[English] 日本語
Yorodumi
- PDB-3sby: Crystal Structure of SeMet-Substituted Apo-MMACHC (1-244), a huma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sby
TitleCrystal Structure of SeMet-Substituted Apo-MMACHC (1-244), a human B12 processing enzyme
ComponentsMethylmalonic aciduria and homocystinuria type C protein
KeywordsOXIDOREDUCTASE / MMACHC / CblC / Cobalamin / Flavin / Glutathione / Flavin Reductase / Maturase
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
Cyanocobalamin reductase / alkylcobalamin dealkylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.71 Å
AuthorsKoutmos, M. / Gherasim, C. / Smith, J.L. / Banerjee, R.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural basis of multifunctionality in a vitamin B12-processing enzyme.
Authors: Koutmos, M. / Gherasim, C. / Smith, J.L. / Banerjee, R.
History
DepositionJun 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Apr 25, 2012Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methylmalonic aciduria and homocystinuria type C protein
B: Methylmalonic aciduria and homocystinuria type C protein


Theoretical massNumber of molelcules
Total (without water)58,7152
Polymers58,7152
Non-polymers00
Water54030
1
A: Methylmalonic aciduria and homocystinuria type C protein


Theoretical massNumber of molelcules
Total (without water)29,3581
Polymers29,3581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methylmalonic aciduria and homocystinuria type C protein


Theoretical massNumber of molelcules
Total (without water)29,3581
Polymers29,3581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.267, 69.267, 201.848
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Methylmalonic aciduria and homocystinuria type C protein


Mass: 29357.576 Da / Num. of mol.: 2 / Fragment: 12 binding domain, Residues 1-244 / Mutation: L48M, V83M, V107M, V164M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMACHC / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y4U1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUES 48, 83, 107 AND 164 IN CHAINS A AND B HAVE BEEN MUTATED TO MET IN ORDER TO INCORPORATE ...THE RESIDUES 48, 83, 107 AND 164 IN CHAINS A AND B HAVE BEEN MUTATED TO MET IN ORDER TO INCORPORATE MORE METHIONINES FOR PHASING.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.96 M sodium malonate, 10% Jeffamine 600 pH 7.0, 0.1 M Hepes 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97954 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2010
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionRedundancy: 7.7 % / Av σ(I) over netI: 16.06 / Number: 114945 / Rmerge(I) obs: 0.132 / Χ2: 1.55 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 14979 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.815099.710.12.057.6
4.625.8110010.1161.9187.8
4.034.6210010.1071.5997.7
3.664.0310010.1181.6197.7
3.43.6610010.1331.5137.7
3.23.410010.1671.5137.7
3.043.210010.1921.3557.7
2.913.0410010.2571.2737.6
2.82.9110010.3351.2597.6
2.72.810010.471.3877.5
ReflectionResolution: 2.7→59.99 Å / Num. all: 14979 / Num. obs: 14979 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.133 / Χ2: 1.794 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.87.50.47314911.4151100
2.8-2.917.60.33814931.3171100
2.91-3.047.60.2614891.3631100
3.04-3.27.70.19414951.5021100
3.2-3.47.70.16914941.7341100
3.4-3.667.70.13615041.7711100
3.66-4.037.70.11914811.9441100
4.03-4.627.70.10615121.9451100
4.62-5.817.80.11514912.3591100
5.81-507.60.09915292.547199.7

-
Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.68 / FOM acentric: 0.68 / FOM centric: 0.6 / Reflection: 14730 / Reflection acentric: 14452 / Reflection centric: 278
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
4.8-7.70.870.880.671985192857
3.9-4.80.870.870.672480243050
3.4-3.90.780.780.642508246246
2.9-3.40.590.590.44393433756
2.7-2.90.370.370.352720268535

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.15phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-IceEpicsdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.71→59.99 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.85 / WRfactor Rfree: 0.315 / WRfactor Rwork: 0.2517 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7802 / SU B: 14.727 / SU ML: 0.314 / SU Rfree: 0.4057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2903 755 5.1 %RANDOM
Rwork0.2283 ---
all0.276 14932 --
obs0.2314 14911 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.63 Å2 / Biso mean: 42.6535 Å2 / Biso min: 18.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.28 Å20 Å2
2--0.57 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.71→59.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3615 0 0 30 3645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223737
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.9625099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3815443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85522.652181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35815573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5141532
X-RAY DIFFRACTIONr_chiral_restr0.0760.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0222958
X-RAY DIFFRACTIONr_mcbond_it0.3831.52254
X-RAY DIFFRACTIONr_mcangle_it0.72823657
X-RAY DIFFRACTIONr_scbond_it0.92531483
X-RAY DIFFRACTIONr_scangle_it1.5394.51442
LS refinement shellResolution: 2.706→2.776 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 63 -
Rwork0.287 1058 -
all-1121 -
obs--99.91 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more