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- PDB-2xvz: Cobalt chelatase CbiK (periplasmatic) from Desulvobrio vulgaris H... -

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Basic information

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


sirohydrochlorin ferrochelatase / sirohydrochlorin ferrochelatase activity / sirohydrochlorin cobaltochelatase / 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 / MAD / Resolution: 2.4 Å
AuthorsRomao, C.V. / Lobo, S.A.L. / Carrondo, M.A. / Saraiva, L.M. / Matias, P.M.
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.L. / Carrondo, M.A. / Brindley, A.A. / Deery, E. / Matias, P.M. / Pickersgill, R.W. / Saraiva, L.M. / Warren, M.J.
History
DepositionOct 28, 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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)30,57817
Polymers28,7681
Non-polymers1,81116
Water2,018112
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)122,31468
Polymers115,0714
Non-polymers7,24364
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 area17730 Å2
ΔGint-654.9 kcal/mol
Surface area41440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.441, 121.441, 121.100
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

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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 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 GOLD (DE3)
References: UniProt: Q72EC8, sirohydrochlorin cobaltochelatase

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Non-polymers , 8 types, 128 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.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE ON THE DATABASE HAS A SIGNAL PEPTIDE, THE SEQUENCE OF THE STRUCTURE PRESENTED STARTS ...THE SEQUENCE ON THE DATABASE HAS A SIGNAL PEPTIDE, THE SEQUENCE OF THE STRUCTURE PRESENTED STARTS ON RESIDUE 29

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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: 3.7 Å3/Da / Density % sol: 66.7 % / 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 1M COBALT CHLORIDE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.42363
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 12, 2007 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.42363 Å / Relative weight: 1
ReflectionResolution: 2.4→49.45 Å / Num. obs: 18046 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 1.9 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0063refinement
XDSdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.4→85.75 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.299 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE-CHAINS OF THE AMINO ACID RESIDUES- GLU22, GLU23, ARG25, LYS30, LYS51, MET52 WERE MODELLED WITH 0.5 OF OCCUPANCY DUE TO THE LACK OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE-CHAINS OF THE AMINO ACID RESIDUES- GLU22, GLU23, ARG25, LYS30, LYS51, MET52 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- ARG173, MET193.
RfactorNum. reflection% reflectionSelection details
Rfree0.22022 917 5.1 %RANDOM
Rwork0.1696 ---
obs0.17211 17055 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.804 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→85.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 106 112 2202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222144
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9892.0512925
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7925262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63823.05985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79515322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9931517
X-RAY DIFFRACTIONr_chiral_restr0.1150.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211609
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_it1.0821.51313
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0722096
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3083831
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.224.5829
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 74 -
Rwork0.215 1205 -
obs--98.23 %

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