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- PDB-2ycl: complete structure of the corrinoid,iron-sulfur protein including... -

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Basic information

Entry
Database: PDB / ID: 2ycl
Titlecomplete structure of the corrinoid,iron-sulfur protein including the N-terminal domain with a 4Fe-4S cluster
Components
  • CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT
  • CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN
KeywordsTRANSFERASE
Function / homology
Function and homology information


acetyl-CoA catabolic process / methyltransferase activity / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Rossmann fold - #11600 / CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel / Acetyl-CoA decarbonylase/synthase complex, gamma subunit / CO dehydrogenase/acetyl-CoA synthase delta subunit / 4Fe-4S domain / Putative Fe-S cluster / 4Fe-4S domain profile. / Dihydropteroate synthase-like / Dihydropteroate synthase-like / TIM Barrel ...Rossmann fold - #11600 / CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel / Acetyl-CoA decarbonylase/synthase complex, gamma subunit / CO dehydrogenase/acetyl-CoA synthase delta subunit / 4Fe-4S domain / Putative Fe-S cluster / 4Fe-4S domain profile. / Dihydropteroate synthase-like / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COBALAMIN / IRON/SULFUR CLUSTER / CO dehydrogenase/acetyl-CoA synthase, iron-sulfur protein / Carbon monoxide dehydrogenase corrinoid/iron-sulfur protein, gamma subunit
Similarity search - Component
Biological speciesCARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGoetzl, S. / Jeoung, J.H. / Hennig, S.E. / Dobbek, H.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Basis for Electron and Methyl-Group Transfer in a Methyltransferase System Operating in the Reductive Acetyl-Coa Pathway
Authors: Goetzl, S. / Jeoung, J.H. / Hennig, S.E. / Dobbek, H.
History
DepositionMar 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Other / Version format compliance
Revision 1.2Oct 24, 2012Group: Non-polymer description
Revision 1.3Dec 20, 2023Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_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
A: CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT
B: CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0624
Polymers82,3802
Non-polymers1,6822
Water14,322795
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-39.6 kcal/mol
Surface area29130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.219, 43.476, 101.855
Angle α, β, γ (deg.)90.00, 119.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2102-

HOH

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Components

#1: Protein CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT


Mass: 48469.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
Strain: Z-2901 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3ACS3
#2: Protein CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN


Mass: 33910.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
Strain: Z-2901 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3ACS0
#3: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 795 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→35 Å / Num. obs: 48286 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 18.68 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.36
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.55 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H9A

2h9a


Resolution: 1.95→33.745 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 2415 5 %
Rwork0.1915 --
obs0.1946 48268 99.51 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.296 Å2 / ksol: 0.427 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.1642 Å20 Å2-4.1454 Å2
2--1.2701 Å20 Å2
3----6.4344 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5758 0 99 795 6652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126104
X-RAY DIFFRACTIONf_angle_d1.6478353
X-RAY DIFFRACTIONf_dihedral_angle_d13.6442323
X-RAY DIFFRACTIONf_chiral_restr0.092966
X-RAY DIFFRACTIONf_plane_restr0.0111071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.98980.36231410.28542681X-RAY DIFFRACTION100
1.9898-2.03310.35551410.26382669X-RAY DIFFRACTION100
2.0331-2.08030.35241420.26762688X-RAY DIFFRACTION100
2.0803-2.13240.30471400.25272659X-RAY DIFFRACTION100
2.1324-2.190.3241420.23822701X-RAY DIFFRACTION100
2.19-2.25440.31241380.26472623X-RAY DIFFRACTION99
2.2544-2.32720.35851400.26482671X-RAY DIFFRACTION99
2.3272-2.41030.28721430.2252701X-RAY DIFFRACTION100
2.4103-2.50680.32261400.2122671X-RAY DIFFRACTION100
2.5068-2.62090.28451420.1982700X-RAY DIFFRACTION100
2.6209-2.7590.25351420.1882696X-RAY DIFFRACTION100
2.759-2.93180.22871420.17862686X-RAY DIFFRACTION100
2.9318-3.1580.22771430.17132723X-RAY DIFFRACTION100
3.158-3.47550.24411420.1692691X-RAY DIFFRACTION100
3.4755-3.97770.20611440.15432736X-RAY DIFFRACTION99
3.9777-5.00890.17371430.13052735X-RAY DIFFRACTION100
5.0089-33.75050.18611500.16232822X-RAY DIFFRACTION99

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