[English] 日本語
Yorodumi
- PDB-6lhm: Structure of human PYCR2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lhm
TitleStructure of human PYCR2
ComponentsPyrroline-5-carboxylate reductase 2
KeywordsOXIDOREDUCTASE / PYCR2 / carboxylate / P5CR / decamer / pentamer / Pyrroline-5-carboxylate reductase
Function / homology
Function and homology information


glutamine family amino acid metabolic process / pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / proline biosynthetic process / L-proline biosynthetic process / Glutamate and glutamine metabolism / cellular response to oxidative stress / mitochondrial matrix / mitochondrion
Similarity search - Function
Delta 1-pyrroline-5-carboxylate reductase signature. / Pyrroline-5-carboxylate reductase / Pyrroline-5-carboxylate reductase, dimerisation domain / Pyrroline-5-carboxylate reductase dimerisation / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Pyrroline-5-carboxylate reductase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBaburajendran, N.
CitationJournal: Neuron / Year: 2020
Title: Loss of PYCR2 Causes Neurodegeneration by Increasing Cerebral Glycine Levels via SHMT2.
Authors: Escande-Beillard, N. / Loh, A. / Saleem, S.N. / Kanata, K. / Hashimoto, Y. / Altunoglu, U. / Metoska, A. / Grandjean, J. / Ng, F.M. / Pomp, O. / Baburajendran, N. / Wong, J. / Hill, J. / ...Authors: Escande-Beillard, N. / Loh, A. / Saleem, S.N. / Kanata, K. / Hashimoto, Y. / Altunoglu, U. / Metoska, A. / Grandjean, J. / Ng, F.M. / Pomp, O. / Baburajendran, N. / Wong, J. / Hill, J. / Beillard, E. / Cozzone, P. / Zaki, M. / Kayserili, H. / Hamada, H. / Shiratori, H. / Reversade, B.
History
DepositionDec 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Pyrroline-5-carboxylate reductase 2
B: Pyrroline-5-carboxylate reductase 2
C: Pyrroline-5-carboxylate reductase 2
D: Pyrroline-5-carboxylate reductase 2
E: Pyrroline-5-carboxylate reductase 2


Theoretical massNumber of molelcules
Total (without water)158,6895
Polymers158,6895
Non-polymers00
Water0
1
A: Pyrroline-5-carboxylate reductase 2


Theoretical massNumber of molelcules
Total (without water)31,7381
Polymers31,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pyrroline-5-carboxylate reductase 2


Theoretical massNumber of molelcules
Total (without water)31,7381
Polymers31,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pyrroline-5-carboxylate reductase 2


Theoretical massNumber of molelcules
Total (without water)31,7381
Polymers31,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pyrroline-5-carboxylate reductase 2


Theoretical massNumber of molelcules
Total (without water)31,7381
Polymers31,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Pyrroline-5-carboxylate reductase 2


Theoretical massNumber of molelcules
Total (without water)31,7381
Polymers31,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.903, 110.312, 155.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein
Pyrroline-5-carboxylate reductase 2 / / P5CR 2


Mass: 31737.818 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PYCR2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96C36, pyrroline-5-carboxylate reductase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Carboxylic acids, 0.1M Buffer system 3 pH 8.5, 50% v/v Precipitant Mix 3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.4→46.904 Å / Num. obs: 24754 / % possible obs: 97.68 % / Redundancy: 8.2 % / CC1/2: 0.829 / Net I/σ(I): 8.75
Reflection shellResolution: 3.4→3.522 Å / Num. unique obs: 20319 / CC1/2: 0.659

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZZ

2izz


Resolution: 3.4→46.904 Å / SU ML: 0.67 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.86
RfactorNum. reflection% reflection
Rfree0.3601 1961 8.11 %
Rwork0.3291 --
obs0.3317 24194 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.4 Å2 / Biso mean: 76.6374 Å2 / Biso min: 33.54 Å2
Refinement stepCycle: final / Resolution: 3.4→46.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9211 0 0 0 9211
Num. residues----1317
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4001-3.48510.62481270.5361138187
3.4851-3.57930.48851380.4558152996
3.5793-3.68460.49181260.4648155397
3.6846-3.80340.43481590.3996157398
3.8034-3.93930.51831230.4595148593
3.9393-4.0970.42611340.3449155998
4.097-4.28330.2881400.30841614100
4.2833-4.50890.32211410.29351613100
4.5089-4.79120.33231490.2921605100
4.7912-5.16070.33261340.29561644100
5.1607-5.67920.35071470.31461620100
5.6792-6.49920.35981470.30541643100
6.4992-8.18120.24361400.26081669100
8.1812-46.90.27581560.2459174599
Refinement TLS params.Method: refined / Origin x: -7.2772 Å / Origin y: 26.959 Å / Origin z: -20.3521 Å
111213212223313233
T0.1677 Å2-0.0273 Å20.0896 Å2-0.4808 Å20.0624 Å2--0.2764 Å2
L0.7275 °20.0245 °2-0.0856 °2-1.1188 °2-0.2362 °2--1.6924 °2
S-0.0276 Å °0.3163 Å °0.01 Å °-0.0785 Å °0.0705 Å °0.0407 Å °0.5312 Å °-0.2289 Å °-0.0099 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 271
2X-RAY DIFFRACTION1allB3 - 271
3X-RAY DIFFRACTION1allC3 - 271
4X-RAY DIFFRACTION1allD1 - 273
5X-RAY DIFFRACTION1allE10 - 273

+
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