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- PDB-4c7y: Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), soaked wi... -

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Basic information

Entry
Database: PDB / ID: 4c7y
TitleAldehyde Oxidoreductase from Desulfovibrio gigas (MOP), soaked with sodium dithionite and sodium sulfide
ComponentsALDEHYDE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / MOLYBDENUM ENZYME / MOP / ACTIVATION / INACTIVATION
Function / homology
Function and homology information


aldehyde dehydrogenase (FAD-independent) / aldehyde dehydrogenase (FAD-independent) activity / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily ...Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde Oxidoreductase; domain 3 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / DNA polymerase; domain 1 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / FE2/S2 (INORGANIC) CLUSTER / ISOPROPYL ALCOHOL / Chem-PCD / HYDROGEN PEROXIDE / Aldehyde oxidoreductase
Similarity search - Component
Biological speciesDESULFOVIBRIO GIGAS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsCorreia, H.D. / Romao, M.J. / Santos-Silva, T.
CitationJournal: Plos One / Year: 2013
Title: Kinetic and Structural Studies of Aldehyde Oxidoreductase from Desulfovibrio Gigas Reveal a Dithiolene-Based Chemistry for Enzyme Activation and Inhibition by H2O2.
Authors: Marangon, J. / Correia, H.D. / Brondino, C.D. / Moura, J.J.G. / Romao, M.J. / Gonzalez, P.J. / Santos-Silva, T.
History
DepositionSep 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.2Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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: ALDEHYDE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,65212
Polymers97,1571
Non-polymers1,49511
Water22,1941232
1
A: ALDEHYDE OXIDOREDUCTASE
hetero molecules

A: ALDEHYDE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,30324
Polymers194,3132
Non-polymers2,99022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
Buried area7770 Å2
ΔGint-153.3 kcal/mol
Surface area56350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.250, 143.250, 162.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2034-

HOH

21A-2212-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ALDEHYDE OXIDOREDUCTASE / MOLYBDENUM IRON SULFUR PROTEIN


Mass: 97156.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO GIGAS (bacteria)
References: UniProt: Q46509, aldehyde dehydrogenase (FAD-independent)

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Non-polymers , 8 types, 1243 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PCD / (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V) / MOLYBDENUM COFACTOR / MOCO


Mass: 844.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26MoN8O16P2S2
#8: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1232 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.47 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: VAPOR DIFFUSION, SITTING DROP, AT 277 K. CRYSTALLIZED USING 30% ISOPROPANOL, 0.2M MGCL2, 0.2M HEPES PH 7.6. ISOPROPANOL WAS REMOVED AND CRYSTALS WERE SOAKED WITH 30MM SODIUM DITHIONITE AND ...Details: VAPOR DIFFUSION, SITTING DROP, AT 277 K. CRYSTALLIZED USING 30% ISOPROPANOL, 0.2M MGCL2, 0.2M HEPES PH 7.6. ISOPROPANOL WAS REMOVED AND CRYSTALS WERE SOAKED WITH 30MM SODIUM DITHIONITE AND 7MM SODIUM SULFIDE FOR 24H.

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Sep 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.57→25.68 Å / Num. obs: 135137 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.5
Reflection shellResolution: 1.57→1.65 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VLB

1vlb


Resolution: 1.57→124.06 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.039 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15792 6793 5 %RANDOM
Rwork0.1344 ---
obs0.13557 128341 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.09 Å20 Å2
2---0.19 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.57→124.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6815 0 70 1232 8117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0557296
X-RAY DIFFRACTIONr_bond_other_d0.0190.0356957
X-RAY DIFFRACTIONr_angle_refined_deg1.6272.1159966
X-RAY DIFFRACTIONr_angle_other_deg0.8553.05116118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.455974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74924.902306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.551151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5681533
X-RAY DIFFRACTIONr_chiral_restr0.0920.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0438392
X-RAY DIFFRACTIONr_gen_planes_other0.0290.0641578
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_it1.150.5563697
X-RAY DIFFRACTIONr_mcbond_other1.1490.5563696
X-RAY DIFFRACTIONr_mcangle_it1.6060.8344637
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3910.7483599
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: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 507 -
Rwork0.191 9398 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: 8.381 Å / Origin y: -48.127 Å / Origin z: -0.942 Å
111213212223313233
T0.0403 Å2-0.001 Å2-0.0049 Å2-0.0422 Å20.0015 Å2--0.0026 Å2
L0.3703 °20.0245 °2-0.0883 °2-0.3116 °2-0.081 °2--0.4976 °2
S-0.002 Å °0.0329 Å °0.0096 Å °-0.0079 Å °-0.0036 Å °-0.0219 Å °0.013 Å °-0.0033 Å °0.0056 Å °

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