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- PDB-5z21: The ternary structure of D-lactate dehydrogenase from Fusobacteri... -

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Basic information

Entry
Database: PDB / ID: 5z21
TitleThe ternary structure of D-lactate dehydrogenase from Fusobacterium nucleatum with NADH and oxamate
ComponentsD-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / Ternary complex / Rossmann Fold / Dehydrogenase / NADH binding
Function / homology
Function and homology information


D-lactate dehydrogenase / D-lactate dehydrogenase (NAD+) activity / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain ...D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXAMIC ACID / 2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFurukawa, N. / Miyanaga, A. / Nakajima, M. / Taguchi, H.
CitationJournal: Biochemistry / Year: 2018
Title: Structural Basis of Sequential Allosteric Transitions in Tetrameric d-Lactate Dehydrogenases from Three Gram-Negative Bacteria.
Authors: Furukawa, N. / Miyanaga, A. / Nakajima, M. / Taguchi, H.
History
DepositionDec 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: D-lactate dehydrogenase
B: D-lactate dehydrogenase
C: D-lactate dehydrogenase
D: D-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,17312
Polymers163,1554
Non-polymers3,0188
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22780 Å2
ΔGint-78 kcal/mol
Surface area46550 Å2
Unit cell
Length a, b, c (Å)117.230, 159.740, 90.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A5 - 333
2010B5 - 333
1020A8 - 333
2020C8 - 333
1030A5 - 333
2030D5 - 333
1040B8 - 333
2040C8 - 333
1050B4 - 334
2050D4 - 334
1060C8 - 333
2060D8 - 333

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
D-lactate dehydrogenase


Mass: 40788.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131) (bacteria)
Strain: ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131 / Gene: FN0511 / Plasmid: pColdI / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q8RG11, D-lactate dehydrogenase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2 mM NADH, 25 mM oxamate, 100 mM acetate buffer pH 5, 4% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 17, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.3→42.01 Å / Num. obs: 75787 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.05 / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 10924 / CC1/2: 0.738 / Rpim(I) all: 0.254 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
ADSCdata collection
SCALAdata scaling
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J49

1j49


Resolution: 2.3→42.01 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.892 / SU B: 14.647 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.228 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25142 3810 5 %RANDOM
Rwork0.22546 ---
obs0.22679 71921 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.925 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.3→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10490 0 200 98 10788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0210866
X-RAY DIFFRACTIONr_bond_other_d0.0080.0210556
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.99314682
X-RAY DIFFRACTIONr_angle_other_deg1.332324264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2151315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9925496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.069151985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5221552
X-RAY DIFFRACTIONr_chiral_restr0.0970.21681
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212125
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022443
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5411.995272
X-RAY DIFFRACTIONr_mcbond_other1.5411.995271
X-RAY DIFFRACTIONr_mcangle_it2.4052.9796583
X-RAY DIFFRACTIONr_mcangle_other2.4052.9796584
X-RAY DIFFRACTIONr_scbond_it1.6382.1615594
X-RAY DIFFRACTIONr_scbond_other1.6382.1615595
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6683.1728100
X-RAY DIFFRACTIONr_long_range_B_refined3.96315.50312352
X-RAY DIFFRACTIONr_long_range_B_other3.9615.50112343
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A207300.1
12B207300.1
21A201720.1
22C201720.1
31A208520.09
32D208520.09
41B203540.1
42C203540.1
51B213210.09
52D213210.09
61C203530.1
62D203530.1
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 254 -
Rwork0.259 5262 -
obs--100 %
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)
10.2332-0.01740.14970.3862-0.2220.2423-0.0137-0.0093-0.01820.1870.03730.0531-0.0714-0.0545-0.02350.1650.02290.05040.12320.02330.0468-1.850437.7317101.6025
20.2394-0.0581-0.00630.6179-0.18370.2923-0.03840.030.07890.12060.0048-0.2801-0.0187-0.00020.03360.0411-0.0232-0.08910.10630.01850.204121.289958.425184.1393
30.1524-0.4355-0.02591.86420.24980.17580.171-0.0092-0.0727-0.6463-0.24210.2365-0.122-0.03710.07110.27910.0737-0.12450.1489-0.00870.0682-6.584835.203756.7514
40.20910.01450.03751.4935-0.0560.11690.0611-0.0564-0.0979-0.2265-0.0439-0.4577-0.0344-0.0837-0.01710.0820.02380.06440.07550.03910.221120.392615.559368.3281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 333
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2B3 - 333
4X-RAY DIFFRACTION2B401 - 402
5X-RAY DIFFRACTION3C7 - 333
6X-RAY DIFFRACTION3C401 - 402
7X-RAY DIFFRACTION4D3 - 333
8X-RAY DIFFRACTION4D401 - 402

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