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- PDB-5g5h: Escherichia coli Periplasmic Aldehyde Oxidase R440H mutant -

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Basic information

Entry
Database: PDB / ID: 5g5h
TitleEscherichia coli Periplasmic Aldehyde Oxidase R440H mutant
Components(Aldehyde oxidoreductase ...) 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 / periplasmic space / oxidoreductase activity / 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 / 2Fe-2S ferredoxin-like superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_conn_type / struct_ref / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Oct 23, 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: Aldehyde oxidoreductase iron-sulfur-binding subunit PaoA
B: Aldehyde oxidoreductase FAD-binding subunit PaoB
C: Aldehyde oxidoreductase molybdenum-binding subunit PaoC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,60233
Polymers136,4333
Non-polymers4,17030
Water11,908661
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18960 Å2
ΔGint-230.9 kcal/mol
Surface area38110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.839, 78.263, 151.732
Angle α, β, γ (deg.)90.00, 99.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Aldehyde oxidoreductase ... , 3 types, 3 molecules ABC

#1: Protein Aldehyde oxidoreductase iron-sulfur-binding subunit PaoA


Mass: 24370.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: paoA, yagT, b0286, JW0280 / Plasmid: PTRCHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ESCHERICHIA COLI TP1000 / References: UniProt: P77165, carboxylate reductase
#2: Protein Aldehyde oxidoreductase FAD-binding subunit PaoB


Mass: 33900.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: paoB, yagS, b0285, JW0279 / Plasmid: PTRCHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ESCHERICHIA COLI TP1000 / References: UniProt: P77324, carboxylate reductase
#3: Protein Aldehyde oxidoreductase molybdenum-binding subunit PaoC


Mass: 78161.203 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: paoC, yagR, b0284, JW0278 / Plasmid: PTRCHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ESCHERICHIA COLI TP1000 / References: UniProt: P77489, carboxylate reductase

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Non-polymers , 10 types, 691 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.: 8 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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


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


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


Mass: 161.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HMoO2S
#12: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 48.55 % / 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: ESRF / Beamline: BM14 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→48.27 Å / Num. obs: 55360 / % possible obs: 98 % / Observed criterion σ(I): 1.81 / Redundancy: 7.2 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.81 / % possible all: 84.2

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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: 2.3→48.27 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.892 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 2811 5.1 %RANDOM
Rwork0.16378 ---
obs0.16664 52541 97.95 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.324 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20.01 Å2
2---0.15 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9104 0 173 661 9938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0259452
X-RAY DIFFRACTIONr_bond_other_d0.010.0229035
X-RAY DIFFRACTIONr_angle_refined_deg1.8572.32912859
X-RAY DIFFRACTIONr_angle_other_deg1.2043.12520770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42951222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7523.964386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.918151510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4251567
X-RAY DIFFRACTIONr_chiral_restr0.0730.21475
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.02410767
X-RAY DIFFRACTIONr_gen_planes_other0.0070.0232053
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_it0.9181.5654882
X-RAY DIFFRACTIONr_mcbond_other0.9171.5634878
X-RAY DIFFRACTIONr_mcangle_it1.5252.3426095
X-RAY DIFFRACTIONr_mcangle_other1.5252.3436096
X-RAY DIFFRACTIONr_scbond_it1.2861.754570
X-RAY DIFFRACTIONr_scbond_other1.2861.754570
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0912.5576746
X-RAY DIFFRACTIONr_long_range_B_refined4.43413.30710948
X-RAY DIFFRACTIONr_long_range_B_other4.43413.30710948
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 154 -
Rwork0.258 3318 -
obs--83.82 %
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)
11.67620.0179-0.280.7815-0.30461.0576-0.0239-0.14980.16280.13580.0210.038-0.1216-0.1020.0030.03080.01580.01140.0297-0.0180.1703106.812-106.58544.454
20.8705-0.25850.07150.7042-0.06651.2105-0.0226-0.1881-0.14820.08870.01960.04450.109-0.0680.0030.0366-0.00240.05060.06820.03860.1718108.635-130.02756.213
30.75750.0257-0.00830.3769-0.06540.3479-0.02650.0456-0.0021-0.03230.0085-0.0255-0.00810.00540.0180.0065-0.00290.02060.0031-0.00370.1511122.916-113.6521.579
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 225
2X-RAY DIFFRACTION2B1 - 316
3X-RAY DIFFRACTION3C1 - 730

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