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- PDB-2xvy: Cobalt chelatase CbiK (periplasmic) from Desulvobrio vulgaris Hil... -

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Basic information

Entry
Database: PDB / ID: 2xvy
TitleCobalt chelatase CbiK (periplasmic) from Desulvobrio vulgaris Hildenborough (co-crystallised with cobalt and SHC)
ComponentsCHELATASE, PUTATIVE
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


sirohydrochlorin ferrochelatase / sirohydrochlorin cobaltochelatase / sirohydrochlorin ferrochelatase activity / sirohydrochlorin cobaltochelatase activity / anaerobic cobalamin biosynthetic process / cobalt ion binding / protein tetramerization / periplasmic space / heme binding
Similarity search - Function
Anaerobic cobalt chelatase / Cobalt chelatase (CbiK) / Rossmann fold - #1400 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / PEROXIDE ION / Sirohydrochlorin cobaltochelatase CbiKP
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRomao, C.V. / Lobo, S.A.L. / Carrondo, M.A. / Saraiva, L.M. / Matias, P.M.
CitationJournal: Environ. Microbiol. / Year: 2017
Title: Desulfovibrio vulgaris CbiK(P) cobaltochelatase: evolution of a haem binding protein orchestrated by the incorporation of two histidine residues.
Authors: Lobo, S.A. / Videira, M.A. / Pacheco, I. / Wass, M.N. / Warren, M.J. / Teixeira, M. / Matias, P.M. / Romao, C.V. / Saraiva, L.M.
History
DepositionOct 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Mar 1, 2017Group: Database references
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 / pdbx_struct_special_symmetry / 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.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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Assembly

Deposited unit
A: CHELATASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,74219
Polymers28,7681
Non-polymers1,97418
Water4,288238
1
A: CHELATASE, PUTATIVE
hetero molecules

A: CHELATASE, PUTATIVE
hetero molecules

A: CHELATASE, PUTATIVE
hetero molecules

A: CHELATASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,96976
Polymers115,0714
Non-polymers7,89872
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_555-x,y,-z1
Buried area24260 Å2
ΔGint-610.6 kcal/mol
Surface area38920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.810, 120.810, 119.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-1270-

HEM

21A-1270-

HEM

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CHELATASE, PUTATIVE / COBALT CHELATASE CBIK


Mass: 28767.809 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / Plasmid: PET-28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q72EC8, sirohydrochlorin cobaltochelatase

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Non-polymers , 7 types, 256 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.6 Å3/Da / Density % sol: 65.9 % / Description: NONE
Crystal growpH: 8.5
Details: CRYSTALLIZATION SOLUTION: 100MM TRIS-HCL PH8.5, 2M AMMONIUM SULFATE. THE DROP WAS MADE BY ADDING 1UL OF PROTEIN PLUS 1.8UL OF CRYSTALLIZATION SOLUTION AND 0.2UL OF 2MM SIROHYDROCHLORIN AND 0. ...Details: CRYSTALLIZATION SOLUTION: 100MM TRIS-HCL PH8.5, 2M AMMONIUM SULFATE. THE DROP WAS MADE BY ADDING 1UL OF PROTEIN PLUS 1.8UL OF CRYSTALLIZATION SOLUTION AND 0.2UL OF 2MM SIROHYDROCHLORIN AND 0.2UL OF COBALT CHLORIDE IN AEROBIC CONDITIONS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0332
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 12, 2007
Details: COLLIMATING RHODIUM COATED MIRROR (BEFORE MONOCHROMATOR) AND FOCUSSING TOROIDAL RHODIUM COATED MIRROR (AFTER MONOCHROMATOR)
RadiationMonochromator: SI 111 CHANNEL-CUT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→49.24 Å / Num. obs: 46830 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.8
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.9 / % possible all: 84.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0063refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XVZ

2xvz


Resolution: 1.7→85.44 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.518 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE-CHAINS OF THE AMINO ACID RESIDUES- GLU22, GLU23, LYS51, MET52, GLU93, LYS110, ARG218 WERE MODELLED WITH 0.5 OF OCCUPANCY DUE TO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE-CHAINS OF THE AMINO ACID RESIDUES- GLU22, GLU23, LYS51, MET52, GLU93, LYS110, ARG218 WERE MODELLED WITH 0.5 OF OCCUPANCY DUE TO THE LACK OF ELECTRON DENSITY PROBABLY DUE TO DISORDER. THE FOLLOWING AMINO ACID RESIDUES WERE MODELLED WITH DOUBLE CONFORMATION- MET31, ARG34, GLU133, ARG173, VAL198, LEU206, LEU209, ASP227, ARG236.
RfactorNum. reflection% reflectionSelection details
Rfree0.18779 2379 5.1 %RANDOM
Rwork0.17215 ---
obs0.17296 44493 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.875 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.7→85.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 120 238 2337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222194
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7622.0542987
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0265264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7222.92189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7615336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1161519
X-RAY DIFFRACTIONr_chiral_restr0.1230.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211635
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_it1.0881.51324
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91522123
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0363870
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.834.5863
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: 1.704→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 129 -
Rwork0.299 2405 -
obs--71.95 %

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