[English] 日本語
Yorodumi
- PDB-3fmx: Crystal structure of Tartrate dehydrogenase from Pseudomonas puti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fmx
TitleCrystal structure of Tartrate dehydrogenase from Pseudomonas putida complexed with NADH
ComponentsTartrate dehydrogenase/decarboxylase
KeywordsOXIDOREDUCTASE / Lyase / Magnesium / Manganese / NAD
Function / homology
Function and homology information


D-malate dehydrogenase (decarboxylating) / tartrate dehydrogenase / tartrate decarboxylase / tartrate dehydrogenase activity / D-malate dehydrogenase (decarboxylating) (NAD+) activity / tartrate decarboxylase activity / NAD binding / magnesium ion binding / cytoplasm
Similarity search - Function
Tartrate dehydrogenase / : / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / AMMONIUM ION / Tartrate dehydrogenase/decarboxylase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMalik, R. / Viola, R.E.
CitationJournal: To be Published
Title: Structural Characterization of Tartrate Dehydrogenase: a versatile enzyme catalyzing multiple reactions
Authors: Malik, R. / Viola, R.E.
History
DepositionDec 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2013Group: Non-polymer description
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
X: Tartrate dehydrogenase/decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2003
Polymers40,5171
Non-polymers6832
Water30617
1
X: Tartrate dehydrogenase/decarboxylase
hetero molecules

X: Tartrate dehydrogenase/decarboxylase
hetero molecules

X: Tartrate dehydrogenase/decarboxylase
hetero molecules

X: Tartrate dehydrogenase/decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,80212
Polymers162,0684
Non-polymers2,7348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area19010 Å2
ΔGint-94 kcal/mol
Surface area48210 Å2
MethodPISA
2
X: Tartrate dehydrogenase/decarboxylase
hetero molecules

X: Tartrate dehydrogenase/decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4016
Polymers81,0342
Non-polymers1,3674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area7870 Å2
ΔGint-37 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.906, 182.906, 66.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

-
Components

#1: Protein Tartrate dehydrogenase/decarboxylase / TDH / D-malate dehydrogenase [decarboxylating]


Mass: 40516.922 Da / Num. of mol.: 1 / Mutation: D79G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ttuC / Plasmid: pET 3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: Q51945, tartrate dehydrogenase, tartrate decarboxylase, D-malate dehydrogenase (decarboxylating)
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 4 Å3/Da / Density % sol: 69.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.65 M ammonium sulfate, 0.2 M ammonium tartrate, 0.01 M DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.03 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 14251 / % possible obs: 84.7 %
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.3 % / % possible all: 80.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FLK

3flk


Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.822 / SU B: 18.902 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R: 0.793 / ESU R Free: 0.466 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29684 604 4.9 %RANDOM
Rwork0.26017 ---
obs0.26191 11632 85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.794 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 0 45 17 2875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222907
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9683954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5615358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20123.824136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.11615454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0041520
X-RAY DIFFRACTIONr_chiral_restr0.090.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022251
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.21651
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21936
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 47 -
Rwork0.355 884 -
obs--90.21 %

+
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