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- PDB-6dvh: Lactate Monooxygenase from Mycobacterium smegmatis - C203A mutant -

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Basic information

Entry
Database: PDB / ID: 6dvh
TitleLactate Monooxygenase from Mycobacterium smegmatis - C203A mutant
ComponentsLactate 2-monooxygenase
KeywordsOXIDOREDUCTASE / alpha-hydroxy acid oxidase / flavoenzyme / lactate metabolism
Function / homology
Function and homology information


lactate 2-monooxygenase / lactate 2-monooxygenase activity / FMN binding
Similarity search - Function
Lactate 2-monooxygenase, FMN-binding domain / Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel ...Lactate 2-monooxygenase, FMN-binding domain / Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / L-lactate 2-monooxygenase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKean, K.M. / Karplus, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-9982727 United States
CitationJournal: Protein Sci. / Year: 2019
Title: Structure and role for active site lid of lactate monooxygenase from Mycobacterium smegmatis.
Authors: Kean, K.M. / Karplus, P.A.
History
DepositionJun 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactate 2-monooxygenase
B: Lactate 2-monooxygenase
C: Lactate 2-monooxygenase
D: Lactate 2-monooxygenase
E: Lactate 2-monooxygenase
F: Lactate 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,03430
Polymers256,5676
Non-polymers4,46724
Water24,7531374
1
A: Lactate 2-monooxygenase
C: Lactate 2-monooxygenase
hetero molecules

A: Lactate 2-monooxygenase
C: Lactate 2-monooxygenase
hetero molecules

A: Lactate 2-monooxygenase
C: Lactate 2-monooxygenase
hetero molecules

A: Lactate 2-monooxygenase
C: Lactate 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,42944
Polymers342,0898
Non-polymers6,34136
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area47660 Å2
ΔGint-611 kcal/mol
Surface area95490 Å2
MethodPISA
2
B: Lactate 2-monooxygenase
D: Lactate 2-monooxygenase
hetero molecules

B: Lactate 2-monooxygenase
D: Lactate 2-monooxygenase
hetero molecules

B: Lactate 2-monooxygenase
D: Lactate 2-monooxygenase
hetero molecules

B: Lactate 2-monooxygenase
D: Lactate 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,42944
Polymers342,0898
Non-polymers6,34136
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area47930 Å2
ΔGint-629 kcal/mol
Surface area96120 Å2
MethodPISA
3
E: Lactate 2-monooxygenase
hetero molecules

E: Lactate 2-monooxygenase
hetero molecules

E: Lactate 2-monooxygenase
hetero molecules

E: Lactate 2-monooxygenase
hetero molecules

F: Lactate 2-monooxygenase
hetero molecules

F: Lactate 2-monooxygenase
hetero molecules

F: Lactate 2-monooxygenase
hetero molecules

F: Lactate 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,27732
Polymers342,0898
Non-polymers5,18824
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
crystal symmetry operation5_546-x+1/2,y-1/2,-z+11
crystal symmetry operation6_556x+1/2,-y+1/2,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_656-y+1,-x,-z+11
Buried area45930 Å2
ΔGint-500 kcal/mol
Surface area95310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.620, 149.620, 274.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-875-

