[English] 日本語
Yorodumi
- PDB-5a4d: Crystal structure of the chloroplastic gamma-ketol reductase from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5a4d
TitleCrystal structure of the chloroplastic gamma-ketol reductase from Arabidopsis thaliana bound to 13KOTE and NADP
ComponentsPUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
KeywordsOXIDOREDUCTASE / GAMMA-KETOL REDUCTASE / ARABIDOPSIS THALIANA / CHLOROPLAST / 13KOTE
Function / homology
Function and homology information


chloroplast inner membrane / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / plant-type vacuole / chloroplast envelope / chloroplast thylakoid membrane / chloroplast / oxidoreductase activity / plasma membrane / cytosol
Similarity search - Function
Zinc-binding dehydrogenase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Zinc-binding dehydrogenase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(13-oxo-9(Z),11(E),15(Z)-octadecatrienoic acid) / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chloroplast envelope quinone oxidoreductase homolog
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.807 Å
AuthorsMas-y-mas, S. / Curien, G. / Giustini, C. / Rolland, N. / Ferrer, J.L. / Cobessi, D.
CitationJournal: Front Plant Sci / Year: 2017
Title: Crystal Structure of the Chloroplastic Oxoene Reductase ceQORH from Arabidopsis thaliana.
Authors: Mas Y Mas, S. / Curien, G. / Giustini, C. / Rolland, N. / Ferrer, J.L. / Cobessi, D.
History
DepositionJun 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3Aug 9, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
B: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
C: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
D: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
E: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
F: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
G: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
H: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,55022
Polymers275,8488
Non-polymers7,70214
Water0
1
A: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5173
Polymers34,4811
Non-polymers1,0362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2242
Polymers34,4811
Non-polymers7431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5173
Polymers34,4811
Non-polymers1,0362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5173
Polymers34,4811
Non-polymers1,0362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2242
Polymers34,4811
Non-polymers7431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5173
Polymers34,4811
Non-polymers1,0362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5173
Polymers34,4811
Non-polymers1,0362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5173
Polymers34,4811
Non-polymers1,0362
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.160, 128.600, 150.120
Angle α, β, γ (deg.)90.00, 97.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 6:101 OR RESSEQ 103:329 )
211CHAIN B AND (RESSEQ 6:101 OR RESSEQ 103:329 )
311CHAIN C AND (RESSEQ 6:101 OR RESSEQ 103:329 )
411CHAIN D AND (RESSEQ 6:101 OR RESSEQ 103:329 )
511CHAIN E AND (RESSEQ 6:78 OR RESSEQ 88:101 OR RESSEQ 103:120 OR RESSEQ 123:329 )
611CHAIN F AND (RESSEQ 6:101 OR RESSEQ 103:329 )
711CHAIN G AND (RESSEQ 6:101 OR RESSEQ 103:329 )
811CHAIN H AND (RESSEQ 6:101 OR RESSEQ 103:329 )

NCS oper:
IDCodeMatrixVector
1given(0.9959, 0.007356, 0.0905), (0.007143, -1, 0.002678), (0.09052, -0.002021, -0.9959)-6.626, 5.462, 142.5
2given(-0.9994, -0.03351, -0.009692), (-0.0223, 0.4, 0.9162), (-0.02683, 0.9159, -0.4005)128.7, -64.3, 102.9
3given(-0.9956, 0.03462, -0.08656), (0.06518, -0.4053, -0.9119), (-0.06665, -0.9135, 0.4013)134, 68.28, 51.65
4given(0.5627, -0.01612, -0.8265), (-0.01981, 0.9993, -0.03298), (0.8264, 0.03493, 0.562)49.76, -16.76, 40.42
5given(0.6948, 0.01217, -0.7191), (0.02341, -0.9997, 0.005706), (-0.7188, -0.0208, -0.6949)43.92, 22.67, 104.4
6given(-0.6268, -0.09294, 0.7736), (0.6907, 0.3932, 0.6069), (-0.3606, 0.9147, -0.1823)82.42, -33.57, 69.19
7given(-0.6609, 0.08553, 0.7456), (-0.7119, -0.3859, -0.5868), (0.2376, -0.9185, 0.316)80.28, 39.93, 82.43

-
Components

#1: Protein
PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC / GAMMA-KETOL REDUCTASE


Mass: 34481.008 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Organelle: CHLOROPLAST / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9SV68, Oxidoreductases
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-KZH / (13-oxo-9(Z),11(E),15(Z)-octadecatrienoic acid)


