[English] 日本語
Yorodumi
- PDB-7x1l: Malate dehydrogenase from Geobacillus stearothermophilus (gs-MDH)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7x1l
TitleMalate dehydrogenase from Geobacillus stearothermophilus (gs-MDH) delta E311 mutant complexed with Nicotinamide Adenine Dinucleotide (NAD+)
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogease
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid metabolic process / tricarboxylic acid cycle
Similarity search - Function
Malate dehydrogenase, type 3 / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsShimozawa, Y. / Himiyama, T. / Nakamura, T. / Nishiya, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K06616 Japan
Japan Society for the Promotion of Science (JSPS)20K15403 Japan
Japan Society for the Promotion of Science (JSPS)20K05740 Japan
CitationJournal: Protein Eng.Des.Sel. / Year: 2022
Title: Reducing substrate inhibition of malate dehydrogenase from Geobacillus stearothermophilus by C-terminal truncation.
Authors: Shimozawa, Y. / Matsuhisa, H. / Nakamura, T. / Himiyama, T. / Nishiya, Y.
History
DepositionFeb 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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: Malate dehydrogenase
B: Malate dehydrogenase
E: Malate dehydrogenase
F: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,80012
Polymers214,8196
Non-polymers3,9816
Water3,261181
1
A: Malate dehydrogenase
B: Malate dehydrogenase
E: Malate dehydrogenase
F: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8668
Polymers143,2134
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-94 kcal/mol
Surface area41270 Å2
MethodPISA
2
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules

C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8668
Polymers143,2134
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area19390 Å2
ΔGint-101 kcal/mol
Surface area41940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.850, 82.724, 136.703
Angle α, β, γ (deg.)90.000, 98.588, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Malate dehydrogenase /


Mass: 35803.199 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mdh / Production host: Escherichia coli (E. coli) / References: UniProt: A0A143T1U9, malate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M CHES (pH 8.8), 20 % (w/v) PEG 8000, 2 mM NAD+

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.28→48.633 Å / Num. obs: 122192 / % possible obs: 99.8 % / Redundancy: 3.9 % / CC1/2: 0.999 / Net I/σ(I): 7.8
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 4 % / Num. unique obs: 5972 / CC1/2: 0.997

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BY8

7by8


Resolution: 2.28→48.633 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.66 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.228
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.28 6081 4.977 %
Rwork0.2329 116109 -
all0.235 --
obs-122190 99.812 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 64.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.017 Å20 Å2-0.003 Å2
2---0.004 Å2-0 Å2
3----0.011 Å2
Refinement stepCycle: LAST / Resolution: 2.28→48.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13820 0 264 181 14265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01314302
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713881
X-RAY DIFFRACTIONr_angle_refined_deg1.51.64619410
X-RAY DIFFRACTIONr_angle_other_deg1.221.57832204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99351819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29423.311607
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25152512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9311570
X-RAY DIFFRACTIONr_chiral_restr0.0650.21967
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215787
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022669
X-RAY DIFFRACTIONr_nbd_refined0.1950.22694
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.212796
X-RAY DIFFRACTIONr_nbtor_refined0.1550.26856
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.26770
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2381
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1490.220
X-RAY DIFFRACTIONr_nbd_other0.2040.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.211
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0320.21
X-RAY DIFFRACTIONr_mcbond_it5.3866.577300
X-RAY DIFFRACTIONr_mcbond_other5.3866.5697299
X-RAY DIFFRACTIONr_mcangle_it7.159.8479111
X-RAY DIFFRACTIONr_mcangle_other7.159.8489112
X-RAY DIFFRACTIONr_scbond_it5.927.2397000
X-RAY DIFFRACTIONr_scbond_other5.927.2397001
X-RAY DIFFRACTIONr_scangle_it8.55410.59910298
X-RAY DIFFRACTIONr_scangle_other8.55410.59910299
X-RAY DIFFRACTIONr_lrange_it10.51277.56814997
X-RAY DIFFRACTIONr_lrange_other10.51577.56714982
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.28-2.3390.3164320.29484810.29589470.810.82199.620.265
2.339-2.4030.3394030.27683210.27987520.80.83699.68010.251
2.403-2.4730.3134340.25480780.25785340.8320.86199.74220.235
2.473-2.5480.3193820.24278810.24582800.8460.87799.79470.227
2.548-2.6320.3243750.24976480.25380360.8370.86399.83820.235
2.632-2.7240.3294030.23973500.24377650.8460.87999.84550.232
2.724-2.8260.3033860.23771090.2475050.8630.88799.86680.235
2.826-2.9410.3023570.23868700.24172330.860.88599.9170.24
2.941-3.0720.3073470.24165900.24569400.8720.89399.95680.248
3.072-3.2210.2813470.23362710.23566200.8860.90899.96980.243
3.221-3.3940.2713250.23659980.23863240.90.91199.98420.253
3.394-3.5990.2793340.23256470.23459840.9030.91899.94990.256
3.599-3.8460.262920.22353220.22556230.9150.92999.83990.254
3.846-4.1520.2542520.20650040.20852720.9160.93499.69650.246
4.152-4.5450.2392470.19745990.19948470.9310.9499.97940.249
4.545-5.0760.2372260.19641540.19843810.9230.93899.97720.252
5.076-5.8510.2891910.23537010.23838930.8950.91499.97430.307
5.851-7.140.2971510.24531700.24833220.8840.90999.96990.32
7.14-9.990.2821160.23324910.23526090.9060.92899.92330.3
9.99-48.6330.278810.32714240.32415350.8970.86398.04560.449

+
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