HOH

21A-997-

HOH

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Components

#1: Protein
Lactate 2-monooxygenase / / Lactate oxidase


Mass: 42761.113 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P21795, lactate 2-monooxygenase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1374 / 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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate, pH 4.6, 0.4 M lithium sulfate, 0.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30.9 Å / Num. obs: 338277 / % possible obs: 99.9 % / Redundancy: 26.7 % / CC1/2: 1 / Net I/σ(I): 15.5
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 27.5 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 24764 / CC1/2: 0.23 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30.903 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 33982 10.06 %
Rwork0.169 --
obs0.1716 337920 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→30.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18082 0 276 1374 19732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01219262
X-RAY DIFFRACTIONf_angle_d1.11226355
X-RAY DIFFRACTIONf_dihedral_angle_d13.63411208
X-RAY DIFFRACTIONf_chiral_restr0.0612809
X-RAY DIFFRACTIONf_plane_restr0.0083418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.397511270.380810023X-RAY DIFFRACTION100
1.7193-1.73950.37210920.365110029X-RAY DIFFRACTION100
1.7395-1.76080.344811160.33910041X-RAY DIFFRACTION100
1.7608-1.7830.353611310.32710008X-RAY DIFFRACTION100
1.783-1.80650.328211130.319510040X-RAY DIFFRACTION100
1.8065-1.83120.325311700.30859966X-RAY DIFFRACTION100
1.8312-1.85740.299711290.28810068X-RAY DIFFRACTION100
1.8574-1.88510.317611050.291310045X-RAY DIFFRACTION100
1.8851-1.91460.297811350.283510061X-RAY DIFFRACTION100
1.9146-1.9460.33611520.32210013X-RAY DIFFRACTION100
1.946-1.97950.251711740.244410024X-RAY DIFFRACTION100
1.9795-2.01550.255611010.224610066X-RAY DIFFRACTION100
2.0155-2.05430.23510880.209910109X-RAY DIFFRACTION100
2.0543-2.09620.229311260.20810062X-RAY DIFFRACTION100
2.0962-2.14180.212611470.186910059X-RAY DIFFRACTION100
2.1418-2.19160.197811150.17710068X-RAY DIFFRACTION100
2.1916-2.24640.208311440.179610079X-RAY DIFFRACTION100
2.2464-2.30710.224110880.189510132X-RAY DIFFRACTION100
2.3071-2.37490.183211070.151610146X-RAY DIFFRACTION100
2.3749-2.45160.165411150.145810105X-RAY DIFFRACTION100
2.4516-2.53910.176811730.14810094X-RAY DIFFRACTION100
2.5391-2.64080.169711010.148410156X-RAY DIFFRACTION100
2.6408-2.76090.177111230.147210167X-RAY DIFFRACTION100
2.7609-2.90630.168911060.141810212X-RAY DIFFRACTION100
2.9063-3.08830.17311710.143910162X-RAY DIFFRACTION100
3.0883-3.32640.175511560.14810227X-RAY DIFFRACTION100
3.3264-3.66070.162811560.135410220X-RAY DIFFRACTION100
3.6607-4.18930.155611470.129210323X-RAY DIFFRACTION100
4.1893-5.27380.151911450.127310440X-RAY DIFFRACTION100
5.2738-30.90820.207812290.182110793X-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)
10.77430.07730.04620.4589-0.05811.0003-0.027-0.03540.12780.0506-0.01570.0523-0.2846-0.18650.02410.23620.0712-0.030.1329-0.03280.30561.363327.361910.1689
20.7501-0.01120.06571.3275-0.21551.5162-0.0173-0.13220.0330.251-0.0829-0.2092-0.25940.30090.06770.2673-0.0435-0.06570.32990.0520.311730.292780.208734.1452
30.81540.01820.03790.6804-0.01781.6474-0.0542-0.19920.23280.2242-0.02370.01-0.6264-0.0480.05730.54840.0512-0.04830.2694-0.10810.284570.093530.141253.8542
40.9521-0.0283-0.1071.1319-0.04351.7431-0.0424-0.2857-0.08040.1951-0.0112-0.21350.16610.45650.04780.6433-0.0006-0.11170.84150.09620.401130.203970.348477.7579
50.75760.1326-0.15220.7798-0.05521.2318-0.1098-0.14230.18440.144-0.1521-0.0747-1.10160.59770.18221.7379-0.3101-0.27011.29950.08960.549189.401126.995103.23
60.448-0.1237-0.23730.9695-0.01051.2082-0.13650.1216-0.00890.0832-0.1062-0.21580.93510.86460.17591.81280.39540.221.66460.17080.541421.760953.4695127.2934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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