[English] 日本語
Yorodumi
- PDB-4nd2: Crystal structure of the lactate dehydrogenase from cryptosporidi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nd2
TitleCrystal structure of the lactate dehydrogenase from cryptosporidium parvum complexed with substrate (pyruvic acid) and cofactor analog (3-acetylpyridine adenine dinucleotide)
ComponentsLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / NAD Binding
Function / homology
Function and homology information


L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / nucleotide binding
Similarity search - Function
Malate dehydrogenase, type 3 / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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 3 / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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
3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE / PYRUVIC ACID / L-lactate dehydrogenase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChattopadhyay, D. / Cook, W.J.
CitationJournal: Int.J.Biol.Macromol. / Year: 2014
Title: Biochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase.
Authors: Cook, W.J. / Senkovich, O. / Hernandez, A. / Speed, H. / Chattopadhyay, D.
History
DepositionOct 25, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionDec 17, 2014ID: 2EWD
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase
B: Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5479
Polymers67,7702
Non-polymers1,7777
Water7,476415
1
A: Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase
B: Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase
hetero molecules

A: Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase
B: Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,09418
Polymers135,5394
Non-polymers3,55514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area22610 Å2
ΔGint-97 kcal/mol
Surface area41500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.830, 95.830, 185.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase


Mass: 33884.855 Da / Num. of mol.: 2 / Fragment: unp residues 17-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd7_480, LDH1 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)PLYSS / References: UniProt: Q5CYZ2, L-lactate dehydrogenase
#2: Chemical ChemComp-A3D / 3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE


Mass: 662.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28N6O14P2
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsPEPTIDE SEQUENCE FOR THIS ENTRY WAS TRANSLATED FROM DNA SEQUENCING OF ACTUAL CLONE USED FOR PROTEIN ...PEPTIDE SEQUENCE FOR THIS ENTRY WAS TRANSLATED FROM DNA SEQUENCING OF ACTUAL CLONE USED FOR PROTEIN EXPRESSION. AUTHORS DO NOT KNOW IF THE SEQUENCE DIFFERENCES ARE PCR ERRORS OR MUTATIONS CORRESPONDING DNA POLYMORPHISM OR THERE WERE ERRORS IN PROTEIN DATABASE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The protein was incubated with 1 mM pyruvate and 100 uM APAD+ for 1 hour on ice prior to crystallization. Reservoir solution was 1.45-1.65 M ammonium sulfate in 0.1 M sodium cacodylate, pH 7. ...Details: The protein was incubated with 1 mM pyruvate and 100 uM APAD+ for 1 hour on ice prior to crystallization. Reservoir solution was 1.45-1.65 M ammonium sulfate in 0.1 M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9998 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 67287 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 10.7 % / Rmerge(I) obs: 0.054
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.186 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T2D

1t2d


Resolution: 2→49.61 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.013 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20788 6816 10.1 %RANDOM
Rwork0.19132 ---
obs0.19299 60473 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.258 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.77 Å2-0 Å2
2--0.77 Å2-0 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 2→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 118 415 5241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194909
X-RAY DIFFRACTIONr_bond_other_d0.0010.024762
X-RAY DIFFRACTIONr_angle_refined_deg0.9251.9886659
X-RAY DIFFRACTIONr_angle_other_deg0.664310982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6455632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85725.333180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.66215816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9041516
X-RAY DIFFRACTIONr_chiral_restr0.0470.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025498
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021016
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
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 476 -
Rwork0.218 4312 -
obs--97.5 %

+
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