[English] 日本語
Yorodumi
- PDB-6cip: Pyruvate:ferredoxin oxidoreductase from Moorella thermoacetica wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cip
TitlePyruvate:ferredoxin oxidoreductase from Moorella thermoacetica with acetyl-TPP bound
ComponentsPYRUVATE-FERREDOXIN OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / pyruvate:ferredoxin oxidoreductase / thiamine pyrophosphate / coenzyme A / gated electron transfer
Function / homology
Function and homology information


pyruvate synthase / pyruvate synthase activity / thiamine pyrophosphate binding / electron transport chain / 4 iron, 4 sulfur cluster binding / response to oxidative stress / iron ion binding
Similarity search - Function
Pyruvate-flavodoxin oxidoreductase / Pyruvate-flavodoxin oxidoreductase, EKR domain / Pyruvate-flavodoxin oxidoreductase, EKR domain superfamily / Domain of unknown function / 4Fe-4S double cluster binding domain / Domain of unknown function / Pyruvate:ferredoxin oxidoreductase, core domain II / Pyruvate:ferredoxin oxidoreductase core domain II / Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain / : ...Pyruvate-flavodoxin oxidoreductase / Pyruvate-flavodoxin oxidoreductase, EKR domain / Pyruvate-flavodoxin oxidoreductase, EKR domain superfamily / Domain of unknown function / 4Fe-4S double cluster binding domain / Domain of unknown function / Pyruvate:ferredoxin oxidoreductase, core domain II / Pyruvate:ferredoxin oxidoreductase core domain II / Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain / : / Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg / Pyruvate-flavodoxin oxidoreductase, central domain / Pyruvate/ketoisovalerate oxidoreductase, catalytic domain / Pyruvate ferredoxin/flavodoxin oxidoreductase / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
2-ACETYL-THIAMINE DIPHOSPHATE / IRON/SULFUR CLUSTER / Pyruvate:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.189 Å
AuthorsChen, P.Y.-T. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM39451 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Binding site for coenzyme A revealed in the structure of pyruvate:ferredoxin oxidoreductase fromMoorella thermoacetica.
Authors: Chen, P.Y. / Aman, H. / Can, M. / Ragsdale, S.W. / Drennan, C.L.
History
DepositionFeb 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 3, 2018Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
B: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
C: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
D: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
E: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
F: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)774,49143
Polymers764,5396
Non-polymers9,95237
Water48627
1
A: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
B: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,22815
Polymers254,8462
Non-polymers3,38113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21530 Å2
ΔGint-286 kcal/mol
Surface area76150 Å2
MethodPISA
2
C: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
D: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,13214
Polymers254,8462
Non-polymers3,28512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21430 Å2
ΔGint-277 kcal/mol
Surface area75010 Å2
MethodPISA
3
E: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
F: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,13214
Polymers254,8462
Non-polymers3,28512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21410 Å2
ΔGint-278 kcal/mol
Surface area75150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)342.005, 108.263, 240.437
Angle α, β, γ (deg.)90.00, 109.32, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
PYRUVATE-FERREDOXIN OXIDOREDUCTASE


Mass: 127423.125 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (strain ATCC 39073 / JCM 9320) (bacteria)
Strain: ATCC 39073 / JCM 9320 / Gene: Moth_0064 / Production host: Moorella thermoacetica (bacteria)
References: UniProt: Q2RMD6, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With an iron-sulfur protein as acceptor

-
Non-polymers , 5 types, 64 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-HTL / 2-ACETYL-THIAMINE DIPHOSPHATE / 2-ACETYL-3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-4-METHYL-5-(4,6,6-TRIHYDROXY-3,5-DIOXA-4,6-DIPHOSPHAHEX-1-YL)THIAZO LIUM INNER SALT P,P'-DIOXIDE


Mass: 467.351 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H21N4O8P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 15-16% (w/v) PEG 4000, 0.21 M (NH4)2SO4 and 0.10 M MES pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.189→100 Å / Num. obs: 132748 / % possible obs: 97.2 % / Redundancy: 3.2 % / Rsym value: 0.092 / Net I/σ(I): 3.3
Reflection shellResolution: 3.19→3.26 Å / Num. unique obs: 5773 / Rsym value: 0.58

