[English] 日本語
Yorodumi
- PDB-6rtt: Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuli... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rtt
TitlePiperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus complexed with picolinic acid
ComponentsSemialdehyde dehydrogenase Pcd
KeywordsOXIDOREDUCTASE / antibiotic biosynthesis / Streptomyces clavuligerus
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity
Similarity search - Function
Aldehyde dehydrogenase family 7 member A1-like / 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 family 7 member A1-like / 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
PYRIDINE-2-CARBOXYLIC ACID / aldehyde dehydrogenase (NAD(+))
Similarity search - Component
Biological speciesStreptomyces clavuligerus ATCC 27064 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHasse, D. / Huelsemann, J. / Carlsson, G. / Andersson, I.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structure and mechanism of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus.
Authors: Hasse, D. / Hulsemann, J. / Carlsson, G.H. / Valegard, K. / Andersson, I.
History
DepositionMay 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Semialdehyde dehydrogenase Pcd
B: Semialdehyde dehydrogenase Pcd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,65016
Polymers108,1782
Non-polymers1,47214
Water13,259736
1
A: Semialdehyde dehydrogenase Pcd
B: Semialdehyde dehydrogenase Pcd
hetero molecules

A: Semialdehyde dehydrogenase Pcd
B: Semialdehyde dehydrogenase Pcd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,30032
Polymers216,3564
Non-polymers2,94428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area27530 Å2
ΔGint-152 kcal/mol
Surface area58990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.820, 130.060, 157.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-906-

HOH

21A-1025-

HOH

31B-1002-

HOH

41B-1054-

HOH

-
Components

#1: Protein Semialdehyde dehydrogenase Pcd


Mass: 54088.996 Da / Num. of mol.: 2 / Mutation: S140T, A503T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus ATCC 27064 (bacteria)
Gene: pcd / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: O85725
#2: Chemical
ChemComp-6PC / PYRIDINE-2-CARBOXYLIC ACID / PICOLINIC ACID / Picolinic acid


Mass: 123.109 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate pH 5, 2.2 M ammonium sulphate, 0.2 M lithium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.65→45.33 Å / Num. obs: 128777 / % possible obs: 99 % / Redundancy: 7.4 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.088 / Net I/σ(I): 18.65
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.29 / Num. unique obs: 5590 / CC1/2: 0.816 / Rrim(I) all: 0.706 / % possible all: 92

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RTR

6rtr


Resolution: 1.65→45.33 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.184 6439 5 %
Rwork0.162 122338 -
obs0.163 128777 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.06 Å2 / Biso mean: 21.0336 Å2 / Biso min: 6.25 Å2
Refinement stepCycle: final / Resolution: 1.65→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7474 0 92 736 8302
Biso mean--28.12 27.71 -
Num. residues----1007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.66870.29461420.2656269263
1.6687-1.68830.28761520.2481289568
1.6883-1.70890.30551600.2364302871
1.7089-1.73060.27121700.2154323876
1.7306-1.75330.20961860.2123352282
1.7533-1.77740.24882030.2121385890
1.7774-1.80280.22482160.1905411797
1.8028-1.82970.21852240.1854425699
1.8297-1.85830.22042260.1814427899
1.8583-1.88870.20622220.1787422099
1.8887-1.92130.2112220.1762422999
1.9213-1.95620.20132240.1683425699
1.9562-1.99390.20262250.1562426799
1.9939-2.03460.19782260.1571428899
2.0346-2.07880.17912230.1511424099
2.0788-2.12720.1812260.148429399
2.1272-2.18030.16832240.15434267100
2.1803-2.23930.17522250.15054266100
2.2393-2.30520.17652260.15374290100
2.3052-2.37960.18372260.15424307100
2.3796-2.46460.19252250.16274273100
2.4646-2.56330.18692260.16094300100
2.5633-2.67990.19772280.16454320100
2.6799-2.82120.17472260.16794307100
2.8212-2.99790.18432280.16524329100
2.9979-3.22940.19692280.16514335100
3.2294-3.55420.17942300.1594354100
3.5542-4.06830.15272300.14334384100
4.0683-5.12440.14672310.13824378100
5.1244-45.330.16832390.16214551100

+
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