[English] 日本語
Yorodumi
- PDB-4lh1: Structure of mouse 1-Pyrroline-5-Carboxylate Dehydrogenase (ALDH4... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lh1
TitleStructure of mouse 1-Pyrroline-5-Carboxylate Dehydrogenase (ALDH4A1) complexed with malonate
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / Proline catabolism Substrate recognition / Rossmann Fold
Function / homology
Function and homology information


Proline catabolism / Glyoxylate metabolism and glycine degradation / 1-pyrroline-5-carboxylate dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONIC ACID / Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.673 Å
AuthorsPemberton, T.A. / Tanner, J.J.
CitationJournal: Arch.Biochem.Biophys. / Year: 2013
Title: Structural basis of substrate selectivity of Delta (1)-pyrroline-5-carboxylate dehydrogenase (ALDH4A1): Semialdehyde chain length.
Authors: Pemberton, T.A. / Tanner, J.J.
History
DepositionJun 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)124,5936
Polymers123,9082
Non-polymers6854
Water13,475748
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-40 kcal/mol
Surface area34000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.921, 93.999, 132.068
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 / 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 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CHT0, EC: 1.5.1.12
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 42.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15-25% PEG 3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 148 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 3, 2012
RadiationMonochromator: osmic blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.672→19.647 Å / Num. all: 120594 / Num. obs: 120594 / % possible obs: 98.5 % / Redundancy: 4.4 % / Rsym value: 0.067 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.67-1.763.20.3582.151398161330.35891.2
1.76-1.873.80.2912.662712165780.29199.1
1.87-24.20.1854.165937157350.18599.9
2-2.164.70.1295.968904147320.129100
2.16-2.364.80.0928.264748135810.092100
2.36-2.644.80.06710.859414123330.067100
2.64-3.054.80.05412.752672109060.05499.9
3.05-3.744.80.04414.54495792730.04499.9
3.74-5.294.80.03716.33524272740.03799.9
5.29-19.6474.70.03515.71894040490.03597.7

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
XDSdata reduction
PHENIXphasing
RefinementResolution: 1.673→19.631 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8862 / SU ML: 0.19 / σ(F): 0 / Phase error: 18.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 6014 4.99 %
Rwork0.1696 114483 -
obs0.1711 120497 98.55 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.663 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso max: 58.69 Å2 / Biso mean: 15.178 Å2 / Biso min: 4.43 Å2
Baniso -1Baniso -2Baniso -3
1--2.2238 Å20 Å20 Å2
2--2.1011 Å2-0 Å2
3---0.1226 Å2
Refinement stepCycle: LAST / Resolution: 1.673→19.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8175 0 46 748 8969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068463
X-RAY DIFFRACTIONf_angle_d1.03211523
X-RAY DIFFRACTIONf_chiral_restr0.071272
X-RAY DIFFRACTIONf_plane_restr0.0051507
X-RAY DIFFRACTIONf_dihedral_angle_d11.9023029
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6725-1.69150.29721550.29182794294973
1.6915-1.71140.28671750.26713637381294
1.7114-1.73220.29191960.23743735393198
1.7322-1.75420.27781870.22643764395198
1.7542-1.77720.28211930.21513804399798
1.7772-1.80160.25121940.21493794398899
1.8016-1.82730.26121800.20963824400499
1.8273-1.85450.28391780.20883823400199
1.8545-1.88350.26042180.20623784400299
1.8835-1.91430.2462020.186438314033100
1.9143-1.94730.20371990.171638234022100
1.9473-1.98270.22091950.160838644059100
1.9827-2.02080.19292040.158438344038100
2.0208-2.0620.18662120.160838294041100
2.062-2.10680.21181930.166238704063100
2.1068-2.15570.22962010.158338514052100
2.1557-2.20960.18822010.155938514052100
2.2096-2.26920.19111810.166238674048100
2.2692-2.33590.18262210.155238434064100
2.3359-2.41120.20361950.155438994094100
2.4112-2.49720.18982050.158538764081100
2.4972-2.5970.18442090.159138454054100
2.597-2.71490.19512300.171338404070100
2.7149-2.85760.22271900.173239244114100
2.8576-3.0360.18412210.173638774098100
3.036-3.26940.2092210.187638914112100
3.2694-3.59660.17762190.164738894108100
3.5966-4.11290.15562120.143239304142100
4.1129-5.16620.14962100.128739674177100
5.1662-19.63260.17212170.16784123434099
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2714-0.0322-0.05750.12830.06830.1819-0.0042-0.01250.0274-0.010.0201-0.0283-0.01570.0403-0.01630.041-0.00150.00210.04820.00170.050619.58380.77433.3398
20.3287-0.05550.00390.16040.04190.0864-0.0174-0.05990.01250.0016-0.00840.0108-0.0136-0.02950.02270.0510.00860.00030.0526-0.00780.0558-12.32037.122318.1677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA30 - 563
2X-RAY DIFFRACTION2Chain BB19 - 563

+
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