[English] 日本語
Yorodumi
- PDB-4oe5: Structure of Human ALDH4A1 Crystallized in Space Group P21 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oe5
TitleStructure of Human ALDH4A1 Crystallized in Space Group P21
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / ALDH4A1 / ROSSMANN FOLD / NAD / MITOCHONDRIA
Function / homology
Function and homology information


Proline catabolism / proline metabolic process / 4-hydroxyproline catabolic process / proline catabolic process / 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 / electron transfer activity ...Proline catabolism / proline metabolic process / 4-hydroxyproline catabolic process / proline catabolic process / 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 / electron transfer 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
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTanner, J.J.
CitationJournal: Biochemistry / Year: 2014
Title: Structural Studies of Yeast Delta (1)-Pyrroline-5-carboxylate Dehydrogenase (ALDH4A1): Active Site Flexibility and Oligomeric State.
Authors: Pemberton, T.A. / Srivastava, D. / Sanyal, N. / Henzl, M.T. / Becker, D.F. / Tanner, J.J.
History
DepositionJan 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 18, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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
C: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
D: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,2608
Polymers240,5204
Non-polymers7394
Water4,342241
1
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)120,7615
Polymers120,2602
Non-polymers5013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-19 kcal/mol
Surface area37100 Å2
MethodPISA
2
C: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
D: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4983
Polymers120,2602
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-15 kcal/mol
Surface area37140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.960, 121.335, 93.397
Angle α, β, γ (deg.)90.000, 104.230, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 60130.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH4, ALDH4A1, P5CDH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS
References: UniProt: P30038, L-glutamate gamma-semialdehyde dehydrogenase
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 - 25 % (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES at pH 7.0 - 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 139296 / % possible obs: 96.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.049 / Χ2: 0.956 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.023.30.453133560.764193
2.02-2.13.30.333134340.784193.3
2.1-2.23.40.219135860.823194.4
2.2-2.313.40.168137230.866195.4
2.31-2.463.40.123138850.887196.3
2.46-2.653.50.095139940.919197.2
2.65-2.913.60.066141250.987198
2.91-3.333.70.046142981.118198.8
3.33-4.23.70.032143521.273199.2
4.2-503.70.023145431.014199.3

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V9G

3v9g


Resolution: 1.95→42.411 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8145 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 6972 5.01 %random
Rwork0.1938 ---
obs0.1959 139239 96.21 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.47 Å2 / Biso mean: 33.1479 Å2 / Biso min: 10.62 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15149 0 46 241 15436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715562
X-RAY DIFFRACTIONf_angle_d1.01221236
X-RAY DIFFRACTIONf_chiral_restr0.0682418
X-RAY DIFFRACTIONf_plane_restr0.0052771
X-RAY DIFFRACTIONf_dihedral_angle_d12.3595348
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 (%)
1.9484-2.01810.30116490.2279123291297890
2.0181-2.09880.28056930.2199128191351293
2.0988-2.19440.27966790.2093128971357694
2.1944-2.31010.26197150.2031130741378995
2.3101-2.45480.26456960.2033131951389196
2.4548-2.64430.26247070.204133341404197
2.6443-2.91030.26556880.2107134661415498
2.9103-3.33130.26847100.2247136391434999
3.3313-4.19650.20466810.1799137141439599
4.1965-42.42070.1847540.1632138001455499
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)
11.3616-0.3880.4610.7737-0.21690.6860.01690.23140.0875-0.0878-0.00070.0992-0.0432-0.0578-0.0210.149-0.02150.01510.22070.03240.1306-9.5167-5.182411.4309
21.59020.29070.24871.26740.06670.4165-0.02260.19210.02470.11040.0167-0.1602-0.01670.08630.00020.1714-0.040.02560.193-0.02520.187927.03225.803421.165
31.5011-0.67460.55960.94260.01930.47640.0007-0.1370.0114-0.04770.0247-0.07990.0071-0.0477-0.020.17340.0353-0.00180.1362-0.00560.106818.5915-6.887264.9814
41.09410.47040.17421.04380.35660.44020.0336-0.03450.0233-0.077-0.11880.2040.0112-0.11750.06080.17060.0553-0.01830.1789-0.03360.2345-16.3176.782652.8798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA23 - 551
2X-RAY DIFFRACTION2Chain BB23 - 551
3X-RAY DIFFRACTION3Chain CC23 - 551
4X-RAY DIFFRACTION4Chain DD23 - 551

+
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