[English] 日本語
Yorodumi
- PDB-4pab: Crystal structure of the precursor form of rat DMGDH complexed wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pab
TitleCrystal structure of the precursor form of rat DMGDH complexed with tetrahydrofolate
ComponentsDimethylglycine dehydrogenase
KeywordsOXIDOREDUCTASE / dimethylglycine dehydrogenase / rat / tetrahydrofolate
Function / homology
Function and homology information


dimethylglycine dehydrogenase / dimethylglycine dehydrogenase activity / Choline catabolism / amino-acid betaine catabolic process / choline catabolic process / choline metabolic process / tetrahydrofolate interconversion / folic acid binding / flavin adenine dinucleotide binding / mitochondrial matrix ...dimethylglycine dehydrogenase / dimethylglycine dehydrogenase activity / Choline catabolism / amino-acid betaine catabolic process / choline catabolic process / choline metabolic process / tetrahydrofolate interconversion / folic acid binding / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / cytoplasm
Similarity search - Function
FAD dependent oxidoreductase, central domain / FAD dependent oxidoreductase central domain / Aminomethyltransferase beta-barrel domains / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain ...FAD dependent oxidoreductase, central domain / FAD dependent oxidoreductase central domain / Aminomethyltransferase beta-barrel domains / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain / Aminomethyltransferase folate-binding domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / Gyrase A; domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / THIOCYANATE ION / (6S)-5,6,7,8-TETRAHYDROFOLATE / Dimethylglycine dehydrogenase / Dimethylglycine dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLuka, Z. / Pakhomova, S. / Loukachevitch, L.V. / Newcomer, M.E. / Wagner, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK15289 United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Folate in demethylation: The crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate.
Authors: Luka, Z. / Pakhomova, S. / Loukachevitch, L.V. / Newcomer, M.E. / Wagner, C.
History
DepositionApr 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dimethylglycine dehydrogenase
B: Dimethylglycine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,00814
Polymers195,0822
Non-polymers2,92712
Water12,989721
1
A: Dimethylglycine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0047
Polymers97,5411
Non-polymers1,4636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dimethylglycine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0047
Polymers97,5411
Non-polymers1,4636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.182, 107.215, 114.466
Angle α, β, γ (deg.)90.00, 92.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 38 - 859 / Label seq-ID: 40 - 861

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Dimethylglycine dehydrogenase / Dimethylglycine dehydrogenase / mitochondrial


Mass: 97540.859 Da / Num. of mol.: 2 / Mutation: A204V, I267V, T402K, E509R, N746D, N774D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dmgdh / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5RKL4, UniProt: Q63342*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O6
#4: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M NaSCN, 20% PEG 3350, 0.1 M Tris pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→48.19 Å / Num. all: 167803 / Num. obs: 167803 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 21.6 Å2 / Rsym value: 0.037 / Net I/σ(I): 22.2
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.5 / % possible all: 90.2

-
Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PJ5

1pj5


Resolution: 1.85→48.19 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.995 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23053 3356 2 %RANDOM
Rwork0.20648 ---
obs0.20697 163455 96.39 %-
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: 35.572 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å2-0 Å22.73 Å2
2--1.23 Å20 Å2
3----2.76 Å2
Refinement stepCycle: 1 / Resolution: 1.85→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13063 0 194 721 13978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01913621
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212863
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.97718493
X-RAY DIFFRACTIONr_angle_other_deg0.856329635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98751653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03923.681614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.317152274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5621590
X-RAY DIFFRACTIONr_chiral_restr0.0740.21981
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115319
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023151
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_it0.8951.9196606
X-RAY DIFFRACTIONr_mcbond_other0.8751.9146593
X-RAY DIFFRACTIONr_mcangle_it1.3662.8668243
X-RAY DIFFRACTIONr_mcangle_other1.3662.8668242
X-RAY DIFFRACTIONr_scbond_it1.2482.1067015
X-RAY DIFFRACTIONr_scbond_other1.232.1027005
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9743.09710238
X-RAY DIFFRACTIONr_long_range_B_refined4.04416.4916033
X-RAY DIFFRACTIONr_long_range_B_other3.97616.215684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 52989 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 211 -
Rwork0.355 10865 -
obs--86.99 %
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)
13.8559-0.6281-0.52794.4838-0.46094.33260.04880.6348-0.3853-0.4671-0.02110.00160.3397-0.0658-0.02770.14820.00430.04370.1359-0.05910.071162.942-9.51557.943
21.313-0.0704-0.35780.69190.13512.91470.09520.04140.0868-0.1202-0.0214-0.1703-0.07160.3573-0.07380.0837-0.02940.06590.07610.00170.096569.4260.99572.08
34.8342-0.42411.32981.4577-0.4453.19750.19340.26420.53-0.1522-0.1119-0.3446-0.68520.7571-0.08160.3282-0.21950.17110.224-0.01080.290776.51318.21573.009
40.94640.0172-0.85050.59830.05421.79640.04910.04070.0154-0.00780.02090.0269-0.0888-0.1475-0.06990.02710.0082-0.01880.02490.01770.038245.322-2.67390.799
54.28440.11870.20793.63521.11224.5002-0.0117-0.6669-0.41020.3968-0.0147-0.03270.5998-0.08570.02650.13570.01560.04130.1150.08250.07613.529-9.75356.749
61.31030.0332-0.31250.6858-0.25413.42250.021-0.04940.05610.12320.0140.1733-0.0412-0.4235-0.03510.02860.00520.03220.0621-0.00740.09027.0981.16742.843
75.06630.36931.32791.46890.32633.92030.0739-0.28850.47370.1426-0.04770.3519-0.7858-0.7908-0.02620.29490.21090.10320.19210.00230.26250.36318.55342.055
80.86-0.0887-0.92030.5620.08622.3951-0.0384-0.0701-0.01130.00430.027-0.0240.10680.30580.01150.01960.0159-0.02050.0446-0.00280.032831.171-2.86624.171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 67
2X-RAY DIFFRACTION2A68 - 258
3X-RAY DIFFRACTION3A259 - 360
4X-RAY DIFFRACTION4A361 - 857
5X-RAY DIFFRACTION5B38 - 67
6X-RAY DIFFRACTION6B68 - 258
7X-RAY DIFFRACTION7B259 - 360
8X-RAY DIFFRACTION8B361 - 857

+
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