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- PDB-6cin: Crystal structure of pyruvate:ferredoxin oxidoreductase from Moor... -

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Basic information

Entry
Database: PDB / ID: 6cin
TitleCrystal structure of pyruvate:ferredoxin oxidoreductase from Moorella thermoacetica
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
IRON/SULFUR CLUSTER / THIAMINE DIPHOSPHATE / Pyruvate:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
D: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
E: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
F: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)774,23843
Polymers764,5396
Non-polymers9,70037
Water7,909439
1
A: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
B: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,14415
Polymers254,8462
Non-polymers3,29713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21240 Å2
ΔGint-291 kcal/mol
Surface area77200 Å2
MethodPISA
2
C: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
D: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,04714
Polymers254,8462
Non-polymers3,20112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21400 Å2
ΔGint-302 kcal/mol
Surface area75520 Å2
MethodPISA
3
E: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
F: PYRUVATE-FERREDOXIN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,04714
Polymers254,8462
Non-polymers3,20112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21240 Å2
ΔGint-295 kcal/mol
Surface area76270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)340.611, 106.634, 239.079
Angle α, β, γ (deg.)90.00, 109.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

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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

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Non-polymers , 5 types, 476 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-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#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.: 439 / 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: 54.12 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 247841 / % possible obs: 98.5 % / Redundancy: 3.3 % / Rsym value: 0.075 / Net I/σ(I): 9.4
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 11915 / Rsym value: 0.582

