[English] 日本語
Yorodumi
- PDB-6n97: Methylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n97
TitleMethylmalonyl-CoA decarboxylase in complex with 2-sulfonate-propionyl-amino(dethia)-CoA
ComponentsMethylmalonyl-CoA decarboxylase
KeywordsLYASE / crotonase / beta-keto / isostere
Function / homology
Function and homology information


methyl/ethyl malonyl-CoA decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / fatty acid beta-oxidation / cytosol
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / (2R)-sulfonatepropionyl-amino(dethia)-CoA / NICKEL (II) ION / (2S)-sulfonatepropionyl-amino(dethia)-CoA / Methylmalonyl-CoA decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsStunkard, L.M. / Dixon, A.D. / Huth, T.J. / Lohman, J.R.
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-CoA Decarboxylase Structure-Function Studies.
Authors: Stunkard, L.M. / Dixon, A.D. / Huth, T.J. / Lohman, J.R.
History
DepositionNov 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methylmalonyl-CoA decarboxylase
B: Methylmalonyl-CoA decarboxylase
C: Methylmalonyl-CoA decarboxylase
D: Methylmalonyl-CoA decarboxylase
E: Methylmalonyl-CoA decarboxylase
F: Methylmalonyl-CoA decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,62924
Polymers175,1436
Non-polymers13,48618
Water33,0401834
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27150 Å2
ΔGint-152 kcal/mol
Surface area50250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.961, 114.614, 192.338
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Methylmalonyl-CoA decarboxylase / MMCD / Transcarboxylase


Mass: 29190.557 Da / Num. of mol.: 6 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: scpB, mmcD, ygfG, b2919, JW2886 / Plasmid: pRSF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P52045, Lyases; Carbon-carbon lyases; Carboxy-lyases

-
Non-polymers , 5 types, 1852 molecules

#2: Chemical
ChemComp-YZS / (2S)-sulfonatepropionyl-amino(dethia)-CoA / (2~{S})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]me thoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylamino]- 1-oxidanylidene-propane-2-sulfonic acid


Mass: 886.610 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C24H41N8O20P3S
#3: Chemical
ChemComp-KGP / (2R)-sulfonatepropionyl-amino(dethia)-CoA / (2~{R})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylamino]-1-oxidanylidene-propane-2-sulfonic acid


Mass: 886.610 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H41N8O20P3S
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1834 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 150 mM sodium chloride, 100 mM imidazole, 0.4 M Monosodium phosphate/1.6 M Dipotassium phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 25, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 1242089 / Num. obs: 189024 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Rsym value: 0.093 / Χ2: 1.028 / Net I/av σ(I): 17.4 / Net I/σ(I): 7.6 / Num. measured all: 1242089
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.018 / Mean I/σ(I) obs: 2.387 / Rsym value: 1.018 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
REFMACrefmac_5.8.0238refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0238phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EF8

1ef8


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / Matrix type: sparse / WRfactor Rfree: 0.1874 / WRfactor Rwork: 0.1536 / FOM work R set: 0.8611 / SU B: 2.345 / SU ML: 0.072 / SU R Cruickshank DPI: 0.0967 / SU Rfree: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1794 9378 5 %RANDOM
Rwork0.1475 179523 --
obs0.1491 179523 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.55 Å2 / Biso mean: 24.896 Å2 / Biso min: 4.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0 Å2-0 Å2
2---1.53 Å20 Å2
3---2.27 Å2
Refinement stepCycle: final / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12246 0 772 1912 14930
Biso mean--39.87 36.78 -
Num. residues----1560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01314125
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713069
X-RAY DIFFRACTIONr_angle_refined_deg21.71819446
X-RAY DIFFRACTIONr_angle_other_deg1.4661.61530426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.351782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71722.085710
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.554152384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2891592
X-RAY DIFFRACTIONr_chiral_restr0.1610.21891
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215658
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022975
X-RAY DIFFRACTIONr_mcbond_it2.0382.2936537
X-RAY DIFFRACTIONr_mcbond_other2.0392.2936536
X-RAY DIFFRACTIONr_mcangle_it2.8583.4318242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.746-1.7920.2756550.245119581432488.0550.221
1.792-1.8410.2386470.219125761388895.2120.194
1.841-1.8940.2535920.208123451354395.5250.185
1.894-1.9520.2156130.192119471313195.6520.171
1.952-2.0160.2146090.177116241275695.90.161
2.016-2.0870.2175890.169113201235096.4290.156
2.087-2.1660.1895780.151109791193396.8490.142
2.166-2.2540.1845470.142106161147297.3060.135
2.254-2.3540.1725780.134102311103197.9870.129
2.354-2.4690.1684900.13398921053698.5380.131
2.469-2.6030.1884980.13794901008899.0090.137
2.603-2.760.1914520.1388984949799.3580.14
2.76-2.9510.1894380.1468501896599.710.151
2.951-3.1870.1784110.1487952837599.8570.156
3.187-3.4910.173920.1457335773499.9090.157
3.491-3.9020.1483640.1276641700899.9570.145
3.902-4.5050.143190.1145900622399.9360.135
4.505-5.5140.1482750.1195026530499.9430.146
5.514-7.7860.1642060.162395941651000.194
7.786-98.4580.1911250.1692248243397.5340.22

+
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://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