[English] 日本語
Yorodumi
- PDB-2wox: Betaine aldehyde dehydrogenase from Pseudomonas aeruginosa with N... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more