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- PDB-5uos: Crystal Structure of CblC (MMACHC) (1-238), a human B12 processin... -

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Basic information

Entry
Database: PDB / ID: 5uos
TitleCrystal Structure of CblC (MMACHC) (1-238), a human B12 processing enzyme, complexed with an Antivitamin B12
ComponentsMethylmalonic aciduria and homocystinuria type C protein
KeywordsOXIDOREDUCTASE / Vitamin B12 / B12 trafficking / B12 processing / B12 binding
Function / homology
Function and homology information


cyanocobalamin reductase / alkylcobalamin dealkylase / Defective MMACHC causes MAHCC / cyanocobalamin reductase (cyanide-eliminating) (NADP+) activity / Defective MMADHC causes MMAHCD / Cobalamin (Cbl) metabolism / cobalamin metabolic process / demethylation / transferase activity, transferring alkyl or aryl (other than methyl) groups / glutathione binding ...cyanocobalamin reductase / alkylcobalamin dealkylase / Defective MMACHC causes MAHCC / cyanocobalamin reductase (cyanide-eliminating) (NADP+) activity / Defective MMADHC causes MMAHCD / Cobalamin (Cbl) metabolism / cobalamin metabolic process / demethylation / transferase activity, transferring alkyl or aryl (other than methyl) groups / glutathione binding / demethylase activity / cobalamin binding / glutathione metabolic process / FAD binding / oxidoreductase activity / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
Methylmalonic aciduria and homocystinuria type C family / Methylmalonic aciduria and homocystinuria type C family
Similarity search - Domain/homology
2-PHENYLAMINO-ETHANESULFONIC ACID / 1-ethynyl-2,4-difluorobenzene / COBALAMIN / GLUTATHIONE / Cyanocobalamin reductase / alkylcobalamin dealkylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsShanmuganathan, A. / Karasik, A. / Ruetz, M. / Banerjee, R. / Krautler, B. / Koutmos, M.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association13SDG14560056 United States
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Antivitamin B12 Inhibition of the Human B12 -Processing Enzyme CblC: Crystal Structure of an Inactive Ternary Complex with Glutathione as the Cosubstrate.
Authors: Ruetz, M. / Shanmuganathan, A. / Gherasim, C. / Karasik, A. / Salchner, R. / Kieninger, C. / Wurst, K. / Banerjee, R. / Koutmos, M. / Krautler, B.
History
DepositionFeb 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6828
Polymers27,4901
Non-polymers2,1927
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-34 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.432, 114.432, 150.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsMonomer confirmed by gel filtration

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methylmalonic aciduria and homocystinuria type C protein / CblC / Cyanocobalamin reductase (cyanide-eliminating)


Mass: 27489.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMACHC / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y4U1, Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor

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Non-polymers , 7 types, 82 molecules

#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Chemical ChemComp-8FS / 1-ethynyl-2,4-difluorobenzene


Mass: 138.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H4F2
#4: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Chemical ChemComp-171 / 2-PHENYLAMINO-ETHANESULFONIC ACID


Mass: 201.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO3S
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 5.25 Å3/Da / Density % sol: 76.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.2 M NaCl, 0.1 M CHES:NaOH pH 9.5, 1.26 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 9, 2016
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.51→99.1 Å / Num. obs: 17391 / % possible obs: 86.3 % / Redundancy: 12.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.027 / Rsym value: 0.098 / Net I/σ(I): 21.2
Reflection shellResolution: 2.51→2.62 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1967 / CC1/2: 0.853 / Rpim(I) all: 0.198 / Rsym value: 0.721 / % possible all: 87.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimless0.5.27data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SC0

3sc0


Resolution: 2.51→99.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.713 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21384 863 5 %RANDOM
Rwork0.17645 ---
obs0.17832 16527 84.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.619 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å2-0.69 Å20 Å2
2---1.37 Å20 Å2
3---4.46 Å2
Refinement stepCycle: 1 / Resolution: 2.51→99.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 145 75 2148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192143
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1782.0462955
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7485238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98922.81296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95415303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3331517
X-RAY DIFFRACTIONr_chiral_restr0.0720.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0221692
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_it2.7044.99955
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2597.4711192
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7135.2471187
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.67966.5433096
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: 2.513→2.578 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 60 -
Rwork0.277 1214 -
obs--86.14 %

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