Mass: 292.413 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H28O3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.68 % / Description: NONE
Crystal growDetails: 0,2 M SODIUM CHLORIDE, 0,1 M TRIS PH 8,5, 15,5 % PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.040051
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DOUBLE SI 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.040051 Å / Relative weight: 1
ReflectionResolution: 2.81→49.58 Å / Num. obs: 75277 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 57.86 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.67
Reflection shellResolution: 2.81→2.98 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.19 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.807→49.581 Å / SU ML: 0.38 / σ(F): 1.36 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 3786 5 %
Rwork0.1882 --
obs0.1901 75172 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.36 Å2
Refinement stepCycle: LAST / Resolution: 2.807→49.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19052 0 448 0 19500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819996
X-RAY DIFFRACTIONf_angle_d1.21427244
X-RAY DIFFRACTIONf_dihedral_angle_d13.8437349
X-RAY DIFFRACTIONf_chiral_restr0.0433187
X-RAY DIFFRACTIONf_plane_restr0.0053441
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2356X-RAY DIFFRACTIONPOSITIONAL
12B2356X-RAY DIFFRACTIONPOSITIONAL0.044
13C2369X-RAY DIFFRACTIONPOSITIONAL0.048
14D2362X-RAY DIFFRACTIONPOSITIONAL0.051
15E2281X-RAY DIFFRACTIONPOSITIONAL0.05
16F2367X-RAY DIFFRACTIONPOSITIONAL0.049
17G2357X-RAY DIFFRACTIONPOSITIONAL0.052
18H2379X-RAY DIFFRACTIONPOSITIONAL0.049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8071-2.84260.38871290.32462506X-RAY DIFFRACTION94
2.8426-2.880.31791340.29352638X-RAY DIFFRACTION100
2.88-2.91950.34341390.27862657X-RAY DIFFRACTION100
2.9195-2.96120.3451460.28232629X-RAY DIFFRACTION100
2.9612-3.00540.34161360.26582633X-RAY DIFFRACTION100
3.0054-3.05230.31491380.25962681X-RAY DIFFRACTION100
3.0523-3.10230.31471280.25862621X-RAY DIFFRACTION100
3.1023-3.15580.29211470.25372657X-RAY DIFFRACTION100
3.1558-3.21320.3021470.23492639X-RAY DIFFRACTION100
3.2132-3.2750.2721310.24532655X-RAY DIFFRACTION100
3.275-3.34180.31191370.2382644X-RAY DIFFRACTION100
3.3418-3.41450.3051290.22282697X-RAY DIFFRACTION100
3.4145-3.49390.25181240.21212638X-RAY DIFFRACTION100
3.4939-3.58120.22691490.19752662X-RAY DIFFRACTION100
3.5812-3.6780.25531290.1992642X-RAY DIFFRACTION100
3.678-3.78620.22651250.18872649X-RAY DIFFRACTION100
3.7862-3.90840.24171330.182709X-RAY DIFFRACTION100
3.9084-4.0480.21771390.17962603X-RAY DIFFRACTION100
4.048-4.210.2131310.15982685X-RAY DIFFRACTION100
4.21-4.40150.16681480.14822645X-RAY DIFFRACTION100
4.4015-4.63340.17521440.14272659X-RAY DIFFRACTION100
4.6334-4.92350.17731580.1462656X-RAY DIFFRACTION100
4.9235-5.30320.19171530.13972620X-RAY DIFFRACTION100
5.3032-5.83610.16931520.17012695X-RAY DIFFRACTION100
5.8361-6.67890.18791600.1672640X-RAY DIFFRACTION100
6.6789-8.4080.17421560.15662669X-RAY DIFFRACTION100
8.408-49.5890.19181440.16572557X-RAY DIFFRACTION93
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)
11.7468-0.09310.72642.8821-0.86552.74730.0469-0.0560.02050.1020.0173-0.2230.12420.193-0.0610.1995-0.02340.04170.33340.01580.250181.4474-0.73754.9494
21.75280.5891-0.12862.9364-0.51742.67870.2494-0.6491-0.13351.3357-0.2544-0.51520.4-0.03640.00761.2305-0.092-0.25680.7093-0.00350.459579.81977.160894.9004
31.44650.32880.59094.3836-0.44033.30610.4417-0.2950.07340.9149-0.20951.07750.5813-0.3455-0.21330.813-0.27860.24860.56860.09520.624347.1512-16.82877.865
42.0775-0.1976-0.34642.348-0.42423.06230.0474-0.30750.06550.4657-0.13420.5237-0.2889-0.35730.07780.3999-0.04440.13230.3984-0.15740.533947.612823.062768.8285
52.4786-1.3418-1.27033.97540.26461.82090.73680.9158-0.3119-2.3865-1.39281.4372-0.5241-0.43830.39261.53130.5627-0.82990.874-0.49820.871929.832415.0406-17.9651
61.5567-1.18170.59412.8695-1.0942.06250.00420.15770.0847-0.1306-0.1324-0.2621-0.28310.15160.11390.2854-0.09970.01280.35580.06090.252561.066524.89727.2086
73.9647-0.01260.95392.20330.02641.96730.1281-0.0910.15530.2197-0.2280.35660.0185-0.24940.08280.2564-0.00460.13760.2839-0.10550.437228.52350.008121.7564
82.1512-0.6263-0.39556.3756-1.94283.27910.2079-0.4181-0.08870.32860.11761.9724-0.0865-0.4107-0.22470.3718-0.07560.16210.5177-0.06011.024421.683541.026316.1008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 329)
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 6 THROUGH 329)
3X-RAY DIFFRACTION3CHAIN 'C' AND (RESID 4 THROUGH 329)
4X-RAY DIFFRACTION4CHAIN 'D' AND (RESID 3 THROUGH 329)
5X-RAY DIFFRACTION5CHAIN 'E' AND (RESID 6 THROUGH 329)
6X-RAY DIFFRACTION6CHAIN 'F' AND (RESID 3 THROUGH 329)
7X-RAY DIFFRACTION7CHAIN 'G' AND (RESID 3 THROUGH 329)
8X-RAY DIFFRACTION8CHAIN 'H' AND (RESID 4 THROUGH 329)

+
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