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- PDB-4q3n: Crystal structure of MGS-M5, a lactate dehydrogenase enzyme from ... -

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Basic information

Entry
Database: PDB / ID: 4q3n
TitleCrystal structure of MGS-M5, a lactate dehydrogenase enzyme from a Medee basin deep-sea metagenome library
ComponentsMGS-M5
KeywordsHYDROLASE / metagenome / metagenomic library / ROSSMANN FOLD / DEHYDROGENASE / OXIDOREDUCTASE / L-LACTATE DEHYDROGENASE
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / glycolytic 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
ACETATE ION / TRIETHYLENE GLYCOL / L-lactate dehydrogenase
Similarity search - Component
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsStogios, P.J. / Xu, X. / Cui, H. / Alcaide, M. / Ferrer, M. / Savchenko, A.
CitationJournal: Environ Microbiol / Year: 2015
Title: Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats.
Authors: Alcaide, M. / Stogios, P.J. / Lafraya, A. / Tchigvintsev, A. / Flick, R. / Bargiela, R. / Chernikova, T.N. / Reva, O.N. / Hai, T. / Leggewie, C.C. / Katzke, N. / La Cono, V. / Matesanz, R. / ...Authors: Alcaide, M. / Stogios, P.J. / Lafraya, A. / Tchigvintsev, A. / Flick, R. / Bargiela, R. / Chernikova, T.N. / Reva, O.N. / Hai, T. / Leggewie, C.C. / Katzke, N. / La Cono, V. / Matesanz, R. / Jebbar, M. / Jaeger, K.E. / Yakimov, M.M. / Yakunin, A.F. / Golyshin, P.N. / Golyshina, O.V. / Savchenko, A. / Ferrer, M.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: MGS-M5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,14918
Polymers34,8181
Non-polymers1,33117
Water6,359353
1
A: MGS-M5
hetero molecules

A: MGS-M5
hetero molecules

A: MGS-M5
hetero molecules

A: MGS-M5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,59672
Polymers139,2714
Non-polymers5,32468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454y-1/2,x+1/2,-z-1/21
crystal symmetry operation10_565-x,-y+1,z1
crystal symmetry operation16_554-y+1/2,-x+1/2,-z-1/21
Buried area31130 Å2
ΔGint-170 kcal/mol
Surface area42770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.818, 92.818, 203.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-693-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MGS-M5


Mass: 34817.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Gene: MGS-M5 / Plasmid: p15-TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A0A0B5KUB4*PLUS

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Non-polymers , 7 types, 370 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Details

Source detailsTHE SAMPLE HAS BEEN OBTAINED FROM LAKE MATAPAN DEEP-SEA AND IDENTIFIED USING THE TECHNIQUE METAGENOME LIBRARY

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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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 0.2 M calcium acetate, 9% PEG 8K, trypsin in 1/70 molar ratio protein:trypsin cryoprotectant: 12% glycerol then paratone, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 6, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→35 Å / Num. obs: 31973 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 45.3
Reflection shellResolution: 1.97→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 5.31 / % possible all: 99.9

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: dev_1538)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LDN

1ldn


Resolution: 1.97→34.31 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 18.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1838 1998 6.25 %
Rwork0.1453 --
obs0.1476 31945 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2443 0 85 353 2881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172617
X-RAY DIFFRACTIONf_angle_d1.4893528
X-RAY DIFFRACTIONf_dihedral_angle_d13.276993
X-RAY DIFFRACTIONf_chiral_restr0.092397
X-RAY DIFFRACTIONf_plane_restr0.008453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9687-2.01790.2921410.21182116X-RAY DIFFRACTION100
2.0179-2.07250.2231390.18832085X-RAY DIFFRACTION100
2.0725-2.13340.21071400.17332101X-RAY DIFFRACTION100
2.1334-2.20230.19511410.15422122X-RAY DIFFRACTION100
2.2023-2.2810.20241410.1582098X-RAY DIFFRACTION100
2.281-2.37230.19561410.15092117X-RAY DIFFRACTION100
2.3723-2.48020.19911410.14792112X-RAY DIFFRACTION100
2.4802-2.61090.19521420.14972125X-RAY DIFFRACTION100
2.6109-2.77450.20061420.1482118X-RAY DIFFRACTION100
2.7745-2.98860.17111420.14332156X-RAY DIFFRACTION100
2.9886-3.28910.17721440.14512149X-RAY DIFFRACTION100
3.2891-3.76450.18611430.12982151X-RAY DIFFRACTION100
3.7645-4.74090.15011470.11772189X-RAY DIFFRACTION100
4.7409-34.31490.17791540.15722308X-RAY DIFFRACTION100
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)
12.0666-0.0399-0.29643.6776-0.93492.5988-0.0375-0.2401-0.12040.29190.0760.1630.1893-0.1125-0.06180.1909-0.04880.01410.23230.00880.2141-9.078737.9186-31.9811
24.36661.0144-1.40661.1957-0.51441.6402-0.0485-0.3375-0.19520.09750.03040.07180.22020.09040.01870.2663-0.0162-0.02170.19150.01140.21085.695826.8371-35.1486
31.5402-0.24490.10241.2038-0.06821.7391-0.0264-0.1417-0.22080.06810.0427-0.0460.30820.244-0.01870.28110.0038-0.00940.22180.03190.226411.36725.564-36.0861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 1:92
2X-RAY DIFFRACTION2chain A and resi 93:194
3X-RAY DIFFRACTION3chain A and resi 195:314

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