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- PDB-7o1t: Fe(CO)2CNCl species bound [HydE from T. Maritima -

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Basic information

Entry
Database: PDB / ID: 7o1t
TitleFe(CO)2CNCl species bound [HydE from T. Maritima
Components[FeFe] hydrogenase maturase subunit HydE
KeywordsMETAL BINDING PROTEIN / Radical SAM protein / Hydrogenase maturase / metalloprotein
Function / homology
Function and homology information


water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / organonitrogen compound biosynthetic process / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity ...water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / organonitrogen compound biosynthetic process / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity / oxidoreductase activity / metal ion binding
Similarity search - Function
Biotin and Thiamin Synthesis associated domain / [FeFe]-hydrogenase maturation HydE, radical SAM / HydE/PylB-like / Biotin and thiamin synthesis-associated domain / Biotin and Thiamin Synthesis associated domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
S-adenosyl-L-cysteine / CARBON MONOXIDE / CYANIDE ION / CYSTEINE / : / IODIDE ION / PYRUVIC ACID / IRON/SULFUR CLUSTER / [FeFe] hydrogenase maturase subunit HydE
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRohac, R. / Martin, L. / Liu, L. / Basu, D. / Tao, L. / Britt, R.D. / Rauchfuss, T. / Nicolet, Y.
Funding support France, United States, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-IDEX-02 France
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1R35GM126961 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)GM-61153 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Crystal Structure of the [FeFe]-Hydrogenase Maturase HydE Bound to Complex-B.
Authors: Rohac, R. / Martin, L. / Liu, L. / Basu, D. / Tao, L. / Britt, R.D. / Rauchfuss, T.B. / Nicolet, Y.
History
DepositionMar 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [FeFe] hydrogenase maturase subunit HydE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,99416
Polymers41,0091
Non-polymers1,98415
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-69 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.540, 82.830, 70.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein [FeFe] hydrogenase maturase subunit HydE


Mass: 41009.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1269, THEMA_07990, Tmari_1274
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9X0Z6, Oxidoreductases; Acting on a sulfur group of donors

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Non-polymers , 11 types, 497 molecules

#2: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#7: Chemical ChemComp-5X8 / S-adenosyl-L-cysteine


Type: L-peptide linking / Mass: 370.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18N6O5S
#8: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG; LiSO4; Tris pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→43 Å / Num. obs: 113796 / % possible obs: 99.3 % / Redundancy: 4.7 % / CC1/2: 0.997 / Net I/σ(I): 8.76
Reflection shellResolution: 1.5→1.54 Å / Num. unique obs: 11102 / CC1/2: 0.52

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CIW

3ciw


Resolution: 1.5→9.93 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.27 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1946 5687 5 %
Rwork0.1673 108109 -
obs0.1686 113796 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.69 Å2 / Biso mean: 24.5153 Å2 / Biso min: 10.45 Å2
Refinement stepCycle: final / Resolution: 1.5→9.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 86 482 3395
Biso mean--28.1 38.15 -
Num. residues----356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.520.33331850.3463474365997
1.52-1.540.36172010.33033555375699
1.54-1.560.3411800.30143649382999
1.56-1.570.34751640.2853580374499
1.57-1.60.35161890.28493586377599
1.6-1.620.33981860.272635503736100
1.62-1.640.31081790.25223612379199
1.64-1.660.28271880.246335963784100
1.66-1.690.21671960.2263616381299
1.69-1.720.27092030.217736073810100
1.72-1.750.2151760.206236113787100
1.75-1.780.20641880.196336013789100
1.78-1.810.23781820.190536293811100
1.81-1.850.21412210.187235733794100
1.85-1.890.22351920.183736343826100
1.89-1.930.22441900.192636423832100
1.93-1.980.18781710.163435843755100
1.98-2.030.17861920.158236243816100
2.03-2.090.18361940.15836153809100
2.09-2.160.19261760.145736163792100
2.16-2.240.20032280.154835723800100
2.24-2.330.19632140.162536293843100
2.33-2.430.19721910.154336403831100
2.43-2.560.17881890.153235723761100
2.56-2.710.17332310.149735893820100
2.71-2.920.16931800.143636363816100
2.92-3.20.19942000.139936033803100
3.2-3.640.1381760.136836233799100
3.65-4.520.1261700.123836603830100
4.52-9.930.15761550.148536313786100
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)
14.9659-2.3482-1.06354.40760.8032.67830.18390.0415-0.0678-0.332-0.0226-0.34290.05460.5096-0.05430.2096-0.0547-0.05550.38240.0540.443624.425114.2691-21.2494
23.9331-0.5017-1.80031.15840.84333.9670.0287-0.04440.03020.0422-0.0287-0.2612-0.04210.4402-0.00220.1075-0.0264-0.02830.20030.04210.199710.880815.61-14.664
30.9925-0.1179-0.19250.5479-0.07041.7153-0.0030.06440.0779-0.00890.00760.0397-0.1195-0.1273-0.00830.13310.0127-0.00310.11960.01250.1364-19.491820.5042-21.1226
41.2773-0.12460.09810.5629-0.24381.50360.03320.04930.0554-0.033-0.0419-0.0518-0.03190.14470.00540.1313-0.00590.00540.11620.01840.1392-2.641415.9294-21.8808
52.66720.3389-0.51710.9827-0.12190.8542-0.0518-0.0023-0.1439-0.03720.0009-0.02010.0925-0.03690.0320.1409-0.0093-0.00210.11620.00990.1469-11.04547.8229-12.2871
60.4608-0.3735-0.10930.31190.11110.0654-0.0686-0.1428-0.29080.08850.15330.03590.139-0.0568-0.09250.2185-0.0042-0.01910.2630.00040.2977-19.85832.8301-17.837
72.2172-0.21310.29040.79270.2621.81210.0146-0.3262-0.03510.1080.0415-0.084-0.02230.0559-0.06540.17760.00030.00910.20060.00070.1502-9.331214.9363-3.0637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -9 through 11 )A-9 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 46 )A12 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 189 )A47 - 189
4X-RAY DIFFRACTION4chain 'A' and (resid 190 through 268 )A190 - 268
5X-RAY DIFFRACTION5chain 'A' and (resid 269 through 299 )A269 - 299
6X-RAY DIFFRACTION6chain 'A' and (resid 300 through 317 )A300 - 317
7X-RAY DIFFRACTION7chain 'A' and (resid 318 through 401 )A318 - 401

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