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- PDB-2xwq: Anaerobic cobalt chelatase from Archeaoglobus fulgidus (CbiX) in ... -

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Basic information

Entry
Database: PDB / ID: 2xwq
TitleAnaerobic cobalt chelatase from Archeaoglobus fulgidus (CbiX) in complex with metalated sirohydrochlorin product
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 / 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
COBALT SIROHYDROCHLORIN / Sirohydrochlorin cobaltochelatase
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 1.3Dec 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 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

Downloads & links

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Assembly

Deposited unit
A: SIROHYDROCHLORIN COBALTOCHELATASE
B: SIROHYDROCHLORIN COBALTOCHELATASE
C: SIROHYDROCHLORIN COBALTOCHELATASE
D: SIROHYDROCHLORIN COBALTOCHELATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6026
Polymers60,7624
Non-polymers1,8392
Water3,297183
1
A: SIROHYDROCHLORIN COBALTOCHELATASE
B: SIROHYDROCHLORIN COBALTOCHELATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3013
Polymers30,3812
Non-polymers9201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-37.9 kcal/mol
Surface area10850 Å2
MethodPISA
2
C: SIROHYDROCHLORIN COBALTOCHELATASE
D: SIROHYDROCHLORIN COBALTOCHELATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3013
Polymers30,3812
Non-polymers9201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-35.9 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.010, 99.000, 116.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99515, 0.0965, 0.01898), (0.09467, 0.8875, 0.45097), (0.02667, 0.45058, -0.89234)7.48496, -6.19439, 24.90189
2given(0.27026, -0.32378, 0.90671), (-0.22656, -0.9367, -0.26695), (0.93575, -0.13328, -0.32651)-8.82397, 11.24481, 14.95735
3given(-0.26527, 0.21278, -0.9404), (0.23639, -0.93122, -0.27738), (-0.93475, -0.29589, 0.19672)17.64079, 9.17131, 16.48726

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Components

#1: Protein
SIROHYDROCHLORIN COBALTOCHELATASE / CBIXS


Mass: 15190.501 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR DE3 / Variant (production host): PLYSS
References: UniProt: O29537, sirohydrochlorin cobaltochelatase
#2: Chemical ChemComp-SIR / COBALT SIROHYDROCHLORIN


Mass: 919.749 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H44CoN4O16
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOBALT-SIROHYDROCHLORIN (SIR): METAL AT THE CENTER OF THE SHC IS UNKNOWN, COBALT WAS USED FOR THE ...COBALT-SIROHYDROCHLORIN (SIR): METAL AT THE CENTER OF THE SHC IS UNKNOWN, COBALT WAS USED FOR THE PURPOSE OF MODELLING.

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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: 2.27 Å3/Da / Density % sol: 46 % / 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: 1.0079
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 26, 2010 / Details: MIRRORS
RadiationMonochromator: SILICON MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0079 Å / Relative weight: 1
ReflectionResolution: 2→50.3 Å / Num. obs: 253190 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.2
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.9 / % 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: 2.01→45.57 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 5.98 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28234 1847 5 %RANDOM
Rwork0.21656 ---
obs0.21979 35176 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.913 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.01→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 126 183 4349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224404
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3842.0495990
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7265498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9722.157204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.4115744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8981548
X-RAY DIFFRACTIONr_chiral_restr0.1290.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213452
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_it1.171.52480
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01124002
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.10431924
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8324.51988
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: 2.012→2.064 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 137 -
Rwork0.344 2582 -
obs--100 %

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