[English] 日本語
Yorodumi
- PDB-3zh2: Structure of Plasmodium falciparum lactate dehydrogenase in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zh2
TitleStructure of Plasmodium falciparum lactate dehydrogenase in complex with a DNA aptamer
Components
  • DNA APTAMER
  • L-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / Malate-aspartate shuttle / L-malate dehydrogenase (NAD+) activity / L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / glycolytic process / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 3 / 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 ...Malate dehydrogenase, type 3 / 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
DNA / DNA (> 10) / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCheung, Y.W. / Kwok, J. / Law, A.W.L. / Watt, R.M. / Kotaka, M. / Tanner, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural Basis for Discriminatory Recognition of Plasmodium Lactate Dehydrogenase by a DNA Aptamer
Authors: Cheung, Y.W. / Kwok, J. / Law, A.W.L. / Watt, R.M. / Kotaka, M. / Tanner, J.A.
History
DepositionDec 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE
C: L-LACTATE DEHYDROGENASE
D: L-LACTATE DEHYDROGENASE
E: DNA APTAMER
G: DNA APTAMER


Theoretical massNumber of molelcules
Total (without water)158,1136
Polymers158,1136
Non-polymers00
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20360 Å2
ΔGint-120 kcal/mol
Surface area48610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.461, 159.489, 88.660
Angle α, β, γ (deg.)90.00, 102.18, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21G

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DC / End label comp-ID: DC / Refine code: 4 / Auth seq-ID: 3 - 25 / Label seq-ID: 3 - 25

Dom-IDAuth asym-IDLabel asym-ID
1EE
2GF

NCS oper:
IDCodeMatrixVector
1given(-0.131, -0.009, -0.991), (-0.003, -1, 0.009), (-0.991, 0.004, 0.131)45.048, 0.749, 39.525
2given(-0.985, -0.172, 0.017), (-0.172, 0.971, -0.163), (0.011, -0.164, -0.986)88.077, 6.774, -10.771
3given(0.113, 0.176, 0.978), (0.176, -0.972, 0.154), (0.978, 0.155, -0.141)44.506, -6.398, -49.136
4given(1), (1), (1)
5given(-0.985217, -0.169551, 0.024504), (-0.171206, 0.969439, -0.175717), (0.006038, -0.177314, -0.984136)88.42956, 6.2313, -10.32197

-
Components

#1: Protein
L-LACTATE DEHYDROGENASE


Mass: 34148.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76NM3, L-lactate dehydrogenase
#2: DNA chain DNA APTAMER


Mass: 10758.911 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 4.08 Å3/Da / Density % sol: 69.87 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M KCL, 0.1 M MAGNESIUM ACETATE, 0.05 M SODIUM CACODYLATE PH 6.5, 10% W/V PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 121507 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.5 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LDG

1ldg


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.052 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25664 6098 5 %RANDOM
Rwork0.2058 ---
obs0.20832 115368 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.213 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å22.07 Å2
2---1.79 Å20 Å2
3---3.41 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9455 1118 0 644 11217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01810856
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1091.89414941
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64551242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28325.956366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.479151739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0491524
X-RAY DIFFRACTIONr_chiral_restr0.1330.21724
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217532
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 474 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Emedium positional0.30.5
2Gmedium positional0.30.5
1Emedium thermal2.272
2Gmedium thermal2.272
LS refinement shellResolution: 2.104→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 385 -
Rwork0.287 6828 -
obs--79.47 %
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)
10.4139-0.0591-0.06860.3015-0.00340.0711-0.00110.0211-0.03860.0613-0.01170.08030.00110.00990.01280.1337-0.00170.00530.1282-0.00130.127327.6089-14.99012.4048
20.2492-0.0269-0.08110.3764-0.13270.09420.022-0.03520.05860.0687-0.00650.03240.00470.0131-0.01540.1708-0.0022-0.00640.1302-0.02040.105539.430715.823411.8803
30.45580.15160.01130.1647-0.0950.15710.0224-0.0005-0.0418-0.0318-0.001-0.06360.01950.0328-0.02140.10330.01050.01480.1248-0.00840.166463.4433-12.8484-10.3901
40.4007-0.1693-0.1020.470.18210.07910.0420.11870.0736-0.0768-0.0352-0.021-0.0137-0.0344-0.00680.15930.0065-0.01910.1750.03270.067646.859113.449-24.8846
52.71561.7719-0.03251.16580.00332.50870.1719-0.28790.12660.1128-0.24390.0428-0.0709-0.82280.0720.1311-0.01880.14780.3737-0.08270.19519.89-5.321425.8398
63.4461-1.16860.03490.41510.12672.22810.11690.36160.0576-0.0388-0.09350.0172-0.12330.7967-0.02330.1057-0.02070.08850.48260.02220.142479.5462-4.411-35.4696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 316
2X-RAY DIFFRACTION2B3 - 316
3X-RAY DIFFRACTION3C2 - 316
4X-RAY DIFFRACTION4D3 - 316
5X-RAY DIFFRACTION5E1 - 27
6X-RAY DIFFRACTION6G1 - 27

+
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