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- PDB-5g5g: Escherichia coli Periplasmic Aldehyde Oxidase -

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Basic information

Entry
Database: PDB / ID: 5g5g
TitleEscherichia coli Periplasmic Aldehyde Oxidase
Components(PUTATIVE XANTHINE DEHYDROGENASE ...) x 3
KeywordsOXIDOREDUCTASE / PAOABC / XANTHINE OXIDASE FAMILY / HETEROTRIMER / E.COLI DETOXIFICATION
Function / homology
Function and homology information


carboxylate reductase / carboxylate reductase activity / oxidoreductase activity, acting on the aldehyde or oxo group of donors / cellular detoxification of aldehyde / molybdenum ion binding / oxidoreductase complex / catabolic process / FAD binding / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding ...carboxylate reductase / carboxylate reductase activity / oxidoreductase activity, acting on the aldehyde or oxo group of donors / cellular detoxification of aldehyde / molybdenum ion binding / oxidoreductase complex / catabolic process / FAD binding / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / periplasmic space / iron ion binding / DNA damage response / metal ion binding
Similarity search - Function
: / : / : / [2Fe-2S]-binding domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase ...: / : / : / [2Fe-2S]-binding domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / CO dehydrogenase flavoprotein, C-terminal 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 / FAD-binding, type PCMH, subdomain 1 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / Enolase-like; domain 1 / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 2Fe-2S ferredoxin-like superfamily / DNA polymerase; domain 1 / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / IODIDE ION / PTERIN CYTOSINE DINUCLEOTIDE / DIOXOTHIOMOLYBDENUM(VI) ION / IRON/SULFUR CLUSTER / Aldehyde oxidoreductase iron-sulfur-binding subunit PaoA / Aldehyde oxidoreductase FAD-binding subunit PaoB / Aldehyde oxidoreductase molybdenum-binding subunit PaoC
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCorreia, M.A.S. / Otrelo-Cardoso, A.R. / Romao, M.J. / Santos-Silva, T.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: The Escherichia Coli Periplasmic Aldehyde Oxidoreductase is an Exceptional Member of the Xanthine Oxidase Family of Molybdoenzymes.
Authors: Correia, M.A. / Otrelo-Cardoso, A.R. / Schwuchow, V. / Sigfridsson Clauss, K.G. / Haumann, M. / Romao, M.J. / Leimkuhler, S. / Santos-Silva, T.
History
DepositionMay 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 10, 2024Group: 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 / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE XANTHINE DEHYDROGENASE YAGT IRON-SULFUR-BINDING SUBUNIT
B: PUTATIVE XANTHINE DEHYDROGENASE YAGR MOLYBDENUM-BINDING SU SUBUNIT
C: PUTATIVE XANTHINE DEHYDROGENASE YAGS FAD-BINDING SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,90138
Polymers136,4523
Non-polymers4,44935
Water17,673981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20580 Å2
ΔGint-260.1 kcal/mol
Surface area37820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.681, 78.342, 151.909
Angle α, β, γ (deg.)90.00, 99.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2052-

HOH

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Components

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PUTATIVE XANTHINE DEHYDROGENASE ... , 3 types, 3 molecules ABC

#1: Protein PUTATIVE XANTHINE DEHYDROGENASE YAGT IRON-SULFUR-BINDING SUBUNIT


Mass: 24370.664 Da / Num. of mol.: 1
Fragment: PERIPLASMIC ALDEHYDE OXIDASE ALPHA SUBUNIT, RESIDUES 1-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PTRCHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: P77165
#2: Protein PUTATIVE XANTHINE DEHYDROGENASE YAGR MOLYBDENUM-BINDING SU SUBUNIT


Mass: 33900.840 Da / Num. of mol.: 1
Fragment: PERIPLASMIC ALDEHYDE OXIDASE BETA SUBUNIT, RESIDUES 1-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PTRCHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: P77324
#3: Protein PUTATIVE XANTHINE DEHYDROGENASE YAGS FAD-BINDING SUBUNIT


Mass: 78180.258 Da / Num. of mol.: 1
Fragment: PERIPLASMIC ALDEHYDE OXIDASE GAMMA SUBUNIT, RESIDUES 1-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PTRCHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: P77489

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Non-polymers , 10 types, 1016 molecules

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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#11: Chemical ChemComp-MCN / PTERIN CYTOSINE DINUCLEOTIDE


Mass: 696.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N8O13P2S2
#12: Chemical ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HMoO2S
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 981 / 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: 2.39 Å3/Da / Density % sol: 48.62 % / Description: NONE
Crystal growpH: 7.5 / Details: PEG 3350, AMMONIUM IODIDE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→48.32 Å / Num. obs: 137342 / % possible obs: 98.5 % / Observed criterion σ(I): 1.9 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.69
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.9 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1RM6, 1T3Q, 1FFU, 1FFV

1rm6

1t3q

1ffu

1ffv


Resolution: 1.7→48.32 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.426 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.16745 6835 5 %RANDOM
Rwork0.13848 ---
obs0.13988 130506 98.52 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.871 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å20.1 Å2
2---0.27 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9136 0 188 981 10305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0259675
X-RAY DIFFRACTIONr_bond_other_d0.0070.0229236
X-RAY DIFFRACTIONr_angle_refined_deg2.0462.32113187
X-RAY DIFFRACTIONr_angle_other_deg1.2993.12221261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2451269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76724.025400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.103151554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7561570
X-RAY DIFFRACTIONr_chiral_restr0.1030.21507
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02411109
X-RAY DIFFRACTIONr_gen_planes_other0.0150.0232110
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_it0.9121.1444981
X-RAY DIFFRACTIONr_mcbond_other0.8741.1414976
X-RAY DIFFRACTIONr_mcangle_it1.4261.7076246
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4831.3444694
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 497 -
Rwork0.254 9672 -
obs--99 %
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)
11.32840.2426-0.20240.6234-0.2120.7514-0.0064-0.13720.12370.11110.0050.0617-0.1003-0.04430.00150.0320.01820.00610.0322-0.01360.0321190.973-104.06194.197
20.9336-0.0626-0.13050.5347-0.11850.8908-0.044-0.169-0.15570.06990.01450.02120.1278-0.02320.02950.05810.00910.02790.06160.03630.0482192.858-127.336206.081
30.83540.0015-0.09470.3652-0.03620.2928-0.04930.0886-0.0353-0.03850.0236-0.0237-0.0050.00110.02580.0082-0.01040.00380.0212-0.00090.0232207.028-111.155171.386
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 226
2X-RAY DIFFRACTION2B1 - 316
3X-RAY DIFFRACTION3C1 - 731

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