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- PDB-3l4p: Crystal structure of the Aldehyde Dehydrogenase (a.k.a. AOR or MO... -

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Basic information

Entry
Database: PDB / ID: 3l4p
TitleCrystal structure of the Aldehyde Dehydrogenase (a.k.a. AOR or MOP) of Desulfovibrio gigas covalently bound to [AsO3]-
ComponentsAldehyde oxidoreductase
KeywordsOXIDOREDUCTASE / Molybdenum-containing enzymes / Aldehyde oxidoreductase / Xanthine oxidase family / Reduced form / Arsenite inhibition / 2Fe-2S / FAD / Flavoprotein / Iron / Iron-sulfur / Metal-binding / Molybdenum / NAD
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/xanthine dehydrogenase, second molybdopterin binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding ...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/xanthine dehydrogenase, second molybdopterin binding domain / Molybdopterin cofactor-binding domain / 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 / [2Fe-2S] 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
ARSENITE / FE2/S2 (INORGANIC) CLUSTER / ISOPROPYL ALCOHOL / : / Chem-PCD / UREA / Aldehyde oxidoreductase
Similarity search - Component
Biological speciesDesulfovibrio gigas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBoer, D.R. / Romao, M.J.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2007
Title: Correlating EPR and X-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase.
Authors: Thapper, A. / Boer, D.R. / Brondino, C.D. / Moura, J.J. / Romao, M.J.
History
DepositionDec 21, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionFeb 16, 2010ID: 1ZCS
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2019Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,18825
Polymers97,1411
Non-polymers2,04724
Water25,9961443
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aldehyde oxidoreductase
hetero molecules

A: Aldehyde oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,37550
Polymers194,2812
Non-polymers4,09448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2310 Å2
ΔGint-16 kcal/mol
Surface area56640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.890, 142.890, 161.640
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-1457-

CA

21A-1703-

HOH

31A-2123-

HOH

41A-2125-

HOH

51A-2544-

HOH

61A-2797-

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: 97140.508 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 , 10 types, 1467 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#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-AST / ARSENITE


Mass: 122.920 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AsO3
#9: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#10: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1443 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE IDENTITY OF THE UREA MOLECULE (RESIDUE URE 926 IN CHAIN A) HAS NOT BEEN CONFIRMED EXPERIMENTALLY.

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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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 30% isopropanol 0.2M magnesium chloride, 0.1M HEPES pH 7.6 , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 10, 2004
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.45→19.474 Å / Num. obs: 169887 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 1.92 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 16.61
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 1.93 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 3.05 / Num. unique all: 15967 / % possible all: 97.8

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Processing

Software
NameVersionClassification
ProDC(ESRF)data collection
PHENIX(phenix.refine: 1.4_4)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vlb

1vlb


Resolution: 1.45→19.442 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.12 / σ(F): 2.01 / Phase error: 13.96 / Stereochemistry target values: cctbx (Phenix project) / Details: maximum-likelihood target
RfactorNum. reflection% reflection
Rfree0.166 8513 5.01 %
Rwork0.142 161351 -
obs0.143 169864 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.251 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 71.56 Å2 / Biso mean: 14.092 Å2 / Biso min: 2.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.539 Å2-0 Å2-0 Å2
2--1.539 Å20 Å2
3----3.078 Å2
Refinement stepCycle: LAST / Resolution: 1.45→19.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7215 0 92 1444 8751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067480
X-RAY DIFFRACTIONf_angle_d1.26510185
X-RAY DIFFRACTIONf_chiral_restr0.0781116
X-RAY DIFFRACTIONf_plane_restr0.0071335
X-RAY DIFFRACTIONf_dihedral_angle_d16.1592796
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.4670.2722710.2724971524293
1.467-1.4840.252760.22153545630100
1.484-1.5020.222880.20153015589100
1.502-1.5210.1992940.18553265620100
1.521-1.5410.1952490.17853585607100
1.541-1.5620.192550.16853585613100
1.562-1.5840.1912880.16553365624100
1.584-1.6080.1942560.15653575613100
1.608-1.6330.1662960.14853175613100
1.633-1.660.193150.14553255640100
1.66-1.6880.1663000.13953065606100
1.688-1.7190.1872810.13553755656100
1.719-1.7520.1752600.13353485608100
1.752-1.7880.1612650.12953825647100
1.788-1.8270.1492920.13153485640100
1.827-1.8690.1622840.1353425626100
1.869-1.9160.1422910.13153285619100
1.916-1.9670.1532860.12753815667100
1.967-2.0250.1463130.12253565669100
2.025-2.0910.1462830.12553515634100
2.091-2.1650.152720.12454145686100
2.165-2.2520.1542950.12653635658100
2.252-2.3540.142830.12654065689100
2.354-2.4780.1423030.12654235726100
2.478-2.6330.1452600.13154615721100
2.633-2.8360.1672770.13654485725100
2.836-3.120.162590.13555295788100
3.12-3.5690.1492900.12254975787100
3.569-4.4880.1313170.11255395856100
4.488-19.4440.1553140.1315751606599
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)
10.06490.0082-0.05480.0608-0.09850.2774-0.00220.01310.00630.0152-0.0283-0.0341-0.08720.05650.02510.0568-0.0149-0.00810.04920.01620.059755.79891.496315.4546
20-0-0000-0.1018-0.2497-0.06880.08330.0607-0.0070.01680.06720.05160.0902-0.0102-0.00960.0760.00450.085751.2262-8.96121.661
3000000-0.0022-0.08230.05730.0661-0.06930.088-0.1159-0.14930.07650.1222-0.0103-0.01440.09720.01480.108743.6221.961520.1038
40.18240.0090.03270.1872-0.03810.2153-0.0041-0.00050.0032-0.01880.0090.00620.0269-0.0044-0.0050.021-0.0011-0.00260.01260.00010.020143.3911-21.481828.4334
50.06060.0409-0.01050.0439-0.04050.07120.00230.0079-0.0024-0.01340.00070.07360.0072-0.00080.00180.08610.0002-0.00460.0718-0.00630.103950.7165-22.413524.4161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:174)A1 - 174
2X-RAY DIFFRACTION2(chain A and resid 908)A908
3X-RAY DIFFRACTION3(chain A and resid 909)A909
4X-RAY DIFFRACTION4(chain A and resid 175:907)A175 - 907
5X-RAY DIFFRACTION5(chain A and resid 931)A931

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