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- PDB-4l4s: Structural characterisation of the NADH binary complex of human l... -

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Basic information

Entry
Database: PDB / ID: 4l4s
TitleStructural characterisation of the NADH binary complex of human lactate dehydrogenase M isozyme
ComponentsL-lactate dehydrogenase A chain
KeywordsOXIDOREDUCTASE / Glycolysis / anaerobic respiration
Function / homology
Function and homology information


oxidoreductase complex / Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion ...oxidoreductase complex / Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion / extracellular exosome / identical protein binding / membrane / nucleus / cytosol
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 / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsDempster, S. / Harper, S. / Moses, J.E. / Dreveny, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural characterization of the apo form and NADH binary complex of human lactate dehydrogenase.
Authors: Dempster, S. / Harper, S. / Moses, J.E. / Dreveny, I.
History
DepositionJun 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Structure summary
Revision 1.2Jun 4, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: L-lactate dehydrogenase A chain
A: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6804
Polymers75,3492
Non-polymers1,3312
Water66737
1
H: L-lactate dehydrogenase A chain
A: L-lactate dehydrogenase A chain
hetero molecules

H: L-lactate dehydrogenase A chain
A: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,3608
Polymers150,6984
Non-polymers2,6624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area17560 Å2
ΔGint-118 kcal/mol
Surface area53910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.317, 84.317, 276.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein L-lactate dehydrogenase A chain / LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma ...LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma antigen NY-REN-59


Mass: 37674.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHA, PIG19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00338, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.26 Å3/Da / Density % sol: 62.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 % PEG 8000, 100 mM HEPES, 20 % ethylene glycol, 10 % acetonitrile, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.9→84.317 Å / Num. all: 23067 / Num. obs: 23067 / % possible obs: 99.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 43.37 Å2 / Rsym value: 0.203 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.9-3.065.60.77111840532650.77199.9
3.06-3.245.90.5831.31842231350.583100
3.24-3.4760.3811.91740029210.38199.9
3.47-3.745.90.2662.71624227590.266100
3.74-4.15.40.1823.91381525400.18299.5
4.1-4.595.60.1186.21306223330.11899.9
4.59-5.295.90.1126.51217720660.112100
5.29-6.485.60.135.61013717950.13100
6.48-9.175.10.0818.7715614170.08199.6
9.17-29.1915.40.05212.345208360.05297.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.42 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.9 Å29.19 Å
Translation2.9 Å29.19 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
PHENIX1.7.3_928refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.191 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.42 / σ(F): 1.34 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 1183 5.14 %
Rwork0.1849 --
obs0.188 23011 99.78 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.59 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 134.65 Å2 / Biso mean: 39.1416 Å2 / Biso min: 4.67 Å2
Baniso -1Baniso -2Baniso -3
1-4.5568 Å20 Å2-0 Å2
2--4.5568 Å2-0 Å2
3----9.1137 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5134 0 88 37 5259
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)
12.6788-2.15051.29125.30610.12651.00110.70.5343-0.6935-1.221-0.05940.20220.37090.2905-0.58770.737-0.09370.04340.329-0.06810.349731.2414-53.098521.145
21.2507-0.19670.53991.16240.31020.70260.00690.1439-0.1641-0.18910.013-0.09490.11180.03030.00310.11990.03150.00790.1567-0.0738-0.025529.2822-30.932314.6045
32.2429-0.8245-0.32686.4033-2.856.31980.12430.28250.3243-0.1548-0.0547-0.3269-0.76030.1262-0.06440.1551-0.00030.0790.203-0.05070.043520.7178-19.3603-0.1036
40.55570.05950.03210.10470.13340.8918-0.03460.05750.1266-0.07720.00020.0704-0.1224-0.01130.02770.0206-0.0791-0.05750.0516-0.04520.019413.9049-11.268720.2937
53.1187-1.0691-0.40133.96081.77460.79750.03380.44730.0195-0.2784-0.09420.0621-0.0135-0.0777-0.00440.1748-0.0196-0.10480.11850.07010.07795.7884-7.31595.7565
60.4842-1.1878-0.7713.03261.75681.3811-0.2081-0.31120.60560.13170.3421-0.6866-0.22820.3017-0.13760.3639-0.10220.04330.2216-0.08250.235825.8498-0.054543.7907
72.5738-0.42150.70591.1730.13221.14290.0234-0.08950.07450.0068-0.0461-0.1925-0.15340.11940.05070.0516-0.04970.02090.1488-0.01950.082138.3658-11.557128.1725
82.3597-1.1643-1.92284.01341.81524.5337-0.1390.4533-0.2291-0.7146-0.25150.1493-0.0586-0.07940.10280.1852-0.03470.0010.3696-0.04620.191957.3511-13.149220.8027
91.2251.1351-0.03031.4581-0.191.1345-0.00190.0386-0.3449-0.0870.0274-0.47040.33430.386-0.03870.18730.0917-0.02930.3233-0.04690.169951.3788-33.673727.5237
106.2523.5126-2.04637.1122-1.02973.44620.24140.12390.0429-0.1969-0.1216-0.7065-0.04010.2445-0.11420.16690.14540.08530.4829-0.06210.401767.6619-29.257124.7875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resseq 1:20)H1 - 20
2X-RAY DIFFRACTION2chain 'H' and (resseq 21:93)H21 - 93
3X-RAY DIFFRACTION3chain 'H' and (resseq 94:126)H94 - 126
4X-RAY DIFFRACTION4chain 'H' and (resseq 127:308)H127 - 308
5X-RAY DIFFRACTION5chain 'H' and (resseq 309:331)H309 - 331
6X-RAY DIFFRACTION6chain 'A' and (resseq 1:20)A1 - 20
7X-RAY DIFFRACTION7chain 'A' and (resseq 21:93)A21 - 93
8X-RAY DIFFRACTION8chain 'A' and (resseq 94:126)A94 - 126
9X-RAY DIFFRACTION9chain 'A' and (resseq 127:308)A127 - 308
10X-RAY DIFFRACTION10chain 'A' and (resseq 309:331)A309 - 331

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