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- PDB-1i0z: HUMAN HEART L-LACTATE DEHYDROGENASE H CHAIN, TERNARY COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 1i0z
TitleHUMAN HEART L-LACTATE DEHYDROGENASE H CHAIN, TERNARY COMPLEX WITH NADH AND OXAMATE
ComponentsL-LACTATE DEHYDROGENASE H CHAIN
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ROSSMANN FOLD
Function / homology
Function and homology information


L-lactate dehydrogenase / oxidoreductase complex / pyruvate metabolic process / NAD+ metabolic process / L-lactate dehydrogenase (NAD+) activity / Pyruvate metabolism / lactate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane ...L-lactate dehydrogenase / oxidoreductase complex / pyruvate metabolic process / NAD+ metabolic process / L-lactate dehydrogenase (NAD+) activity / Pyruvate metabolism / lactate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane / membrane raft / mitochondrion / extracellular exosome / identical protein binding / membrane / cytosol / 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXAMIC ACID / L-lactate dehydrogenase B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRead, J.A. / Winter, V.J. / Eszes, C.M. / Sessions, R.B. / Brady, R.L.
CitationJournal: Proteins / Year: 2001
Title: Structural basis for altered activity of M- and H-isozyme forms of human lactate dehydrogenase.
Authors: Read, J.A. / Winter, V.J. / Eszes, C.M. / Sessions, R.B. / Brady, R.L.
History
DepositionJan 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Aug 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-LACTATE DEHYDROGENASE H CHAIN
B: L-LACTATE DEHYDROGENASE H CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6056
Polymers73,0962
Non-polymers1,5094
Water5,729318
1
A: L-LACTATE DEHYDROGENASE H CHAIN
B: L-LACTATE DEHYDROGENASE H CHAIN
hetero molecules

A: L-LACTATE DEHYDROGENASE H CHAIN
B: L-LACTATE DEHYDROGENASE H CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,21112
Polymers146,1934
Non-polymers3,0188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area25950 Å2
ΔGint-139 kcal/mol
Surface area44350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.491, 161.683, 137.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit

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Components

#1: Protein L-LACTATE DEHYDROGENASE H CHAIN / LDH-B


Mass: 36548.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHB / Organ: HEART / Plasmid: PKK223-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07195, L-lactate dehydrogenase
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein solution: 15 mg/ml H4-ldh, 50 mM Na-Hepes pH 7.5, 2.5 mM NADH, 1 mM oxamate. Well solution: 21% PEG 8k, 100 mM Na-HEPES ph 7.5., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
22.5 mMNADH1drop
31 mMsodium oxamate1drop
450 mMHEPES1drop
521 %PEG80001reservoir
6100 mMsodium acetate1reservoir
7100 mMsodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 7, 1999
RadiationMonochromator: platinum mirrors/Ge 111 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 39237 / Num. obs: 37680 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.31 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.25
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 8.5 / Num. unique all: 4400 / % possible all: 91.1
Reflection shell
*PLUS
% possible obs: 91.1 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ldh

5ldh


Resolution: 2.1→20 Å / SU B: 4.848 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.247 / ESU R Free: 0.197 / Stereochemistry target values: Engh & Huber
Details: METHOD USED FOR BULK SOLVENT MODELLING: BABINET MODEL WITH MASK. PARAMETERS FOR MASK CALCULATION: VDW PROBE RADIUS = 1.40, ION PROBE RADIUS = 0.80, SHRINKAGE RADIUS = 0.80.
RfactorNum. reflection% reflectionSelection details
Rfree0.23012 1867 5 %RANDOM
Rwork0.17676 ---
obs0.17946 35460 95.22 %-
all-37680 --
Displacement parametersBiso mean: 19.533 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2---0.53 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 100 318 5522
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.022
X-RAY DIFFRACTIONp_mcbond_it0.8291.5
X-RAY DIFFRACTIONp_mcangle_it1.4972
X-RAY DIFFRACTIONp_scbond_it2.5343
X-RAY DIFFRACTIONp_scangle_it4.0214.5
X-RAY DIFFRACTIONp_xyhbond_nbd0.1480.5
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.231 131
Rwork0.169 2370
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.179 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS

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