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- PDB-2xws: ANAEROBIC COBALT CHELATASE (CbiX) FROM ARCHAEOGLOBUS FULGIDUS -

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Basic information

Entry
Database: PDB / ID: 2xws
TitleANAEROBIC COBALT CHELATASE (CbiX) FROM ARCHAEOGLOBUS FULGIDUS
ComponentsSIROHYDROCHLORIN COBALTOCHELATASE
KeywordsLYASE / BETA-ALPHA-BETA / COBALAMIN BIOSYNTHESIS / METAL-BINDING / PARALLEL BETA SHEET
Function / homology
Function and homology information


sirohydrochlorin cobaltochelatase / anaerobic cobalamin biosynthetic process / sirohydrochlorin cobaltochelatase activity / tetrapyrrole binding / cobalt ion binding
Similarity search - Function
Sirohydrochlorin cobaltochelatase / Sirohydrochlorin cobaltochelatase CbiX-like / CbiX / Rossmann fold - #1400 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRomao, C.V. / Ladakis, D. / Lobo, S.A.L. / Carrondo, M.A. / Brindley, A.A. / Deery, E. / Matias, P.M. / Pickersgill, R.W. / Saraiva, L.M. / Warren, M.J.
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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIROHYDROCHLORIN COBALTOCHELATASE


Theoretical massNumber of molelcules
Total (without water)15,1911
Polymers15,1911
Non-polymers00
Water1,58588
1
A: SIROHYDROCHLORIN COBALTOCHELATASE

A: SIROHYDROCHLORIN COBALTOCHELATASE


Theoretical massNumber of molelcules
Total (without water)30,3812
Polymers30,3812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3940 Å2
ΔGint-33.2 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.980, 50.980, 101.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein SIROHYDROCHLORIN COBALTOCHELATASE /


Mass: 15190.501 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR DE3 / Variant (production host): PLYSS
References: UniProt: O29537, sirohydrochlorin cobaltochelatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.23 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.8 / Details: pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9835
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SILICON MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9835 Å / Relative weight: 1
ReflectionResolution: 1.6→29.5 Å / Num. obs: 118464 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 13.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DJ5

2dj5


Resolution: 1.6→33.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.475 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21484 947 5.1 %RANDOM
Rwork0.18537 ---
obs0.18679 17516 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.203 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 0 88 1100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0221039
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4021.9731397
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80622.15751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14815189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.841512
X-RAY DIFFRACTIONr_chiral_restr0.1880.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021793
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_it1.5811.5625
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.51321009
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0013414
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.6234.5387
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: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 74 -
Rwork0.222 1266 -
obs--100 %

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