[English] 日本語
Yorodumi
- PDB-7nrz: Crystal structure of malate dehydrogenase from Trypanosoma cruzi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nrz
TitleCrystal structure of malate dehydrogenase from Trypanosoma cruzi
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Glycosomal enzyme / Trypanosoma cruzi
Function / homology
Function and homology information


intracellular organelle lumen / (S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 1 / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / malate dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSonani, R.R. / Kurpiewska, K. / Lewinski, K. / Dubin, G.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/M/NZ1/00797 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Distinct sequence and structural feature of trypanosoma malate dehydrogenase.
Authors: Sonani, R.R. / Kurpiewska, K. / Lewinski, K. / Dubin, G.
History
DepositionMar 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
C: Malate dehydrogenase
D: Malate dehydrogenase
E: Malate dehydrogenase
F: Malate dehydrogenase
G: Malate dehydrogenase
H: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,01397
Polymers272,8558
Non-polymers6,15889
Water7,188399
1
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,50834
Polymers68,2142
Non-polymers2,29532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,75524
Polymers68,2142
Non-polymers1,54222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Malate dehydrogenase
F: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,63122
Polymers68,2142
Non-polymers1,41820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Malate dehydrogenase
H: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,11817
Polymers68,2142
Non-polymers90415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.040, 148.331, 251.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Malate dehydrogenase


Mass: 34106.832 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053506503.69 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4DRD8, (S)-malate dehydrogenase (NAD+, oxaloacetate-forming)

-
Non-polymers , 6 types, 488 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 79 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density meas: 53.82 Mg/m3 / Density % sol: 55.09 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 30 mM Sodium nitrate, 30 mM Sodium Phosphate 30 mM Ammonium Sulphate, 0.1 M bicine/Trizma pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→23.319 Å / Num. obs: 91983 / % possible obs: 98.86 % / Redundancy: 11.8 % / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 15.18
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8774 / CC1/2: 0.512 / CC star: 0.823 / % possible all: 95.83

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DFD

2dfd


Resolution: 2.6→23.319 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 4647 5.05 %
Rwork0.2031 87323 -
obs0.2038 91970 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.61 Å2 / Biso mean: 57.4447 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.6→23.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19043 0 398 399 19840
Biso mean--65.21 51.72 -
Num. residues----2584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.62950.31471590.3005274395
2.6295-2.66040.35491260.3101282096
2.6604-2.69280.31111610.3043276396
2.6928-2.72690.31521590.2886280097
2.7269-2.76270.32421370.2833287397
2.7627-2.80050.30351670.2737278797
2.8005-2.84040.29431710.2681281298
2.8404-2.88270.28461510.2601282798
2.8827-2.92770.24891460.2545287698
2.9277-2.97560.30091710.2434288399
2.9756-3.02680.26151520.2272888100
3.0268-3.08170.24421410.23832928100
3.0817-3.14090.24591430.2342914100
3.1409-3.20480.2411610.22422941100
3.2048-3.27430.25281510.22192877100
3.2743-3.35030.24251560.21912948100
3.3503-3.43380.22071320.21692944100
3.4338-3.52640.23781280.21562960100
3.5264-3.62970.20681690.19992922100
3.6297-3.74640.21661630.20282944100
3.7464-3.87980.21771630.18932903100
3.8798-4.03430.19411430.18262973100
4.0343-4.21690.19511560.18252965100
4.2169-4.43780.16651480.1792948100
4.4378-4.71370.20931620.17272969100
4.7137-5.07420.18251640.17282950100
5.0742-5.57850.22071570.19142972100
5.5785-6.37130.21291550.20073017100
6.3713-7.97350.16911760.17793038100
7.9735-23.30.151790.153138100
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)
10.8776-0.0372-0.21990.83340.24080.89150.0506-0.06730.05690.1394-0.1264-0.0916-0.12280.07610.00010.3195-0.0477-0.03710.3520.03070.3324-11.993823.1873-17.5084
20.40580.06270.09240.9293-0.08671.29360.07320.03010.0498-0.0733-0.21130.1764-0.2571-0.2134-0.00020.32810.1-0.03030.4202-0.08040.384-36.05218.5977-41.8166
30.43230.1321-0.07441.12220.32071.30830.03660.0378-0.04050.0382-0.1055-0.1980.22030.2689-0.00140.30780.1296-0.00760.45430.0740.401-1.1679-11.4709-38.1866
40.599-0.07760.09931.4487-0.24180.85090.10240.0258-0.08740.3641-0.17170.21560.2736-0.09610.00010.4614-0.0830.07620.3678-0.06180.3819-31.2198-18.6292-22.8922
51.3262-0.2477-0.73850.421-0.15481.0662-0.17810.08460.3485-0.05020.0696-0.1328-0.07220.0983-0.00020.4641-0.0624-0.17880.38720.03370.4893-6.749215.863224.6197
61.4349-0.14030.53680.4594-0.39980.6831-0.3987-0.0484-0.1846-0.0510.1518-0.07240.07750.1372-0.00060.49910.08310.1130.30020.03480.3225-2.926-14.306940.2798
70.78270.3017-0.29150.5158-0.03591.3366-0.20740.00110.15670.04670.01130.0913-0.0334-0.3481-0.00090.3810.1246-0.12130.451-0.09670.4244-43.38958.297243.8413
81.1906-0.28950.26211.158-0.32720.7322-0.30810.1304-0.1678-0.22410.11860.2310.1739-0.3428-0.00020.6519-0.1860.02880.4919-0.09450.4273-39.6163-16.598319.9063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:2201)A1 - 2201
2X-RAY DIFFRACTION2(chain B and resseq 1:2201)B1 - 2201
3X-RAY DIFFRACTION3(chain C and resseq 1:1801)C1 - 1801
4X-RAY DIFFRACTION4(chain D and resseq 1:1901)D1 - 1901
5X-RAY DIFFRACTION5(chain E and resseq 1:1001)E1 - 1001
6X-RAY DIFFRACTION6(chain F and resseq 1:1101)F1 - 1101
7X-RAY DIFFRACTION7(chain G and resseq 1:1601)G1 - 1601
8X-RAY DIFFRACTION8(chain H and resseq 1:901)H1 - 901

+
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