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- PDB-2wox: Betaine aldehyde dehydrogenase from Pseudomonas aeruginosa with N... -

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Basic information

Entry
Database: PDB / ID: 2wox
TitleBetaine aldehyde dehydrogenase from Pseudomonas aeruginosa with NAD(P) H-catalytic thiol adduct.
ComponentsBETAINE ALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ALDEHYDE OXIDATION / NADPH COMPLEX
Function / homology
Function and homology information


betaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / glycine betaine biosynthetic process from choline / metal ion binding
Similarity search - Function
Betaine aldehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Betaine aldehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7PE / BETA-MERCAPTOETHANOL / : / Chem-NDP / NAD/NADP-dependent betaine aldehyde dehydrogenase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGonzalez-Segura, L. / Rudino-Pinera, E. / Diaz-Sanchez, A.G. / Munoz-Clares, R.A.
CitationJournal: Biochem. J. / Year: 2011
Title: Novel NADPH-cysteine covalent adduct found in the active site of an aldehyde dehydrogenase.
Authors: Diaz-Sanchez, A.G. / Gonzalez-Segura, L. / Rudino-Pinera, E. / Lira-Rocha, A. / Torres-Larios, A. / Munoz-Clares, R.A.
History
DepositionJul 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 2.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / database_PDB_caveat / entity_src_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 / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 2.1Apr 24, 2019Group: Data collection / Derived calculations
Category: database_PDB_rev / database_PDB_rev_record / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Dec 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.3Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETAINE ALDEHYDE DEHYDROGENASE
B: BETAINE ALDEHYDE DEHYDROGENASE
C: BETAINE ALDEHYDE DEHYDROGENASE
D: BETAINE ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,51239
Polymers213,0364
Non-polymers6,47635
Water19,6001088
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33250 Å2
ΔGint-116.1 kcal/mol
Surface area55560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.749, 151.749, 242.053
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
BETAINE ALDEHYDE DEHYDROGENASE / BADH


Mass: 53259.066 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PCALBETB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PlysS / References: UniProt: Q9HTJ1, betaine-aldehyde dehydrogenase

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Non-polymers , 6 types, 1123 molecules

#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H30O7
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1088 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 3.79 Å3/Da / Density % sol: 67.53 % / Description: NONE
Crystal growpH: 7.5
Details: CRYSTAL WERE GROWN IN 85 MM HEPES, PH 7.5, 8.5% (V:V) ISOPROPANOL, 17% PEG 4000 AND 2 MM NADPH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 9, 2008
Details: HIGH-RESOLUTION DOUBLE- CRYSTAL SI(220) SAGITTAL FOCUSING, ROSENBAUM- ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: ROSENBAUM-ROCK / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. obs: 143189 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 35.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WME

2wme


Resolution: 2.3→63.414 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 18.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 7099 5 %
Rwork0.1593 --
obs0.1635 141572 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.565 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.3935 Å20 Å20 Å2
2---1.3935 Å20 Å2
3---2.7871 Å2
Refinement stepCycle: LAST / Resolution: 2.3→63.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14976 0 375 1088 16439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03315793
X-RAY DIFFRACTIONf_angle_d1.41821415
X-RAY DIFFRACTIONf_dihedral_angle_d18.3045959
X-RAY DIFFRACTIONf_chiral_restr0.072351
X-RAY DIFFRACTIONf_plane_restr0.0292788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32620.28952240.19524486X-RAY DIFFRACTION100
2.3262-2.35350.29522200.19544502X-RAY DIFFRACTION100
2.3535-2.38220.29512320.19044508X-RAY DIFFRACTION100
2.3822-2.41240.26092540.18334459X-RAY DIFFRACTION100
2.4124-2.44410.29922380.18414502X-RAY DIFFRACTION100
2.4441-2.47760.29042190.17364488X-RAY DIFFRACTION100
2.4776-2.5130.22162400.14624447X-RAY DIFFRACTION100
2.513-2.55050.23872450.15154503X-RAY DIFFRACTION100
2.5505-2.59040.23172350.14724511X-RAY DIFFRACTION100
2.5904-2.63280.22982560.14294454X-RAY DIFFRACTION100
2.6328-2.67820.22072440.13714511X-RAY DIFFRACTION100
2.6782-2.72690.2532380.13954498X-RAY DIFFRACTION100
2.7269-2.77940.22232350.14064498X-RAY DIFFRACTION100
2.7794-2.83610.23992330.12914513X-RAY DIFFRACTION100
2.8361-2.89780.20872610.12664479X-RAY DIFFRACTION100
2.8978-2.96520.22392370.1264511X-RAY DIFFRACTION100
2.9652-3.03930.18812300.11964572X-RAY DIFFRACTION100
3.0393-3.12150.21392260.12754453X-RAY DIFFRACTION100
3.1215-3.21340.20872370.12884557X-RAY DIFFRACTION100
3.2134-3.31710.19782460.12394496X-RAY DIFFRACTION100
3.3171-3.43560.18582600.11684482X-RAY DIFFRACTION99
3.4356-3.57320.16832340.1054502X-RAY DIFFRACTION99
3.5732-3.73580.15612100.10214498X-RAY DIFFRACTION99
3.7358-3.93270.15262350.10324515X-RAY DIFFRACTION99
3.9327-4.17910.16682320.10614464X-RAY DIFFRACTION98
4.1791-4.50170.14852540.09574440X-RAY DIFFRACTION98
4.5017-4.95450.15562070.09754482X-RAY DIFFRACTION97
4.9545-5.67110.18832600.13054396X-RAY DIFFRACTION96
5.6711-7.14340.18712140.14864429X-RAY DIFFRACTION94
7.1434-63.43810.17892430.15954317X-RAY DIFFRACTION90

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