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- PDB-6ciq: Pyruvate:ferredoxin oxidoreductase from Moorella thermoacetica wi... -

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Basic information

Entry
Database: PDB / ID: 6ciq
TitlePyruvate:ferredoxin oxidoreductase from Moorella thermoacetica with coenzyme A bound
ComponentsPYRUVATE-FERREDOXIN OXIDOREDUCTASEPyruvate synthase
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 / 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/ferredoxin oxidoreductase, thiamine diP-bdg ...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
COENZYME A / IRON/SULFUR CLUSTER / THIAMINE DIPHOSPHATE / Pyruvate:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.302 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)389,08621
Polymers382,2693
Non-polymers6,81618
Water52229
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A: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
hetero molecules

A: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,39014
Polymers254,8462
Non-polymers4,54412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area22930 Å2
ΔGint-262 kcal/mol
Surface area77580 Å2
MethodPISA
2
B: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
C: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,39014
Polymers254,8462
Non-polymers4,54412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23380 Å2
ΔGint-258 kcal/mol
Surface area74770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)337.710, 106.993, 120.465
Angle α, β, γ (deg.)90.00, 109.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein PYRUVATE-FERREDOXIN OXIDOREDUCTASE / Pyruvate synthase


Mass: 127423.125 Da / Num. of mol.: 3
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

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Non-polymers , 5 types, 47 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 13% (w/v) PEG 6000, 0.06 M sodium cacodylate pH 6.5

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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: 3.3→100 Å / Num. obs: 58817 / % possible obs: 97.3 % / Redundancy: 3.5 % / Rsym value: 0.159 / Net I/σ(I): 3.5
Reflection shellResolution: 3.3→3.36 Å / Num. unique obs: 2499 / Rsym value: 0.454

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Processing

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

6cin


Resolution: 3.302→80.252 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.5
RfactorNum. reflection% reflection
Rfree0.2227 2951 5.02 %
Rwork0.1838 --
obs0.1858 58800 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.302→80.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26589 0 297 29 26915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327509
X-RAY DIFFRACTIONf_angle_d0.56637420
X-RAY DIFFRACTIONf_dihedral_angle_d15.00116415
X-RAY DIFFRACTIONf_chiral_restr0.0434132
X-RAY DIFFRACTIONf_plane_restr0.0044808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3024-3.35650.3279980.28511882X-RAY DIFFRACTION68
3.3565-3.41440.27281270.2662533X-RAY DIFFRACTION93
3.4144-3.47650.26911490.25232608X-RAY DIFFRACTION95
3.4765-3.54340.25451350.22942667X-RAY DIFFRACTION97
3.5434-3.61570.27721420.22852679X-RAY DIFFRACTION98
3.6157-3.69430.26351440.21772706X-RAY DIFFRACTION98
3.6943-3.78030.27031370.21732713X-RAY DIFFRACTION99
3.7803-3.87480.27551540.21692678X-RAY DIFFRACTION99
3.8748-3.97960.22491380.19642697X-RAY DIFFRACTION98
3.9796-4.09660.20721320.18892656X-RAY DIFFRACTION97
4.0966-4.22890.22311420.18332698X-RAY DIFFRACTION98
4.2289-4.380.22441480.17322713X-RAY DIFFRACTION99
4.38-4.55540.23011450.17122731X-RAY DIFFRACTION99
4.5554-4.76270.23481440.16862726X-RAY DIFFRACTION99
4.7627-5.01370.19921450.15922739X-RAY DIFFRACTION99
5.0137-5.32780.20451430.16442695X-RAY DIFFRACTION98
5.3278-5.7390.22371370.17062716X-RAY DIFFRACTION98
5.739-6.31640.21611490.18012742X-RAY DIFFRACTION99
6.3164-7.22990.20051480.17312734X-RAY DIFFRACTION99
7.2299-9.10680.17881430.14692721X-RAY DIFFRACTION97
9.1068-80.27530.18521510.15662815X-RAY DIFFRACTION98
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)
11.6501-0.03460.02880.6709-0.06420.45660.0209-0.23670.06940.0106-0.06660.0405-0.0489-0.20510.06250.29260.02670.02560.7541-0.00650.3706-35.3192-71.035660.8272
21.6434-0.2833-0.08781.54710.60051.82490.05440.13920.0201-0.12980.0589-0.1241-0.0076-0.0244-0.13140.26890.0140.03270.66460.04610.3549-80.6767-80.412870.2685
31.2189-0.3931-0.42790.96330.34811.2085-0.020.1744-0.2333-0.0860.04220.44210.286-0.8925-0.04060.3947-0.1286-0.07011.31790.08710.6359-110.7199-88.004771.1372
41.09810.27650.43882.2207-0.93893.15140.06120.61740.1848-0.1438-0.03570.1865-0.2559-0.3802-0.04050.37370.0796-0.04351.32830.09380.5081-61.396-63.015637.2553
52.64540.47410.41443.6471-1.36622.83880.52420.3205-0.9354-0.025-0.3704-0.96780.63290.4751-0.10870.58390.183-0.210.6422-0.06190.9989-55.0634-105.309471.3782
61.99260.88370.4521.5787-0.28181.40010.1132-0.79150.27540.5992-0.02431.0976-0.3783-1.0281-0.08010.77820.18880.22712.32180.09231.3882-133.3249-67.212988.5544
71.28470.33290.54061.10850.03211.5841-0.17690.49370.8981-0.0952-0.08180.1219-0.4823-0.15880.12680.51320.0391-0.05840.76390.31871.015-29.2155-38.47532.9337
81.412-0.3992-0.60251.74170.65791.5906-0.2968-0.4046-0.48660.64090.3904-0.00580.99050.2053-0.13531.0070.053-0.03090.73080.2850.624-85.2074-114.365296.6407
91.3927-0.7366-0.22211.4350.32061.6819-0.0649-0.65940.21420.17970.09550.0172-0.0159-0.5069-0.03820.37670.11840.00171.3374-0.04120.4666-100.848-67.5656107.8342
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 'A' and resi 415:631
5X-RAY DIFFRACTION5chain 'B' and resi 415:631
6X-RAY DIFFRACTION6chain 'C' and resi 415:631
7X-RAY DIFFRACTION7chain 'A' and resi 632:1170
8X-RAY DIFFRACTION8chain 'B' and resi 632:1170
9X-RAY DIFFRACTION9chain 'C' and resi 632:1170

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