[English] 日本語
Yorodumi
- PDB-4i1i: Crystal structure of a putative Cytosolic malate dehydrogenase fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i1i
TitleCrystal structure of a putative Cytosolic malate dehydrogenase from Leishmania major Friedlin in complex with NAD
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Leishmania major / Malate dehydrogenase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle / nucleotide binding / cytosol
Similarity search - Function
Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 ...Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Malate dehydrogenase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a putative Cytosolic malate dehydrogenase from Leishmania major Friedlin in complex with NAD
Authors: SSGCID / Abendroth, J. / Edwards, T.E. / Myler, P.
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,22411
Polymers72,9652
Non-polymers1,2599
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-23 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.820, 65.130, 77.490
Angle α, β, γ (deg.)90.000, 110.670, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Malate dehydrogenase


Mass: 36482.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: cMDH, LMJF_28_2860 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4Q7X6, malate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.1 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: EmeraldBio PACT screen a3: 25% PEG 1500, 100mM SPG buffer pH 6.0; LemaA.01212.a.A1.P001468 at 15mg/ml + 2.5mM NAD, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 96750 / Num. obs: 95941 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 25.149 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obsRsym value% possible all
1.5-1.542.60.352.7818894712467110.3594.2
1.54-1.580.2973.9424609696499.3
1.58-1.630.2584.7325037668899.8
1.63-1.680.2115.7424385651399.8
1.68-1.730.1836.5223859635799.8
1.73-1.790.1547.8423144613799.7
1.79-1.860.1259.4422435594199.5
1.86-1.940.1041121370567499.5
1.94-2.020.08812.9620705546999.7
2.02-2.120.07614.7819693519999.5
2.12-2.240.06516.419025500199.3
2.24-2.370.0617.6517794468799.5
2.37-2.540.05718.9716829442199.6
2.54-2.740.05520.1315788415799.5
2.74-30.05121.4414383378199.7
3-3.350.0522.813135346099.4
3.35-3.870.04924.0211509304999.5
3.87-4.740.04724.729717257999.5
4.74-6.710.04524.47596202299.2
6.710.04424.223938113198.1

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
REFMAC5.7.0032phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H7P

4h7p


Resolution: 1.5→48.5 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.17 / WRfactor Rwork: 0.1488 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9116 / SU B: 2.034 / SU ML: 0.038 / SU R Cruickshank DPI: 0.0613 / SU Rfree: 0.0613 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1655 4794 5 %RANDOM
Rwork0.1449 ---
all0.1459 96750 --
obs0.1459 95920 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.59 Å2 / Biso mean: 21.1806 Å2 / Biso min: 9.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.07 Å2
2--0.1 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4567 0 79 623 5269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194807
X-RAY DIFFRACTIONr_bond_other_d0.0010.024673
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9846578
X-RAY DIFFRACTIONr_angle_other_deg0.803310705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3675659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.38223.684171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.23215730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2041533
X-RAY DIFFRACTIONr_chiral_restr0.1020.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021022
X-RAY DIFFRACTIONr_mcbond_it1.1891.2432558
X-RAY DIFFRACTIONr_mcbond_other1.1891.2432557
X-RAY DIFFRACTIONr_mcangle_it1.841.8613198
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 335 -
Rwork0.237 6362 -
all-6697 -
obs-6711 94.23 %
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)
10.27620.0804-0.13860.50060.10110.8276-0.01350.04630.0067-0.0177-0.00230.00450.0294-0.0340.01580.05410.0030.0440.02360.00210.038-5.29920.0862.283
20.5794-0.0327-0.06590.29710.11890.7921-0.0112-0.0712-0.00110.0659-0.01220.02150.0837-0.01420.02330.0886-0.01470.0550.0176-0.01020.0367-13.81616.46795.001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 324
2X-RAY DIFFRACTION1A400 - 405
3X-RAY DIFFRACTION2B2 - 324
4X-RAY DIFFRACTION2B401 - 403

+
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