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C42

2c42


Resolution: 2.6→88.952 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 12231 5 %
Rwork0.1949 --
obs0.1965 244551 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→88.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53090 0 341 439 53870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00354649
X-RAY DIFFRACTIONf_angle_d0.56174271
X-RAY DIFFRACTIONf_dihedral_angle_d16.06732705
X-RAY DIFFRACTIONf_chiral_restr0.0438201
X-RAY DIFFRACTIONf_plane_restr0.0049572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.62950.31863920.30637458X-RAY DIFFRACTION96
2.6295-2.66050.32594030.29467673X-RAY DIFFRACTION97
2.6605-2.69290.34364000.29277584X-RAY DIFFRACTION98
2.6929-2.7270.32824030.27557688X-RAY DIFFRACTION98
2.727-2.76290.31384050.26957663X-RAY DIFFRACTION98
2.7629-2.80080.32364040.277678X-RAY DIFFRACTION97
2.8008-2.84080.30613990.2677557X-RAY DIFFRACTION97
2.8408-2.88320.30564120.27567826X-RAY DIFFRACTION99
2.8832-2.92820.31174050.26627703X-RAY DIFFRACTION99
2.9282-2.97620.29214110.25177799X-RAY DIFFRACTION99
2.9762-3.02760.28834100.25227782X-RAY DIFFRACTION99
3.0276-3.08260.29124110.25097780X-RAY DIFFRACTION99
3.0826-3.14190.26014090.23447758X-RAY DIFFRACTION99
3.1419-3.20610.25654090.22817764X-RAY DIFFRACTION99
3.2061-3.27580.26564070.22677745X-RAY DIFFRACTION99
3.2758-3.3520.26054080.22047734X-RAY DIFFRACTION98
3.352-3.43580.26724060.22327730X-RAY DIFFRACTION98
3.4358-3.52870.23764000.21697582X-RAY DIFFRACTION97
3.5287-3.63250.2464130.21137843X-RAY DIFFRACTION99
3.6325-3.74980.22814100.1957792X-RAY DIFFRACTION100
3.7498-3.88380.20864140.18157877X-RAY DIFFRACTION100
3.8838-4.03930.19364100.16347786X-RAY DIFFRACTION99
4.0393-4.22310.19524120.16117820X-RAY DIFFRACTION99
4.2231-4.44580.17984110.15587805X-RAY DIFFRACTION99
4.4458-4.72430.18374030.15177637X-RAY DIFFRACTION97
4.7243-5.08910.1814170.15167946X-RAY DIFFRACTION99
5.0891-5.60110.21284110.17087791X-RAY DIFFRACTION99
5.6011-6.41140.21194120.17877821X-RAY DIFFRACTION98
6.4114-8.07690.18934120.1687834X-RAY DIFFRACTION98
8.0769-89.00370.1894120.16747864X-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)
11.79070.0486-0.22540.7440.15380.9615-0.0763-0.1280.0670.00380.03010.0313-0.1463-0.17090.05010.35240.08150.04270.53220.02850.3084-34.598-71.55761.1199
21.9815-0.2311-0.30410.7709-0.11280.8303-0.1182-0.05080.0683-0.00420.0419-0.1077-0.09430.11570.07140.3212-0.00710.04640.4119-0.00610.2516-5.1044-71.392752.223
31.7119-0.3574-0.22150.63870.10112.00060.00680.0684-0.1219-0.11720.06460.0270.0963-0.0987-0.07080.34890.08860.00180.53110.06660.3412-79.9414-80.919870.3758
40.679-0.10690.05220.89770.01471.18480.040.2177-0.2544-0.11980.00560.3930.2231-0.8316-0.08780.4402-0.0295-0.06331.14340.05090.6149-109.8582-88.316470.2733
51.683-0.1627-0.09540.99380.2251.5774-0.1977-0.5124-0.2850.24440.18780.03750.19390.1349-0.02130.36580.01550.05540.35770.08440.303-130.2818-27.745441.7442
61.2319-0.08190.42561.1470.27081.4268-0.1231-0.2747-0.31620.26120.3987-0.37110.3730.7591-0.16060.48980.2047-0.07820.8331-0.07950.5614-100.6264-35.886440.6413
72.16490.0133-0.40812.3778-1.07343.2863-0.07820.30960.2324-0.29950.04120.1463-0.1542-0.38920.02690.50860.0967-0.03220.79620.08330.4167-61.4083-61.873638.7143
80.82110.4372-0.12981.54880.30963.93320.0265-0.52270.25240.1043-0.1456-0.0767-0.06230.52260.09720.3999-0.06080.03310.9338-0.10510.495322.0848-64.397475.2065
91.94741.0266-0.50961.8180.12180.32820.3778-0.1504-0.7619-0.2931-0.6225-0.46830.71430.7036-0.17390.78340.36570.02910.73930.17050.7403-53.9935-105.996370.7121
102.7497-0.3835-0.09441.36690.84521.01070.1448-0.06260.12660.0833-0.1280.5629-0.3256-1.04220.05870.54180.37250.11451.71770.11250.8928-134.8464-66.822785.3869
111.3146-0.60610.5711.2364-0.12960.71840.1411-0.1702-0.69850.0779-0.37140.32220.6135-0.4664-0.23720.7951-0.22450.24980.4660.03850.8527-156.9947-52.0839.4212
122.80280.2586-0.22781.7837-1.8281.9251-0.00160.24850.2241-0.10420.1083-0.6732-0.04870.94960.12630.5126-0.27880.15181.3628-0.38611.0019-75.5737-13.18127.4459
131.1984-0.2160.11390.60320.08751.78310.02340.23910.6844-0.1046-0.106-0.0028-0.699-0.51020.12110.92250.21210.02110.75440.14860.771-28.3579-37.935734.115
140.9724-0.03640.4430.7042-0.10071.24-0.0434-0.23690.52430.0839-0.0727-0.0938-0.59390.08150.09190.91490.0408-0.01350.7767-0.17730.7287-10.8903-40.272482.1435
151.2749-0.249-0.25561.24390.42221.33840.031-0.3677-0.35110.2312-0.051-0.05690.6704-0.10130.01411.0053-0.0688-0.03060.77770.21490.7523-85.3719-116.553294.6269
161.5387-0.2777-0.15680.72210.29921.65920.0008-0.46550.01760.1317-0.02530.1545-0.0778-0.58330.01720.51350.18770.03811.00840.06320.4688-100.3916-69.722108.2329
170.61970.06940.21142.0092-0.18531.23510.21010.2528-0.7337-0.20350.19510.57940.49040.1107-0.04970.86030.0264-0.17260.3743-0.05381.0618-126.3423-60.899814.0579
181.4278-0.0628-0.09841.42710.17031.3399-0.01190.58360.1662-0.54410.1021-0.3319-0.3190.6920.08440.6944-0.25760.12850.83370.0220.4548-110.0515-13.75764.668
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 3:414
5X-RAY DIFFRACTION5chain 'E' and resi 2:414
6X-RAY DIFFRACTION6chain 'F' and resi 3:414
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

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