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- PDB-5fle: High resolution NI,FE-CODH-320 mV with CN state -

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Basic information

Entry
Database: PDB / ID: 5fle
TitleHigh resolution NI,FE-CODH-320 mV with CN state
ComponentsCARBON MONOXIDE DEHYDROGENASE 2
KeywordsOXIDOREDUCTASE / CARBON MONOXIDE / NICKEL / IRON / CARBON MONOXIDE DEHYDROGENASE
Function / homology
Function and homology information


anaerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (ferredoxin) activity / carbon-monoxide dehydrogenase (acceptor) activity / hydroxylamine reductase activity / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / plasma membrane / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #30 / Rossmann fold - #2030 / Ni-containing CO dehydrogenase / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL IRON CLSUTER WITH CYANIDE BOUND / : / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Carbon monoxide dehydrogenase 2
Similarity search - Component
Biological speciesCARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsCiaccafava, A. / Tombolelli, D. / Domnik, L. / Fesseler, J. / Jeoung, J.-H. / Dobbek, H. / Mroginski, M.A. / Hildebrandt, P. / Zebger, I.
CitationJournal: Chem Sci / Year: 2016
Title: When the inhibitor tells more than the substrate: the cyanide-bound state of a carbon monoxide dehydrogenase.
Authors: Ciaccafava, A. / Tombolelli, D. / Domnik, L. / Fesseler, J. / Jeoung, J.H. / Dobbek, H. / Mroginski, M.A. / Zebger, I. / Hildebrandt, P.
History
DepositionOct 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: CARBON MONOXIDE DEHYDROGENASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9845
Polymers67,0201
Non-polymers9644
Water12,214678
1
X: CARBON MONOXIDE DEHYDROGENASE 2
hetero molecules

X: CARBON MONOXIDE DEHYDROGENASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,96910
Polymers134,0412
Non-polymers1,9288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8410 Å2
ΔGint-122.7 kcal/mol
Surface area37980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.216, 75.511, 71.132
Angle α, β, γ (deg.)90.00, 111.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-2093-

HOH

21X-2292-

HOH

31X-2343-

HOH

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Components

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Protein , 1 types, 1 molecules X

#1: Protein CARBON MONOXIDE DEHYDROGENASE 2 / / CODH 2


Mass: 67020.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
Strain: Z-2901 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F8A8

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Non-polymers , 5 types, 682 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-82N / NICKEL IRON CLSUTER WITH CYANIDE BOUND


Mass: 380.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CFe3NNiS4
#5: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 678 / 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 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 8
Details: 15% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 6.5,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.23→40.76 Å / Num. obs: 159430 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.55
Reflection shellResolution: 1.23→1.24 Å / Rmerge(I) obs: 0.62 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B53

3b53


Resolution: 1.23→66.17 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.472 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.15321 7972 5 %RANDOM
Rwork0.12108 ---
obs0.1227 151457 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.613 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å21.27 Å2
2---0.49 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.23→66.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 0 23 678 5354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194880
X-RAY DIFFRACTIONr_bond_other_d0.0020.024826
X-RAY DIFFRACTIONr_angle_refined_deg1.942.096714
X-RAY DIFFRACTIONr_angle_other_deg1.4523.01311130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91924.807181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21815832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4851526
X-RAY DIFFRACTIONr_chiral_restr0.1390.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215542
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021006
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4031.4382576
X-RAY DIFFRACTIONr_mcbond_other2.3841.4382574
X-RAY DIFFRACTIONr_mcangle_it2.6312.1673227
X-RAY DIFFRACTIONr_mcangle_other2.6332.1673228
X-RAY DIFFRACTIONr_scbond_it5.6261.742304
X-RAY DIFFRACTIONr_scbond_other5.6241.7392305
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0682.4953404
X-RAY DIFFRACTIONr_long_range_B_refined6.62714.166211
X-RAY DIFFRACTIONr_long_range_B_other5.7512.7685749
X-RAY DIFFRACTIONr_rigid_bond_restr8.09139705
X-RAY DIFFRACTIONr_sphericity_free59.5185114
X-RAY DIFFRACTIONr_sphericity_bonded16.56510172
LS refinement shellResolution: 1.229→1.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 572 -
Rwork0.241 10874 -
obs--97.05 %

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