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CIN

6cin


Resolution: 3.189→97.448 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 6633 5 %
Rwork0.1874 --
obs0.1892 132694 95.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.189→97.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52606 0 359 27 52992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00354188
X-RAY DIFFRACTIONf_angle_d0.5573838
X-RAY DIFFRACTIONf_dihedral_angle_d20.01419321
X-RAY DIFFRACTIONf_chiral_restr0.0628228
X-RAY DIFFRACTIONf_plane_restr0.0049554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1885-3.22470.38751270.36362468X-RAY DIFFRACTION57
3.2247-3.26270.33541940.33673809X-RAY DIFFRACTION86
3.2627-3.30250.38382140.32073844X-RAY DIFFRACTION89
3.3025-3.34430.33662060.30053879X-RAY DIFFRACTION89
3.3443-3.38830.29382110.28144203X-RAY DIFFRACTION96
3.3883-3.43470.29022180.27194264X-RAY DIFFRACTION98
3.4347-3.48380.33272370.26764313X-RAY DIFFRACTION99
3.4838-3.53580.29632260.25434307X-RAY DIFFRACTION99
3.5358-3.5910.28392370.24384338X-RAY DIFFRACTION99
3.591-3.64990.26352110.23814323X-RAY DIFFRACTION99
3.6499-3.71280.28512290.23944359X-RAY DIFFRACTION99
3.7128-3.78040.27482290.22824231X-RAY DIFFRACTION98
3.7804-3.85310.2662340.21964341X-RAY DIFFRACTION98
3.8531-3.93170.26242220.21574268X-RAY DIFFRACTION98
3.9317-4.01720.23792280.19874273X-RAY DIFFRACTION98
4.0172-4.11070.22322080.19364188X-RAY DIFFRACTION96
4.1107-4.21350.2342360.17884317X-RAY DIFFRACTION98
4.2135-4.32740.20012310.17394397X-RAY DIFFRACTION99
4.3274-4.45470.20762330.16374348X-RAY DIFFRACTION99
4.4547-4.59850.1952140.15954330X-RAY DIFFRACTION99
4.5985-4.76290.19792300.15514348X-RAY DIFFRACTION99
4.7629-4.95350.1732310.15134338X-RAY DIFFRACTION98
4.9535-5.1790.18692260.15824322X-RAY DIFFRACTION98
5.179-5.4520.22012290.1644222X-RAY DIFFRACTION96
5.452-5.79360.19822320.16254363X-RAY DIFFRACTION99
5.7936-6.24080.20492280.16624362X-RAY DIFFRACTION99
6.2408-6.86870.20852270.15824407X-RAY DIFFRACTION99
6.8687-7.86220.18122360.15114362X-RAY DIFFRACTION98
7.8622-9.90410.14942300.12984397X-RAY DIFFRACTION98
9.9041-97.49340.21952190.17354140X-RAY DIFFRACTION90
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)
12.4727-0.0417-0.07250.8490.04430.971-0.1243-0.17430.17840.0244-0.05630.02350.0445-0.0660.19990.63750.03760.01550.9655-0.00140.6608-34.7508-68.033661.5552
22.7043-0.25890.00471.0150.02080.5445-0.10310.19470.2684-0.0358-0.0475-0.12470.03950.01820.15180.6005-0.01290.01830.88120.03290.6355-5.0189-67.763852.5403
32.5426-0.2906-0.43211.16770.29521.7101-0.1320.133-0.1597-0.22550.0895-0.04290.0816-0.20040.05770.583-0.05340.01030.7747-0.00840.5271-80.3605-77.268470.867
41.8187-0.2145-0.08961.3151-0.19251.44-0.11550.4313-0.3998-0.26770.12860.38650.2665-0.9188-0.01960.6738-0.2603-0.06931.3907-0.03980.7298-110.5854-84.616570.9195
52.0980.2527-0.24561.2233-0.12771.8742-0.1124-0.4613-0.15460.19820.10850.07740.11190.16380.00410.66370.11470.0430.52980.02520.5332-130.5412-23.006842.2257
