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- PDB-2xwp: ANAEROBIC COBALT CHELATASE (CbiK) FROM SALMONELLA TYPHIMURIUM IN ... -

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Basic information

Entry
Database: PDB / ID: 2xwp
TitleANAEROBIC COBALT CHELATASE (CbiK) FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH METALATED TETRAPYRROLE
ComponentsSIROHYDROCHLORIN COBALTOCHELATASE
KeywordsLYASE / BETA-ALPHA-BETA / COBALAMIN BIOSYNTHESIS / METAL-BINDING / PARALLEL BETA SHEET
Function / homology
Function and homology information


sirohydrochlorin cobaltochelatase / sirohydrochlorin cobaltochelatase activity / anaerobic cobalamin biosynthetic process / tetrapyrrole binding / porphyrin-containing compound biosynthetic process / cobalt ion binding
Similarity search - Function
Anaerobic cobalt chelatase / Cobalt chelatase (CbiK) / Rossmann fold - #1400 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COBALT SIROHYDROCHLORIN / Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesSALMONELLA ENTERICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLadakis, D. / Brindley, A.A. / Deery, E. / Warren, M.J. / Pickersgill, R.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Evolution in a Family of Chelatases Facilitated by the Introduction of Active Site Asymmetry and Protein Oligomerization.
Authors: Romao, C.V. / Ladakis, D. / Lobo, S.A. / Carrondo, M.A. / Brindley, A.A. / Deery, E. / Matias, P.M. / Pickersgill, R.W. / Saraiva, L.M. / Warren, M.J.
History
DepositionNov 4, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations / Other
Category: database_PDB_caveat / pdbx_database_status ...database_PDB_caveat / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 18, 2024Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_chiral
Item: _chem_comp_atom.atom_id / _chem_comp_atom.pdbx_stereo_config ..._chem_comp_atom.atom_id / _chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIROHYDROCHLORIN COBALTOCHELATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2863
Polymers29,2741
Non-polymers1,0122
Water2,612145
1
A: SIROHYDROCHLORIN COBALTOCHELATASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)181,71318
Polymers175,6426
Non-polymers6,07112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area25430 Å2
ΔGint-108.4 kcal/mol
Surface area54940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.630, 110.630, 89.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2028-

HOH

21A-2052-

HOH

31A-2103-

HOH

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Components

#1: Protein SIROHYDROCHLORIN COBALTOCHELATASE


Mass: 29273.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA (bacteria) / Variant: SEROVAR TYPHIMURIUM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR DE3 / Variant (production host): PLYSS
References: UniProt: Q05592, sirohydrochlorin cobaltochelatase
#2: Chemical ChemComp-SIR / COBALT SIROHYDROCHLORIN


Mass: 919.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H44CoN4O16
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.66 Å3/Da / Density % sol: 54 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.978
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→47.9 Å / Num. obs: 176900 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.6 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGO

1qgo


Resolution: 1.9→44.77 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.592 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23928 1297 5.1 %RANDOM
Rwork0.1942 ---
obs0.1965 24372 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.762 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 69 145 2213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0212217
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2481.9933038
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64923.592103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50415380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5361518
X-RAY DIFFRACTIONr_chiral_restr0.150.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211723
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.241.51324
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12222142
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.483893
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4884.5881
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 75 -
Rwork0.334 1717 -
obs--95.37 %

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