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- PDB-7wuz: Structural study of the complex of cblC methylmalonic aciduria an... -

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Basic information

Entry
Database: PDB / ID: 7wuz
TitleStructural study of the complex of cblC methylmalonic aciduria and homocysteinuria-related protein MMACHC with cyanocobalamin
ComponentsCyanocobalamin reductase / alkylcobalamin dealkylase
KeywordsOXIDOREDUCTASE / MMACHC / cyanocobalamin / vitamin B12 / complex structure / STRUCTURAL PROTEIN
Function / homology
Function and homology information


cyanocobalamin reductase / alkylcobalamin dealkylase / Defective MMACHC causes MAHCC / cyanocobalamin reductase (cyanide-eliminating) (NADP+) activity / Defective MMADHC causes MMAHCD / demethylase activity / Cobalamin (Cbl) metabolism / cobalamin metabolic process / demethylation / transferase activity, transferring alkyl or aryl (other than methyl) groups ...cyanocobalamin reductase / alkylcobalamin dealkylase / Defective MMACHC causes MAHCC / cyanocobalamin reductase (cyanide-eliminating) (NADP+) activity / Defective MMADHC causes MMAHCD / demethylase activity / Cobalamin (Cbl) metabolism / cobalamin metabolic process / demethylation / transferase activity, transferring alkyl or aryl (other than methyl) groups / glutathione binding / cobalamin binding / glutathione metabolic process / FAD binding / oxidoreductase activity / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Methylmalonic aciduria and homocystinuria type C family / Methylmalonic aciduria and homocystinuria type C family
Similarity search - Domain/homology
CYANOCOBALAMIN / L(+)-TARTARIC ACID / Cyanocobalamin reductase / alkylcobalamin dealkylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsFeng, Y. / Qin, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31100529 China
CitationJournal: To Be Published
Title: Structural study of the complex of cblC methylmalonic aciduria and homocysteinuria-related protein MMACHC with cyanocobalamin
Authors: Feng, Y. / Qin, X.
History
DepositionFeb 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyanocobalamin reductase / alkylcobalamin dealkylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1934
Polymers27,5911
Non-polymers1,6033
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-6 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.968, 96.327, 47.257
Angle α, β, γ (deg.)90.000, 111.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cyanocobalamin reductase / alkylcobalamin dealkylase / Alkylcobalamin:glutathione S-alkyltransferase / CblC / Cyanocobalamin reductase (cyanide- ...Alkylcobalamin:glutathione S-alkyltransferase / CblC / Cyanocobalamin reductase (cyanide-eliminating) / Methylmalonic aciduria and homocystinuria type C protein / MMACHC


Mass: 27590.656 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, alkylcobalamin dealkylase, cyanocobalamin reductase
#2: Chemical ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C63H89CoN14O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 2000MME, 0.1M Bis-Tris pH 6.5, 0.2 M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.93→55.6 Å / Num. obs: 22121 / % possible obs: 96.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 24.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.044 / Rrim(I) all: 0.102 / Net I/σ(I): 11.8 / Num. measured all: 114741 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.93-2.035.30.5651713332130.8660.2650.6253.296.9
6.1-55.64.80.04335867400.9980.020.04827.299

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.93→33.37 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 1077 4.87 %
Rwork0.1652 21030 -
obs0.1672 22107 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.67 Å2 / Biso mean: 28.9752 Å2 / Biso min: 11.28 Å2
Refinement stepCycle: final / Resolution: 1.93→33.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 108 206 2264
Biso mean--27.31 36.97 -
Num. residues----241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-2.020.22411350.20452631276697
2.02-2.120.23171430.18872601274497
2.12-2.250.23981270.19582662278997
2.25-2.430.24191270.17542674280198
2.43-2.670.22741580.17662652281098
2.67-3.060.23141230.16632709283298
3.06-3.850.18941300.15112395252587
3.85-33.370.17421340.14782706284097
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1275-0.22573.64391.3817-0.61633.34360.28490.3158-0.2826-0.087-0.02580.0911.14530.0983-0.24210.292-0.0032-0.03230.1373-0.01780.2207-30.5761-15.129511.6473
21.84360.5731.13761.47620.03573.93850.13820.0265-0.05210.0678-0.0398-0.02950.26320.3203-0.07220.12630.02830.02040.1325-0.02660.1399-21.1028-6.389620.4283
32.56720.03640.41832.9884-0.2712.4240.0190.2117-0.0436-0.1077-0.0794-0.0242-0.07850.25060.07090.1483-0.00280.00690.1497-0.00570.0983-20.20632.255315.7755
45.6135-1.5845-0.29318.2056-0.99574.51410.42860.04320.4308-0.5054-0.2763-0.117-0.34550.1144-0.06460.33210.0087-0.00880.1584-0.03840.2943-24.647222.787320.9699
51.42990.12490.2691.72430.42022.51-0.0092-0.08060.17180.0677-0.10270.2532-0.308-0.15250.08970.14020.00580.01230.1272-0.01490.1668-31.08735.513222.3364
66.5639-1.20731.14483.12880.7314.4661-0.0691-0.07820.14340.0770.0232-0.17150.2185-0.04690.01850.2482-0.01520.03310.1872-0.00160.1015-18.5824-2.287440.2744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 19 )A-1 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 94 )A20 - 94
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 134 )A95 - 134
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 147 )A135 - 147
5X-RAY DIFFRACTION5chain 'A' and (resid 148 through 216 )A148 - 216
6X-RAY DIFFRACTION6chain 'A' and (resid 217 through 239 )A217 - 239

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