61.582-0.05590.00191.00180.37381.9279-0.1692-0.5182-0.3250.30060.3316-0.39560.25591.0591-0.14150.65840.2805-0.09411.14980.00430.6865-100.5322-30.86941.2411
72.04670.5810.43722.0403-0.60342.1531-0.05090.42260.5196-0.23850.09260.1318-0.0138-0.4019-0.04850.60310.0473-0.04061.11120.13850.6002-61.4663-58.916638.5493
81.52130.09940.40151.36390.52151.94920.1293-0.74430.51430.1122-0.1664-0.08010.04030.48330.00280.5509-0.07880.02271.3966-0.1750.730422.1524-60.683375.7663
91.6492-0.07590.23842.3174-0.51041.8609-0.0931-0.2086-0.8474-0.2677-0.2389-0.19670.57910.4170.28570.90390.10260.26720.73660.0891.1343-54.4803-102.820270.9917
102.1897-0.25140.19351.2990.61682.56460.1008-0.00410.01720.06250.05110.4604-0.3366-1.5557-0.18370.72430.24560.03732.03140.18220.9504-135.2096-62.881886.5276
111.306-0.3898-0.02192.24080.52491.4827-0.1106-0.0983-0.82890.1247-0.34240.39850.5053-0.28360.35491.0264-0.09370.31360.6638-0.00981.2586-156.7462-48.156340.6741
122.221-0.03390.31671.4963-0.60052.1556-0.09270.03040.3325-0.14960.219-0.5268-0.17950.956-0.11060.7555-0.23510.01931.741-0.31381.0324-75.7227-8.509626.7078
131.8077-0.08210.43861.0074-0.07962.2215-0.14990.39291.0094-0.1184-0.1684-0.0939-0.6187-0.23040.30480.77470.1206-0.09850.9890.29651.1751-28.9138-35.007734.4597
141.2162-0.22950.57781.14490.00661.5223-0.2971-0.6760.94760.27320.0123-0.2517-0.46510.14020.24420.81550.0284-0.2381.2716-0.5211.332-10.985-36.914982.3277
151.5079-0.3102-0.02051.54180.5851.0316-0.1825-0.3979-0.63590.09070.02390.00270.787-0.17470.12881.0445-0.13050.12790.9460.28461.0105-86.1115-112.620394.9363
162.0131-0.1934-0.30791.31050.38051.3274-0.1049-1.06690.16690.15240.11160.05370.0252-0.3719-0.02490.53750.1626-0.06681.6069-0.06340.5627-100.9223-65.5868108.3627
171.08210.4670.29131.4838-0.28111.082-0.0470.2595-0.4599-0.09270.01770.12050.55820.272-0.16851.04910.21030.10090.337-0.11631.0393-126.1749-56.440215.4564
182.0569-0.2523-0.30522.0191-0.2531.70710.04480.28970.1598-0.32410.0307-0.2703-0.27210.7706-0.05940.6107-0.12180.03930.7956-0.02590.4713-110.1665-9.35015.2456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and resi 2:414
2X-RAY DIFFRACTION2chain 'B' and resi 2:414
3X-RAY DIFFRACTION3chain 'C' and resi 2:414
4X-RAY DIFFRACTION4chain 'D' and resi 2:414
5X-RAY DIFFRACTION5chain 'E' and resi 2:414
6X-RAY DIFFRACTION6chain 'F' and resi 2:414
7X-RAY DIFFRACTION7chain 'A' and resi 415:631
8X-RAY DIFFRACTION8chain 'B' and resi 415:631
9X-RAY DIFFRACTION9chain 'C' and resi 415:631
10X-RAY DIFFRACTION10chain 'D' and resi 415:631
11X-RAY DIFFRACTION11chain 'E' and resi 415:631
12X-RAY DIFFRACTION12chain 'F' and resi 415:631
13X-RAY DIFFRACTION13chain 'A' and resi 632:1170
14X-RAY DIFFRACTION14chain 'B' and resi 632:1170
15X-RAY DIFFRACTION15chain 'C' and resi 632:1170
16X-RAY DIFFRACTION16chain 'D' and resi 632:1170
17X-RAY DIFFRACTION17chain 'E' and resi 632:1170
18X-RAY DIFFRACTION18chain 'F' and resi 632:1170

+
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