[English] 日本語
Yorodumi
- PDB-6xp3: Structure of human PYCR1 complexed with cyclopentanecarboxylic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xp3
TitleStructure of human PYCR1 complexed with cyclopentanecarboxylic acid
ComponentsPyrroline-5-carboxylate reductase 1, mitochondrial
KeywordsOXIDOREDUCTASE / AMINO-ACID BIOSYNTHESIS / PROLINE BIOSYNTHESIS
Function / homology
Function and homology information


pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / Glutamate and glutamine metabolism / proline biosynthetic process / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrial membrane potential / cellular response to oxidative stress / mitochondrial matrix / mitochondrion / identical protein binding
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
cyclopentanecarboxylic acid / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.93 Å
AuthorsTanner, J.J. / Bogner, A.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM065546 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: In crystallo screening for proline analog inhibitors of the proline cycle enzyme PYCR1.
Authors: Christensen, E.M. / Bogner, A.N. / Vandekeere, A. / Tam, G.S. / Patel, S.M. / Becker, D.F. / Fendt, S.M. / Tanner, J.J.
History
DepositionJul 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 13, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 18, 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 1, mitochondrial
B: Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,82811
Polymers170,2165
Non-polymers6136
Water7,945441
1
A: Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules

A: Pyrroline-5-carboxylate reductase 1, mitochondrial
B: Pyrroline-5-carboxylate reductase 1, mitochondrial
C: Pyrroline-5-carboxylate reductase 1, mitochondrial
D: Pyrroline-5-carboxylate reductase 1, mitochondrial
E: Pyrroline-5-carboxylate reductase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,65722
Polymers340,43210
Non-polymers1,22512
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area58850 Å2
ΔGint-635 kcal/mol
Surface area87390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.702, 178.533, 87.657
Angle α, β, γ (deg.)90.000, 106.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-545-

HOH

21A-556-

HOH

31E-515-

HOH

-
Components

#1: Protein
Pyrroline-5-carboxylate reductase 1, mitochondrial / P5CR 1


Mass: 34043.156 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PYCR1 / Production host: Escherichia coli (E. coli)
References: UniProt: P32322, pyrroline-5-carboxylate reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IQ0 / cyclopentanecarboxylic acid


Mass: 114.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 200 mM Li2SO4, 18% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 10 mM cyclopentanecarboxylic acid. Crystal was soaked in cryobuffer containing 20% ...Details: Reservoir contained 200 mM Li2SO4, 18% (w/v) PEG 3350, and 0.1 M HEPES at pH 7.5. Enzyme solution contained 10 mM cyclopentanecarboxylic acid. Crystal was soaked in cryobuffer containing 20% PEG 200, and 100 mM cyclopentanecarboxylic acid.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97625 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.93→47.18 Å / Num. obs: 116598 / % possible obs: 96.7 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Net I/σ(I): 11.9 / Num. measured all: 408772 / Scaling rejects: 448
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.93-1.963.50.5612016057890.770.350.6641.897.6
10.57-47.183.60.01726317350.9990.010.0236.396.8

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2IZZ

2izz


Resolution: 1.93→47.175 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 5709 4.94 %
Rwork0.1891 109862 -
obs0.1906 115571 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.82 Å2 / Biso mean: 34.9694 Å2 / Biso min: 9.33 Å2
Refinement stepCycle: final / Resolution: 1.93→47.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9842 0 36 441 10319
Biso mean--37.11 32.39 -
Num. residues----1382
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.93-1.95190.34851620.3178372397
1.9519-1.97490.3141980.2677377299
1.9749-1.9990.25922050.2281377899
1.999-2.02430.26142030.22343798100
2.0243-2.05090.3811750.3493365495
2.0509-2.0790.45461370.3939298378
2.079-2.10870.2632080.2279377099
2.1087-2.14020.23972100.18843832100
2.1402-2.17360.25111930.1959377399
2.1736-2.20930.22351770.2054381399
2.2093-2.24740.54271550.4526281474
2.2474-2.28820.33281720.2781338087
2.2882-2.33220.21581950.18633782100
2.3322-2.37980.18741910.1683839100
2.3798-2.43160.21172290.17233764100
2.4316-2.48820.20871870.1765377999
2.4882-2.55040.24321890.1744363395
2.5504-2.61930.19521970.16763818100
2.6193-2.69640.20971690.1912344591
2.6964-2.78340.20022250.17073780100
2.7834-2.88290.19091990.1737380399
2.8829-2.99830.25072160.18123808100
2.9983-3.13470.20942080.17023813100
3.1347-3.30.19181680.1796365795
3.3-3.50660.20281990.1772347791
3.5066-3.77730.18311900.1678343191
3.7773-4.15720.18411900.1529340889
4.1572-4.75830.15911800.13573853100
4.7583-5.9930.19151900.17193843100
5.993-47.1750.15661920.1529383998
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)
10.57260.13960.74530.16220.04122.50080.0447-0.11780.02160.0742-0.0406-0.04690.10050.15950.00420.1103-0.0019-0.02420.1932-0.01140.186725.9873173.587124.0881
21.13080.2463-0.87030.4443-0.10731.80790.0769-0.0320.0643-0.1074-0.0064-0.1323-0.25650.3719-0.05510.1556-0.0309-0.01070.2323-0.01790.203532.8233183.2942-5.9765
30.4418-0.2542-0.03291.1177-0.10271.7513-0.1341-0.1612-0.14160.2701-0.0040.03830.5440.00010.10690.36210.04950.04470.17310.02270.219610.2547139.694218.754
40.9327-0.5088-0.40351.0570.42052.004-0.02660.0469-0.1019-0.1870.0062-0.17820.29570.59620.00350.25890.10080.02360.27220.01490.226426.2158145.3316-7.7892
50.81770.2241-0.61481.34680.03751.49610.1805-0.29250.17210.3518-0.1040.0526-0.40650.1994-0.03920.2559-0.0562-0.00010.2054-0.03450.20820.0503200.695915.8143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and peptide)A0
2X-RAY DIFFRACTION2(chain 'B' and peptide)B0
3X-RAY DIFFRACTION3(chain 'C' and peptide)C0
4X-RAY DIFFRACTION4(chain 'D' and peptide)D0
5X-RAY DIFFRACTION5(chain 'E' and peptide)E0

+
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