[English] 日本語
Yorodumi
- PDB-3giy: Crystal Structures of the G81A Mutant of the Active Chimera of (S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3giy
TitleCrystal Structures of the G81A Mutant of the Active Chimera of (S)-Mandelate Dehydrogenase and its Complex with Two of its Substrates
Components(S)-mandelate dehydrogenase, Peroxisomal (S)-2-hydroxy-acid oxidase
KeywordsOXIDOREDUCTASE / TIM BARREL
Function / homology
Function and homology information


(S)-mandelate dehydrogenase / (S)-mandelate dehydrogenase activity / oxidative photosynthetic carbon pathway / (S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / mandelate catabolic process / response to other organism / L-lactate dehydrogenase activity / aerobic respiration / FMN binding ...(S)-mandelate dehydrogenase / (S)-mandelate dehydrogenase activity / oxidative photosynthetic carbon pathway / (S)-2-hydroxy-acid oxidase / (S)-2-hydroxy-acid oxidase activity / mandelate catabolic process / response to other organism / L-lactate dehydrogenase activity / aerobic respiration / FMN binding / peroxisome / 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
FLAVIN MONONUCLEOTIDE / Glycolate oxidase / (S)-mandelate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
Spinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / refined directly / Resolution: 1.6 Å
AuthorsSukumar, N. / Dewanti, A. / Merli, A. / Rossi, G.L. / Mitra, B. / Mathews, F.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structures of the G81A mutant form of the active chimera of (S)-mandelate dehydrogenase and its complex with two of its substrates.
Authors: Sukumar, N. / Dewanti, A. / Merli, A. / Rossi, G.L. / Mitra, B. / Mathews, F.S.
History
DepositionMar 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: (S)-mandelate dehydrogenase, Peroxisomal (S)-2-hydroxy-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7983
Polymers42,1461
Non-polymers6522
Water5,116284
1
A: (S)-mandelate dehydrogenase, Peroxisomal (S)-2-hydroxy-acid oxidase
hetero molecules

A: (S)-mandelate dehydrogenase, Peroxisomal (S)-2-hydroxy-acid oxidase
hetero molecules

A: (S)-mandelate dehydrogenase, Peroxisomal (S)-2-hydroxy-acid oxidase
hetero molecules

A: (S)-mandelate dehydrogenase, Peroxisomal (S)-2-hydroxy-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,19212
Polymers168,5854
Non-polymers2,6068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Buried area15730 Å2
ΔGint-38 kcal/mol
Surface area50710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.360, 99.360, 87.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein (S)-mandelate dehydrogenase, Peroxisomal (S)-2-hydroxy-acid oxidase / L(+)-mandelate dehydrogenase / MDH / Glycolate oxidase


Mass: 42146.297 Da / Num. of mol.: 1 / Mutation: G81A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria), (gene. exp.) Spinacia oleracea (spinach)
Production host: Escherichia coli (E. coli)
References: UniProt: P20932, UniProt: P05414, (S)-mandelate dehydrogenase, (S)-2-hydroxy-acid oxidase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS BELIEVE THAT UNP ENTRY P20932 INCORRECTLY LISTS RESIDUE 15 AS ARG INSTEAD OF ALA. ...THE AUTHORS BELIEVE THAT UNP ENTRY P20932 INCORRECTLY LISTS RESIDUE 15 AS ARG INSTEAD OF ALA. SEQUENCING OF (S)-MANDELATE DEHYDROGENASE HAS REPEATEDLY CONFIRMED THAT IT IS ALA 15 RATHER THAN ARG 15

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 200mM MES,0.75% ammonium sulfate, 10% ethylene glycol, 20 uM FMN and 4M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2002
RadiationMonochromator: APS BIOCARS 14_BM_C / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 56124 / Num. obs: 53598 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 28.1
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3730 / % possible all: 66.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: refined directly
Starting model: PDB ENTRY 2A7N

2a7n


Resolution: 1.6→27.4 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.171 2470 -RANDOM
Rwork0.134 ---
all-56002 --
obs-51143 91.3 %-
Displacement parametersBiso mean: 22.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.6→27.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 43 284 3079
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_angle_deg1.2
X-RAY DIFFRACTIONo_dihedral_angle_d21.5
X-RAY DIFFRACTIONo_improper_angle_d0.78
X-RAY DIFFRACTIONo_mcbond_it1.131.5
X-RAY DIFFRACTIONo_mcangle_it1.842
X-RAY DIFFRACTIONo_scbond_it1.742
X-RAY DIFFRACTIONo_scangle_it2.642.5
LS refinement shellResolution: 1.6→1.7 Å
RfactorNum. reflection% reflection
Rfree0.3874 246 -
Rwork0.3844 --
obs-6487 66.3 %

+
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