[English] 日本語
Yorodumi
- PDB-6bfg: Crystal structure of monotopic membrane protein (S)-mandelate deh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bfg
TitleCrystal structure of monotopic membrane protein (S)-mandelate dehydrogenase
Components(S)-mandelate dehydrogenase
KeywordsOXIDOREDUCTASE / membrane protein / Flavoprotein / alpha-hydroxy acid enzyme / TIM BARREL
Function / homology
Function and homology information


(S)-mandelate dehydrogenase / (S)-mandelate dehydrogenase activity / mandelate catabolic process / : / fatty acid alpha-oxidation / L-lactate dehydrogenase activity / peroxisome / FMN binding / plasma membrane
Similarity search - Function
Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / (S)-mandelate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSukumar, N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
National Institutes of Health/Office of the DirectorS10OD021527 United States
CitationJournal: Biochimie / Year: 2018
Title: Structure of the monotopic membrane protein (S)-mandelate dehydrogenase at 2.2 angstrom resolution.
Authors: Sukumar, N. / Liu, S. / Li, W. / Mathews, F.S. / Mitra, B. / Kandavelu, P.
History
DepositionOct 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: (S)-mandelate dehydrogenase
B: (S)-mandelate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,38221
Polymers88,6432
Non-polymers2,73819
Water4,684260
1
A: (S)-mandelate dehydrogenase
B: (S)-mandelate dehydrogenase
hetero molecules

A: (S)-mandelate dehydrogenase
B: (S)-mandelate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,76442
Polymers177,2874
Non-polymers5,47738
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area11220 Å2
ΔGint-35 kcal/mol
Surface area55220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.358, 129.879, 143.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B

-
Components

-
Protein / Sugars , 2 types, 3 molecules AB

#10: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#1: Protein (S)-mandelate dehydrogenase / L(+)-mandelate dehydrogenase / MDH


Mass: 44321.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlB / Production host: Escherichia coli (E. coli) / References: UniProt: P20932, (S)-mandelate dehydrogenase

-
Non-polymers , 9 types, 278 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: PEG monoethyl ether 2000, 20% glycerol, 100mM tri-sodium citrate pH 5.6, 5% PEG200, 1.3mM FMN

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 55031 / % possible obs: 93.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.186 / Net I/σ(I): 9.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.2 / % possible all: 69

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P4C

1p4c


Resolution: 2.2→41.4 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.17
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1992 3.62 %RANDOM
Rwork0.197 ---
obs0.198 54963 93.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.39 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5826 0 178 260 6264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126103
X-RAY DIFFRACTIONf_angle_d1.1648245
X-RAY DIFFRACTIONf_dihedral_angle_d14.6073634
X-RAY DIFFRACTIONf_chiral_restr0.059916
X-RAY DIFFRACTIONf_plane_restr0.0081043
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A4396X-RAY DIFFRACTIONPOSITIONAL
12B4396X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1954-2.25030.29281060.27442590X-RAY DIFFRACTION65
2.2503-2.31110.3011020.28152993X-RAY DIFFRACTION75
2.3111-2.37910.35051260.28133350X-RAY DIFFRACTION83
2.3791-2.45590.36951370.29163676X-RAY DIFFRACTION92
2.4559-2.54370.33751540.28443948X-RAY DIFFRACTION98
2.5437-2.64550.30021400.25524007X-RAY DIFFRACTION100
2.6455-2.76590.28991510.23423998X-RAY DIFFRACTION100
2.7659-2.91170.2411590.21274019X-RAY DIFFRACTION100
2.9117-3.0940.24331540.20844056X-RAY DIFFRACTION99
3.094-3.33280.24331500.19253969X-RAY DIFFRACTION98
3.3328-3.6680.20871520.16624049X-RAY DIFFRACTION100
3.668-4.19840.16421490.1484062X-RAY DIFFRACTION99
4.1984-5.28780.17541530.14454088X-RAY DIFFRACTION99
5.2878-41.44940.25981590.19494166X-RAY DIFFRACTION98

+
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