[English] 日本語
Yorodumi
- PDB-5j6b: Crystal structure of Aldehyde dehydrogenase from Burkholderia tha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j6b
TitleCrystal structure of Aldehyde dehydrogenase from Burkholderia thailandensis in covelent complex with NADPH
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / ALDEHYDE DEHYDROGENASE / NADP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal ...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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of Aldehyde dehydrogenase from Burkholderia thailandensis in covelent complex with NADPH
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,27612
Polymers211,1534
Non-polymers3,1238
Water25,7791431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23390 Å2
ΔGint-114 kcal/mol
Surface area57240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.520, 143.660, 167.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Aldehyde dehydrogenase / / Aldehyde dehydrogenase family protein


Mass: 52788.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301) (bacteria)
Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_II0498, DR63_5272 / Plasmid: ButhA.00020.t.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T801
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1431 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: RigakuReagents JCSG+ screen H5: 45% MPD, 200mM Ammonium acetate, 100mM BisTris/HCl pH 5.5; ButhA.00020.t.B1.PW37792 at 22.7 mg/ml + 3mM NADP; cryo: direct; tray: 26729h5, puck sja1-10
PH range: 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 17, 2015
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 146312 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 27.86 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3.55 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
ARPmodel building
Cootmodel building
PHENIX(DEV_2356: ???)refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pqa
Resolution: 1.95→46.4 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 17.87
RfactorNum. reflection% reflection
Rfree0.187 2012 1.38 %
Rwork0.149 --
obs0.149 146283 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.19 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14416 0 196 1431 16043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715091
X-RAY DIFFRACTIONf_angle_d0.8520543
X-RAY DIFFRACTIONf_dihedral_angle_d13.2979177
X-RAY DIFFRACTIONf_chiral_restr0.0512305
X-RAY DIFFRACTIONf_plane_restr0.0052769
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.814-0.1072-0.20180.59090.06121.2954-0.00910.01360.27-0.02360.02710.2237-0.2711-0.0458-0.01980.18990.01850.01320.1180.04180.300985.45177.449331.468
20.41380.0666-0.2541.16390.52720.4195-0.01350.03810.05680.00030.06320.12180.00460.0199-0.06870.15990.0085-0.01170.15190.03860.147694.8761159.50825.2185
30.4041-0.10260.23140.6583-0.22760.7963-0.00710.02510.07240.0377-0.00690.2447-0.0497-0.09610.01810.13310.01770.03250.13380.03450.2381.9422163.604632.3024
42.3418-0.31340.20891.43590.36240.3046-0.013-0.06550.18510.20130.04760.1688-0.1568-0.00150.00830.2380.00520.08230.1422-0.00480.162497.2293160.756654.4704
50.69270.0924-0.02191.00870.15950.5835-0.0623-0.14660.01920.33210.03040.27940.0696-0.07810.01890.23890.02350.09830.15250.0220.169990.7741155.264956.2546
60.34620.44740.31220.58010.47311.5796-0.07110.04820.0274-0.06180.02160.1195-0.15330.08310.01110.13790.01130.00730.13960.04450.185892.5578151.400423.0683
