0181-0.02060.3044-0.02580.13350.25250.03221.191418.859914.770524.1976
40.7923-1.4007-0.53053.40561.49631.65850.0368-0.00310.13680.57350.2085-0.21290.01660.0419-0.27671.38060.37120.15770.4452-0.02010.550128.453322.389638.9091
54.5202-1.941-1.20932.34172.38670.5845-0.3918-0.18860.81830.60430.4733-0.12110.37430.119-0.08190.37750.06620.03190.2712-0.050.642425.750733.533827.4727
60.946-0.46840.07292.7412-0.04380.5012-0.21210.02730.13760.73390.12940.1613-0.18450.02040.07140.3290.0120.0660.20190.00090.572128.828619.127125.927
71.89920.5315-1.22151.00580.97961.2725-0.173-0.0517-0.32440.9082-0.1273-0.7566-0.15180.02990.24070.60030.0689-0.31120.308-0.03240.714745.84558.863834.2986
82.33940.16241.35573.9532-0.87591.5491-0.05260.350.45330.21330.0042-0.9057-0.00960.3820.04820.30290.0412-0.04710.32230.01441.02148.96741.330525.27
90.1929-0.94310.63552.2349-0.60270.5771-0.08130.27810.21520.0043-0.075-0.2383-0.10570.17890.14980.2063-0.035-0.01850.2397-0.02350.605636.11217.161318.8929
101.48963.3086-2.72053.92471.14483.51270.0568-0.36140.5975-0.24870.0754-0.7254-0.35720.5355-0.15740.2764-0.04450.02720.33940.02120.831444.193423.225515.8296
110.666-0.6576-0.08184.86510.82920.4966-0.1273-0.058-0.09491.22310.3702-0.71480.12020.044-0.19730.55940.0608-0.06090.2804-0.0220.627330.523232.170231.2022
12-0.3265-0.5369-0.28453.3463-0.02170.289-0.03980.0515-0.5853-0.12640.13331.76820.0225-0.144-0.06140.22310.0096-0.07590.28290.06981.172416.62528.368319.1221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 28-42A28 - 42
2X-RAY DIFFRACTION2chain A and resseq 43-59A43 - 59
3X-RAY DIFFRACTION3chain A and resseq 60-83A60 - 83
4X-RAY DIFFRACTION4chain A and resseq 84-94A84 - 94
5X-RAY DIFFRACTION5chain A and resseq 95-111A95 - 111
6X-RAY DIFFRACTION6chain A and resseq 112-148A112 - 148
7X-RAY DIFFRACTION7chain A and resseq 149-166A149 - 166
8X-RAY DIFFRACTION8chain A and resseq 167-176A167 - 176
9X-RAY DIFFRACTION9chain A and resseq 177-232A177 - 232
10X-RAY DIFFRACTION10chain A and resseq 233-246A233 - 246
11X-RAY DIFFRACTION11chain A and resseq 247-264A247 - 264
12X-RAY DIFFRACTION12chain A and resseq 265-285A265 - 285

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