[English] 日本語
Yorodumi
- PDB-8tdb: Structure of PYCR1 complexed with NADH and 1-hydroxyethane-1-sulfonate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tdb
TitleStructure of PYCR1 complexed with NADH and 1-hydroxyethane-1-sulfonate
ComponentsPyrroline-5-carboxylate reductase 1, mitochondrial
KeywordsOXIDOREDUCTASE/INHIBITOR / AMINO-ACID BIOSYNTHESIS / OXIDOREDUCTASE / PROLINE BIOSYNTHESIS / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / Glutamate and glutamine metabolism / : / 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
: / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsTanner, J.J. / Meeks, K.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132640 United States
CitationJournal: Protein Sci. / Year: 2024
Title: Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1).
Authors: Meeks, K.R. / Bogner, A.N. / Tanner, J.J.
History
DepositionJul 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
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)171,62115
Polymers167,6635
Non-polymers3,95810
Water3,675204
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)343,24130
Polymers335,32610
Non-polymers7,91620
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area69720 Å2
ΔGint-607 kcal/mol
Surface area84910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.730, 180.678, 88.011
Angle α, β, γ (deg.)90.00, 106.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-502-

HOH

-
Components

#1: Protein
Pyrroline-5-carboxylate reductase 1, mitochondrial / P5C reductase 1 / P5CR 1


Mass: 33532.574 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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GHO / (1R)-1-hydroxyethane-1-sulfonic acid


Mass: 126.132 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 0.01 M MgCl2, 0.1 M HEPES pH 7.5, and 24% Poly(acrylic acid sodium salt) 5,100. Enzyme solution contained 10 mM 1-hydroxyethane-1-sulfonate and 2 mM NADH. Crystal was ...Details: Reservoir contained 0.01 M MgCl2, 0.1 M HEPES pH 7.5, and 24% Poly(acrylic acid sodium salt) 5,100. Enzyme solution contained 10 mM 1-hydroxyethane-1-sulfonate and 2 mM NADH. Crystal was soaked in cryobuffer containing 20% PEG 200 and 50 mM 1-hydroxyethane-1-sulfonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→71.46 Å / Num. obs: 136358 / % possible obs: 98.1 % / Redundancy: 3.8 % / CC1/2: 0.976 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.075 / Rrim(I) all: 0.145 / Χ2: 1.01 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.35 Å / % possible obs: 99.6 % / Redundancy: 4 % / Rmerge(I) obs: 1.057 / Num. measured all: 18208 / Num. unique obs: 4548 / CC1/2: 0.584 / Rpim(I) all: 0.602 / Rrim(I) all: 1.22 / Χ2: 1.07 / Net I/σ(I) obs: 1.5

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4887refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→71.46 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 2709 1.99 %
Rwork0.211 --
obs0.2118 136358 92.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→71.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9623 0 255 204 10082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810091
X-RAY DIFFRACTIONf_angle_d0.96213806
X-RAY DIFFRACTIONf_dihedral_angle_d13.2333385
X-RAY DIFFRACTIONf_chiral_restr0.0481707
X-RAY DIFFRACTIONf_plane_restr0.0081759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.33511670.32977228X-RAY DIFFRACTION96
2.34-2.390.33921560.30447368X-RAY DIFFRACTION97
2.39-2.440.32931660.28737306X-RAY DIFFRACTION97
2.44-2.490.30781400.26427457X-RAY DIFFRACTION97
2.49-2.550.24271300.25737369X-RAY DIFFRACTION97
2.55-2.610.32641740.25447322X-RAY DIFFRACTION97
2.61-2.680.37431500.29037241X-RAY DIFFRACTION95
2.68-2.760.29451460.25947325X-RAY DIFFRACTION97
2.76-2.850.27221480.2277362X-RAY DIFFRACTION97
2.85-2.950.28221310.22987416X-RAY DIFFRACTION97
2.95-3.070.29661220.22916891X-RAY DIFFRACTION92
3.07-3.210.30761160.20977354X-RAY DIFFRACTION96
3.21-3.380.28141470.22947292X-RAY DIFFRACTION96
3.38-3.590.30611560.2346722X-RAY DIFFRACTION89
3.59-3.870.32331000.2454144X-RAY DIFFRACTION55
3.87-4.260.23361110.20696287X-RAY DIFFRACTION82
4.26-4.870.17071510.14217222X-RAY DIFFRACTION96
4.87-6.140.20111320.18217055X-RAY DIFFRACTION93
6.14-71.460.15291660.14787288X-RAY DIFFRACTION96
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)
10.75630.14430.24440.21940.00773.91590.0202-0.2771-0.030.0807-0.0519-0.06960.0790.34620.02680.21890.0116-0.0140.3810.00790.359626.2425173.988523.8256
21.49530.4486-1.37050.351-0.50053.00350.0636-0.0747-0.0286-0.0438-0.0517-0.1151-0.33030.39480.00040.3235-0.0174-0.01170.3346-0.03680.358532.6616183.0327-5.9415
30.4435-0.1858-0.50440.9029-0.56843.1306-0.1641-0.1549-0.1590.1707-0.0088-0.00420.58790.08810.16640.43880.06130.03220.28830.02230.348310.3936139.578218.6225
41.2183-0.4395-1.20710.62750.14682.5994-0.0574-0.0021-0.1229-0.1467-0.0891-0.11230.32110.43950.13040.3860.12080.02140.32130.03090.347126.2222144.8633-8.1846
50.6034-0.0436-0.65981.03410.8153.21240.0671-0.25220.07340.1146-0.02120.0329-0.29880.1824-0.04130.2272-0.0148-0.00860.27150.00670.32070.1333200.94615.7959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1peptide and chain A
2X-RAY DIFFRACTION2peptide and chain B
3X-RAY DIFFRACTION3peptide and chain C
4X-RAY DIFFRACTION4peptide and chain D
5X-RAY DIFFRACTION5peptide and chain E

+
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