[English] 日本語
Yorodumi
- PDB-2cwf: Crystal Structure of delta1-piperideine-2-carboxylate reductase f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cwf
TitleCrystal Structure of delta1-piperideine-2-carboxylate reductase from Pseudomonas syringae complexed with NADPH
Componentsdelta1-piperideine-2-carboxylate reductase
KeywordsOXIDOREDUCTASE / NADPH dependent enzyme
Function / homology
Function and homology information


N-methylalanine dehydrogenase / 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) / delta1-piperideine-2-carboxylate reductase activity / N-methylalanine dehydrogenase activity / pyrroline-2-carboxylate reductase activity / proline metabolic process / methylamine metabolic process / NADP+ binding / protein homodimerization activity / identical protein binding
Similarity search - Function
Hypothetical oxidoreductase yiak; domain 3 / Malate/L-lactate dehydrogenase-like / Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily / Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain / Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain / Malate/L-lactate dehydrogenase / Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 ...Hypothetical oxidoreductase yiak; domain 3 / Malate/L-lactate dehydrogenase-like / Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily / Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain / Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain / Malate/L-lactate dehydrogenase / Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGoto, M. / Muramatsu, H. / Mihara, H. / Kurihara, T. / Esaki, N. / Omi, R. / Miyahara, I. / Hirotsu, K.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structures of Delta1-piperideine-2-carboxylate/Delta1-pyrroline-2-carboxylate reductase belonging to a new family of NAD(P)H-dependent oxidoreductases: conformational change, substrate ...Title: Crystal structures of Delta1-piperideine-2-carboxylate/Delta1-pyrroline-2-carboxylate reductase belonging to a new family of NAD(P)H-dependent oxidoreductases: conformational change, substrate recognition, and stereochemistry of the reaction
Authors: Goto, M. / Muramatsu, H. / Mihara, H. / Kurihara, T. / Esaki, N. / Omi, R. / Miyahara, I. / Hirotsu, K.
History
DepositionJun 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: delta1-piperideine-2-carboxylate reductase
B: delta1-piperideine-2-carboxylate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0714
Polymers72,5802
Non-polymers1,4912
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-55 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.049, 68.578, 178.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein delta1-piperideine-2-carboxylate reductase / DpkA


Mass: 36290.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Species: Pseudomonas syringae group genomosp. 3 / Gene: dpkA / Plasmid: pET21a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q4U331, Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.8 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Na/K Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Dec 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→37.45 Å / Num. all: 77303 / Num. obs: 77180 / % possible obs: 99.8 % / Biso Wilson estimate: 17.6 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 99.1

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→37.37 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2227557.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.209 7775 10.1 %RANDOM
Rwork0.188 ---
obs0.188 77180 99.7 %-
all-77303 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.5307 Å2 / ksol: 0.394357 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20 Å2
2--6.11 Å20 Å2
3----8.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4990 0 96 521 5607
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.582
X-RAY DIFFRACTIONc_scbond_it21.12
X-RAY DIFFRACTIONc_scangle_it13.922.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 1281 10.1 %
Rwork0.219 11400 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwat.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4nph.paramnph.top

+
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://pdbjlvh1.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