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- PDB-3som: crystal structure of human MMACHC -

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Basic information

Entry
Database: PDB / ID: 3som
Titlecrystal structure of human MMACHC
ComponentsMethylmalonic aciduria and homocystinuria type C protein
KeywordsOXIDOREDUCTASE / Structural Genomics / Structural Genomics Consortium / SGC / CblC / Organic aciduria / inborn errors of metabolism / cobalamin / vitamin B12 / cobalt(III)
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 metabolic process / Cobalamin (Cbl) metabolism / demethylation / demethylase activity / glutathione binding ...cyanocobalamin reductase / alkylcobalamin dealkylase / Defective MMACHC causes MAHCC / cyanocobalamin reductase (cyanide-eliminating) (NADP+) activity / Defective MMADHC causes MMAHCD / cobalamin metabolic process / Cobalamin (Cbl) metabolism / demethylation / demethylase activity / glutathione binding / cobalamin binding / FAD binding / glutathione metabolic process / transferase activity / 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
5'-DEOXYADENOSINE / COBALAMIN / 2-AMINO-ETHANETHIOL / CITRATE ANION / Cyanocobalamin reductase / alkylcobalamin dealkylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsKrojer, T. / Froese, D.S. / von Delft, F. / Muniz, J.R. / Gileadi, C. / Vollmar, M. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Krojer, T. / Froese, D.S. / von Delft, F. / Muniz, J.R. / Gileadi, C. / Vollmar, M. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Gravel, R.A. / Yue, W.W. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: Biochemistry / Year: 2012
Title: Structure of MMACHC reveals an arginine-rich pocket and a domain-swapped dimer for its B12 processing function.
Authors: Froese, D.S. / Krojer, T. / Wu, X. / Shrestha, R. / Kiyani, W. / von Delft, F. / Gravel, R.A. / Oppermann, U. / Yue, W.W.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Non-polymer description
Revision 1.2Apr 15, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylmalonic aciduria and homocystinuria type C protein
B: Methylmalonic aciduria and homocystinuria type C protein
C: Methylmalonic aciduria and homocystinuria type C protein
D: Methylmalonic aciduria and homocystinuria type C protein
E: Methylmalonic aciduria and homocystinuria type C protein
F: Methylmalonic aciduria and homocystinuria type C protein
G: Methylmalonic aciduria and homocystinuria type C protein
H: Methylmalonic aciduria and homocystinuria type C protein
I: Methylmalonic aciduria and homocystinuria type C protein
J: Methylmalonic aciduria and homocystinuria type C protein
K: Methylmalonic aciduria and homocystinuria type C protein
L: Methylmalonic aciduria and homocystinuria type C protein
M: Methylmalonic aciduria and homocystinuria type C protein
N: Methylmalonic aciduria and homocystinuria type C protein
O: Methylmalonic aciduria and homocystinuria type C protein
P: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)549,02283
Polymers518,92216
Non-polymers30,10067
Water29,6531646
1
A: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2805
Polymers32,4331
Non-polymers1,8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2034
Polymers32,4331
Non-polymers1,7713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2805
Polymers32,4331
Non-polymers1,8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2805
Polymers32,4331
Non-polymers1,8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2655
Polymers32,4331
Non-polymers1,8334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2805
Polymers32,4331
Non-polymers1,8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5326
Polymers32,4331
Non-polymers2,0995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2805
Polymers32,4331
Non-polymers1,8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5326
Polymers32,4331
Non-polymers2,0995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2805
Polymers32,4331
Non-polymers1,8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2805
Polymers32,4331
Non-polymers1,8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2805
Polymers32,4331
Non-polymers1,8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2805
Polymers32,4331
Non-polymers1,8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2805
Polymers32,4331
Non-polymers1,8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2805
Polymers32,4331
Non-polymers1,8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Methylmalonic aciduria and homocystinuria type C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4057
Polymers32,4331
Non-polymers1,9726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.664, 71.960, 300.055
Angle α, β, γ (deg.)88.53, 85.25, 83.76
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein
Methylmalonic aciduria and homocystinuria type C protein


Mass: 32432.598 Da / Num. of mol.: 16
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

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Non-polymers , 6 types, 1713 molecules

#2: Chemical
ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-DHL / 2-AMINO-ETHANETHIOL / 2,3-DESHYDROLANTHIONINE


Type: L-peptide linking / Mass: 77.149 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H7NS
#5: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C10H13N5O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1646 / 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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 10(w/v) PEG_3350, 0.2M ammonium citrate pH 5.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96860, 0.97880
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 27, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
20.97881
ReflectionResolution: 2.4→19.86 Å / Num. all: 229004 / Num. obs: 229004 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 44.91 Å2 / Rmerge(I) obs: 0.193 / Net I/σ(I): 8.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 2.1 / Num. unique all: 33155 / % possible all: 98

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Processing

Software
NameVersionClassification
GDAdata collection
SHARPphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.86 Å / Cor.coef. Fo:Fc: 0.9351 / Cor.coef. Fo:Fc free: 0.9204 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 11473 5.02 %RANDOM
Rwork0.1817 ---
all0.1829 228734 --
obs0.1829 228734 --
Displacement parametersBiso mean: 33.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.6731 Å20.3217 Å2-0.7474 Å2
2---1.0958 Å2-0.0311 Å2
3---1.7689 Å2
Refine analyzeLuzzati coordinate error obs: 0.273 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29475 0 2056 1646 33177
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132797HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2745380HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d14660SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes652HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4802HARMONIC5
X-RAY DIFFRACTIONt_it32797HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion0.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3801SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact37188SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2348 845 5.05 %
Rwork0.2154 15878 -
all0.2163 16723 -

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