[English] 日本語
Yorodumi
- PDB-3v9l: Crystal structure of mouse 1-pyrroline-5-carboxylate dehydrogenas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v9l
TitleCrystal structure of mouse 1-pyrroline-5-carboxylate dehydrogenase complexed with NAD+
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / Rossmann fold / nucleotide binding / acting on aldehyde or oxo group of donors / NAD or NADP as acceptor / mitochondria
Function / homology
Function and homology information


Proline catabolism / Glyoxylate metabolism and glycine degradation / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / aldehyde dehydrogenase (NAD+) activity / mitochondrial matrix / mitochondrion / identical protein binding / cytosol
Similarity search - Function
Delta-1-pyrroline-5-carboxylate 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 ...Delta-1-pyrroline-5-carboxylate 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsTanner, J.J. / Srivastava, D.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Three-Dimensional Structural Basis of Type II Hyperprolinemia.
Authors: Srivastava, D. / Singh, R.K. / Moxley, M.A. / Henzl, M.T. / Becker, D.F. / Tanner, J.J.
History
DepositionDec 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Sep 13, 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: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,4196
Polymers123,9082
Non-polymers1,5114
Water15,709872
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-45 kcal/mol
Surface area33460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.888, 94.053, 132.425
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial / 1-pyrroline-5-carboxylate dehydrogenase / P5C dehydrogenase / Aldehyde dehydrogenase family 4 member A1


Mass: 61954.215 Da / Num. of mol.: 2 / Fragment: UNP residues 21-562
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aldh4a1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8CHT0, EC: 1.5.1.12
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 872 / 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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: reservoir: 20-25% w/v PEG3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5, cryoprotectant: 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 27, 2011
RadiationMonochromator: Rosenbaum-Rock Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.502→47.027 Å / Num. all: 168338 / Num. obs: 168338 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rsym value: 0.061 / Net I/σ(I): 25.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.502-1.586.80.3994.9161483238650.39997.6
1.58-1.687.30.296.6169246231370.29100
1.68-1.87.40.2039.5159974217640.203100
1.8-1.947.30.1315149214203110.13100
1.94-2.127.40.07723.6138606187210.077100
2.12-2.377.30.05831.5123759169730.058100
2.37-2.747.40.04140.7111856150510.041100
2.74-3.367.40.02955.994752127950.029100
3.36-4.757.30.02374.37258499970.023100
4.75-47.02770.02754034257240.0299.9

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V9J

3v9j


Resolution: 1.502→45.647 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9149 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1758 8525 5.07 %SAME TEST SET AS PDB ENTRY 3V9J
Rwork0.1579 ---
obs0.1588 168202 99.61 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.035 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso max: 45.41 Å2 / Biso mean: 12.0852 Å2 / Biso min: 3.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.7985 Å20 Å2-0 Å2
2--2.1932 Å20 Å2
3----0.0957 Å2
Refinement stepCycle: LAST / Resolution: 1.502→45.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8170 0 100 872 9142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068653
X-RAY DIFFRACTIONf_angle_d1.11111830
X-RAY DIFFRACTIONf_chiral_restr0.071306
X-RAY DIFFRACTIONf_plane_restr0.0051545
X-RAY DIFFRACTIONf_dihedral_angle_d11.6833080
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.502-1.55570.21228320.194152701610296
1.5557-1.6180.19178440.15641590016744100
1.618-1.69160.1829190.15091586116780100
1.6916-1.78080.17588110.14891591516726100
1.7808-1.89240.17948180.14781597916797100
1.8924-2.03850.17148370.15091596416801100
2.0385-2.24360.1748170.15021603616853100
2.2436-2.56830.17288540.15691602216876100
2.5683-3.23560.17648950.16381615217047100
3.2356-45.66860.16658980.16011657817476100

+
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