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- PDB-2v65: Apo LDH from the psychrophile C. gunnari -

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Basic information

Entry
Database: PDB / ID: 2v65
TitleApo LDH from the psychrophile C. gunnari
ComponentsL-LACTATE DEHYDROGENASE A CHAIN
KeywordsOXIDOREDUCTASE / LACTATE DEHYDROGENASE / NAD / FISH / GLYCOLYSIS
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase activity / carboxylic acid metabolic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / 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 ...L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / 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
L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesCHAMPSOCEPHALUS GUNNARI (mackerel icefish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCoquelle, N. / Madern, D. / Vellieux, F.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Activity, Stability and Structural Studies of Lactate Dehydrogenases Adapted to Extreme Thermal Environments.
Authors: Coquelle, N. / Fioravanti, E. / Weik, M. / Vellieux, F. / Madern, D.
History
DepositionJul 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Apr 3, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-LACTATE DEHYDROGENASE A CHAIN
B: L-LACTATE DEHYDROGENASE A CHAIN


Theoretical massNumber of molelcules
Total (without water)72,4062
Polymers72,4062
Non-polymers00
Water5,495305
1
A: L-LACTATE DEHYDROGENASE A CHAIN

A: L-LACTATE DEHYDROGENASE A CHAIN

A: L-LACTATE DEHYDROGENASE A CHAIN

A: L-LACTATE DEHYDROGENASE A CHAIN


Theoretical massNumber of molelcules
Total (without water)144,8124
Polymers144,8124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_544x,-y-1,-z-11
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_554-x,y,-z-11
Buried area20320 Å2
ΔGint-165.1 kcal/mol
Surface area45090 Å2
MethodPISA
2
B: L-LACTATE DEHYDROGENASE A CHAIN

B: L-LACTATE DEHYDROGENASE A CHAIN

B: L-LACTATE DEHYDROGENASE A CHAIN

B: L-LACTATE DEHYDROGENASE A CHAIN


Theoretical massNumber of molelcules
Total (without water)144,8124
Polymers144,8124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation2_555-x,-y,z1
Buried area19700 Å2
ΔGint-154.2 kcal/mol
Surface area44530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.790, 113.790, 109.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-1019-

HOH

21B-1132-

HOH

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Components

#1: Protein L-LACTATE DEHYDROGENASE A CHAIN / LDH-A


Mass: 36202.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHAMPSOCEPHALUS GUNNARI (mackerel icefish)
Tissue: MUSCLE / Plasmid: PET-11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: O93541, L-lactate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.03 % / Description: NONE
Crystal growTemperature: 277 K / pH: 7.8
Details: 0.1M HEPES PH 7.8, 0.2M PROLINE, 14% PEG 3350, 4 DEG C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97773
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97773 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. obs: 28796 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 2.97 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.51
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.08 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V6A

1v6a


Resolution: 2.35→19.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4900337.22 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1432 5 %RANDOM
Rwork0.228 ---
obs0.228 28632 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.421 Å2 / ksol: 0.329238 e/Å3
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20 Å2
2--2.01 Å20 Å2
3----4.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.35→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 0 305 5277
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.582.5
LS refinement shellResolution: 2.35→2.43 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.282 144 5 %
Rwork0.265 2726 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_JPP.PARAMPROTEIN_JPP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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