[English] 日本語
Yorodumi
- PDB-4jz6: Crystal structure of a salicylaldehyde dehydrogenase from Pseudom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jz6
TitleCrystal structure of a salicylaldehyde dehydrogenase from Pseudomonas putida G7 complexed with salicylaldehyde
ComponentsSalicylaldehyde dehydrogenase NahF
KeywordsOXIDOREDUCTASE / Protein-ligand complex / alpha/beta fold / dehydrogenase / NAD+ Binding / N-terminal 6xHis-tagged protein
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
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
SALICYLALDEHYDE / Salicylaldehyde dehydrogenase NahF
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.417 Å
AuthorsCoitinho, J.B. / Nagem, R.A.P.
Citation
Journal: Biochemistry / Year: 2016
Title: Structural and Kinetic Properties of the Aldehyde Dehydrogenase NahF, a Broad Substrate Specificity Enzyme for Aldehyde Oxidation.
Authors: Coitinho, J.B. / Pereira, M.S. / Costa, D.M. / Guimaraes, S.L. / Araujo, S.S. / Hengge, A.C. / Brandao, T.A. / Nagem, R.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Expression, purification and preliminary crystallographic studies of NahF, a salicylaldehyde dehydrogenase from Pseudomonas putida G7 involved in naphthalene degradation.
Authors: Coitinho, J.B. / Costa, D.M. / Guimaraes, S.L. / de Goes, A.M. / Nagem, R.A.
History
DepositionApr 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Salicylaldehyde dehydrogenase NahF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,25111
Polymers54,4081
Non-polymers84310
Water6,756375
1
A: Salicylaldehyde dehydrogenase NahF
hetero molecules

A: Salicylaldehyde dehydrogenase NahF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,50122
Polymers108,8162
Non-polymers1,68620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area10900 Å2
ΔGint-109 kcal/mol
Surface area31760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.470, 169.470, 157.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

21A-832-

HOH

31A-884-

HOH

41A-910-

HOH

51A-941-

HOH

-
Components

#1: Protein Salicylaldehyde dehydrogenase NahF


Mass: 54407.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein was engineered to contain a 6xHis N-terminal tag
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: G7 / Gene: nahF / Plasmid: pET28a(TEV) / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express / References: UniProt: Q1XGL7, EC: 1.2.1.65
#2: Chemical ChemComp-NK / SALICYLALDEHYDE / Salicylaldehyde


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein at 15 mg/ml. Mother liquor with 1.5 M ammonium sulfate, 5%(v/v) 2-propanol in 100 mM sodium acetate acetic acid buffer pH 5.0., VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.608 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 17, 2011
RadiationMonochromator: Curved crystal of silicon (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.608 Å / Relative weight: 1
ReflectionResolution: 2.417→32.17 Å / Num. obs: 51558 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.272 / Net I/σ(I): 10.4
Reflection shellResolution: 2.417→2.55 Å / Redundancy: 13.2 % / % possible all: 99.8

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BXS
Resolution: 2.417→32.168 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 2619 5.08 %random
Rwork0.2089 ---
all0.2108 ---
obs0.2108 51517 99.96 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.779 Å2 / ksol: 0.301 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6396 Å20 Å2-0 Å2
2--0.6396 Å20 Å2
3----1.2792 Å2
Refinement stepCycle: LAST / Resolution: 2.417→32.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 53 375 4101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053784
X-RAY DIFFRACTIONf_angle_d0.9265117
X-RAY DIFFRACTIONf_dihedral_angle_d15.4871380
X-RAY DIFFRACTIONf_chiral_restr0.061582
X-RAY DIFFRACTIONf_plane_restr0.004664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.417-2.4610.41421260.38412517X-RAY DIFFRACTION99
2.461-2.50830.3761470.34852510X-RAY DIFFRACTION100
2.5083-2.55950.35251600.33672502X-RAY DIFFRACTION100
2.5595-2.61510.3421220.31162547X-RAY DIFFRACTION100
2.6151-2.67590.33381390.31512547X-RAY DIFFRACTION100
2.6759-2.74280.38181480.29932515X-RAY DIFFRACTION100
2.7428-2.81690.32461510.28192533X-RAY DIFFRACTION100
2.8169-2.89970.26551300.26382548X-RAY DIFFRACTION100
2.8997-2.99330.30471310.24952552X-RAY DIFFRACTION100
2.9933-3.10020.2781370.22752544X-RAY DIFFRACTION100
3.1002-3.22420.24081390.22282561X-RAY DIFFRACTION100
3.2242-3.37080.25251390.19392564X-RAY DIFFRACTION100
3.3708-3.54830.21791370.18122561X-RAY DIFFRACTION100
3.5483-3.77030.21221430.15682576X-RAY DIFFRACTION100
3.7703-4.06080.16041250.1362605X-RAY DIFFRACTION100
4.0608-4.46850.14391430.11542590X-RAY DIFFRACTION100
4.4685-5.11290.13941440.11362626X-RAY DIFFRACTION100
5.1129-6.43330.19561280.1532671X-RAY DIFFRACTION100
6.4333-32.17090.19481300.16652829X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 64.7522 Å / Origin y: -9.6861 Å / Origin z: 13.6149 Å
111213212223313233
T0.3736 Å2-0.0121 Å20.05 Å2-0.193 Å20.0432 Å2--0.1777 Å2
L0.4679 °20.2009 °20.0019 °2-1.3151 °2-0.1139 °2--0.6524 °2
S-0.0602 Å °-0.1046 Å °-0.0191 Å °0.0817 Å °0.0718 Å °0.1758 Å °0.1276 Å °-0.1804 Å °-0.0143 Å °
Refinement TLS groupSelection details: all

+
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