71.16680.5467-0.14090.678-0.21680.7859-0.08320.0927-0.1333-0.06470.05620.060.156-0.07310.00950.1449-0.02670.0320.11930.00070.174181.2944121.146723.1176
81.07080.66220.36881.08050.56810.4501-0.04390.1122-0.0401-0.0710.08670.0248-0.05230.0529-0.06770.1495-0.03550.01470.15950.03090.119593.606137.935724.1513
90.95390.6199-0.05670.8393-0.34670.5796-0.06340.1250.119-0.04640.04980.20580.0057-0.0896-0.03630.1131-0.0252-0.00170.13670.01370.170878.7358134.754422.5235
100.3825-0.47210.20240.95210.08640.4111-0.11880.4359-0.1109-0.26670.22570.12080.1792-0.0134-0.13850.2966-0.1747-0.06870.44990.020.151484.1522136.7074-3.4766
111.09340.2177-0.42580.33050.06390.7001-0.25070.56790.3028-0.28790.26510.29380.0081-0.30450.05380.2541-0.15-0.14530.45540.16190.257878.1143143.1578-2.8099
120.56330.31930.57640.66070.70592.003-0.06290.10750.16-0.01260.02090.15710.07450.04340.02470.1187-0.02530.0130.11130.03680.162693.0765145.948226.714
130.8911-0.29940.83251.1093-1.17162.92730.04190.2181-0.2932-0.305-0.0076-0.13860.52180.2988-0.02580.29670.05320.05970.222-0.07520.2662131.0513119.58969.4895
143.2965-1.78922.69742.0143-1.78423.17590.23290.0446-0.6004-0.21110.11220.19590.5513-0.0778-0.31660.2277-0.0324-0.0030.1513-0.00380.3031115.7632119.688817.2043
151.1574-0.54720.20851.1533-0.03930.2751-0.0075-0.0168-0.12050.0090.08090.08-0.012-0.0248-0.09460.1227-0.01210.0220.1390.0210.1137115.1208137.245617.1917
160.396-0.0860.06550.55960.14641.5390.00540.0499-0.1022-0.1033-0.0002-0.08960.06710.1494-0.01940.13280.00330.03290.1872-0.0040.1728129.2562131.589517.3813
173.7574-0.9443-1.78163.13821.0072.6177-0.1715-0.1776-0.44160.15710.01380.10460.41720.12470.13830.12380.0285-0.01040.17170.06980.1933123.4211126.258643.1885
181.3833-0.247-0.10771.58080.1021.2367-0.0767-0.2417-0.2040.16230.0981-0.18040.16150.2287-0.00620.13360.0369-0.01820.23420.04830.1842134.5074127.677845.2568
192.22220.1847-0.11151.13260.34171.5687-0.0215-0.08050.0580.12820.02860.0122-0.1220.0595-0.00790.130.01740.01680.1260.01980.108120.926140.602940.4063
200.195-0.10480.44711.5217-1.37052.2974-0.01760.00830.0186-0.11890.08870.07060.05040.0226-0.10890.118-0.0150.02060.1290.01280.1466116.9461145.609117.1127
210.78550.1992-0.28371.498-1.93974.00970.01960.05290.24190.0834-0.0009-0.1422-0.41150.20620.02160.2651-0.12230.03070.22290.00370.2745137.4448179.672119.0125
221.29230.3379-0.49380.5355-0.1491.42180.04-0.06120.1780.02370.0868-0.0019-0.26160.0114-0.09560.2004-0.05850.04230.109-0.0290.1507123.8614171.284825.495
230.4019-0.0279-0.35281.1216-0.2470.56210.04360.07140.0476-0.06850.0680.1359-0.0783-0.011-0.1310.1411-0.0433-0.00930.15890.03190.1217117.3212158.044422.9638
240.57610.07160.20470.5337-0.01850.7955-0.00170.03240.0358-0.06960.0137-0.1064-0.10130.19580.00120.1569-0.05070.04510.16520.02470.1528130.7153162.373317.1323
252.10580.44711.11260.41670.64531.9422-0.0892-0.03720.214-0.18970.08180.0571-0.23710.03810.07050.2823-0.04660.02030.16590.05880.1612115.7254168.2828-4.8283
260.91090.00690.37831.4058-0.27791.47980.0010.21910.097-0.32830.012-0.1351-0.07080.2249-0.00810.292-0.04640.05450.22620.03150.1297124.6881166.4945-10.8064
271.8528-0.0480.11340.7362-0.38441.31920.00050.0581-0.1411-0.21550.0910.07860.1647-0.0738-0.09110.2152-0.0543-0.00580.15330.04030.1276112.7725154.6536-0.6724
280.4208-0.40410.09260.4882-0.49611.3493-0.0324-0.0157-0.07280.02440.05490.0506-0-0.0236-0.05680.1319-0.0340.02360.12730.01790.1428118.2257149.553922.4285

+
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