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- PDB-5z20: The ternary structure of D-lactate dehydrogenase from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 5z20
TitleThe ternary structure of D-lactate dehydrogenase from Pseudomonas aeruginosa with NADH and oxamate
ComponentsD-lactate dehydrogenase (Fermentative)
KeywordsOXIDOREDUCTASE / Ternary complex / Rossmann Fold / Dehydrogenase / NADH binding
Function / homology
Function and homology information


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
FORMIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXAMIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / D-lactate dehydrogenase (Fermentative)
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 (Fermentative)
B: D-lactate dehydrogenase (Fermentative)
C: D-lactate dehydrogenase (Fermentative)
D: D-lactate dehydrogenase (Fermentative)
E: D-lactate dehydrogenase (Fermentative)
F: D-lactate dehydrogenase (Fermentative)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,51726
Polymers226,9976
Non-polymers5,52020
Water16,358908
1
A: D-lactate dehydrogenase (Fermentative)
B: D-lactate dehydrogenase (Fermentative)
C: D-lactate dehydrogenase (Fermentative)
D: D-lactate dehydrogenase (Fermentative)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,99818
Polymers151,3314
Non-polymers3,66714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21870 Å2
ΔGint-51 kcal/mol
Surface area44900 Å2
MethodPISA
2
E: D-lactate dehydrogenase (Fermentative)
F: D-lactate dehydrogenase (Fermentative)
hetero molecules

E: D-lactate dehydrogenase (Fermentative)
F: D-lactate dehydrogenase (Fermentative)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,03816
Polymers151,3314
Non-polymers3,70712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554y,x,-z-11
Buried area20990 Å2
ΔGint-47 kcal/mol
Surface area46930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.690, 155.690, 230.011
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11E-571-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A0 - 328
2010B0 - 328
1020A0 - 329
2020C0 - 329
1030A0 - 327
2030D0 - 327
1040A0 - 329
2040E0 - 329
1050A0 - 328
2050F-6 - 328
1060B0 - 328
2060C0 - 328
1070B-9 - 327
2070D-1 - 327
1080B0 - 328
2080E0 - 328
1090B-10 - 328
2090F-8 - 328
10100C0 - 327
20100D0 - 327
10110C0 - 329
20110E0 - 329
10120C0 - 328
20120F-6 - 328
10130D0 - 327
20130E0 - 327
10140D-1 - 327
20140F-7 - 327
10150E0 - 328
20150F-6 - 328

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
D-lactate dehydrogenase (Fermentative)


Mass: 37832.754 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ldhA, PA0927 / Plasmid: pColdI / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9I530, D-lactate dehydrogenase

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Non-polymers , 7 types, 928 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3NO3
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / 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: 3.59 Å3/Da / Density % sol: 65.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1 mM NADH, 10 mM oxamate, 100 mM sodium formate, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 31, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→37.4 Å / Num. obs: 161477 / % possible obs: 98.8 % / Redundancy: 8.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.045 / Net I/σ(I): 13.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 22650 / CC1/2: 0.79 / Rpim(I) all: 0.293 / % possible all: 95.8

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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: 2.2→37.4 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.189 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19891 8080 5 %RANDOM
Rwork0.17065 ---
obs0.17206 153341 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.734 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.08 Å20 Å2
2--0.08 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.2→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15290 0 366 908 16564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01916022
X-RAY DIFFRACTIONr_bond_other_d0.0110.0215166
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.97421795
X-RAY DIFFRACTIONr_angle_other_deg1.589334553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70951988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50523.003766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.104152406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.62215145
X-RAY DIFFRACTIONr_chiral_restr0.1120.22457
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218465
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023998
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_it2.2952.3357967
X-RAY DIFFRACTIONr_mcbond_other2.2952.3357968
X-RAY DIFFRACTIONr_mcangle_it3.1833.4879950
X-RAY DIFFRACTIONr_mcangle_other3.1833.4889951
X-RAY DIFFRACTIONr_scbond_it3.8472.8328055
X-RAY DIFFRACTIONr_scbond_other3.8472.8328055
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7734.08311846
X-RAY DIFFRACTIONr_long_range_B_refined7.34819.89518463
X-RAY DIFFRACTIONr_long_range_B_other7.34819.89518463
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)
11A194810.09
12B194810.09
21A196500.09
22C196500.09
31A197020.08
32D197020.08
41A198160.08
42E198160.08
51A194830.09
52F194830.09
61B197210.08
62C197210.08
71B198730.07
72D198730.07
81B196660.08
82E196660.08
91B196490.09
92F196490.09
101C199080.07
102D199080.07
111C200210.07
112E200210.07
121C195900.08
122F195900.08
131D198910.07
132E198910.07
141D197360.08
142F197360.08
151E196070.09
152F196070.09
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 551 -
Rwork0.239 10876 -
obs--95.36 %
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)
10.1729-0.09990.06890.0839-0.1120.273-0.01250.0191-0.02550.00090.00570.01040.01030.00640.00680.041-0.0142-0.01390.05170.00330.076426.170447.6237-19.7673
20.3314-0.1427-0.01160.2706-0.03770.12630.0057-0.02230.01320.05360.0336-0.0198-0.07470.0067-0.03930.0795-0.0051-0.00090.04360.00940.038915.88580.8076-13.3535
30.4064-0.0716-0.00080.1744-0.21750.33460.07780.1068-0.0021-0.00330.01820.03550.0039-0.0684-0.0960.0310.0371-0.01820.11330.02050.05332.703667.2032-54.0166
40.3796-0.033-0.01650.09050.00660.26070.08330.0945-0.00390.0234-0.0594-0.0136-0.05930.0398-0.02390.04960.01060.01730.10220.04560.04836.999475.092-53.8599
50.3559-0.2069-0.03910.6660.00480.1471-0.08540.00240.0830.16330.1432-0.0230.02590.0118-0.05780.06780.0661-0.02720.0943-0.00830.037340.715799.7223-97.0597
60.5021-0.34940.28650.3808-0.14690.267-0.038-0.0219-0.0830.13420.09630.0421-0.0098-0.0115-0.05830.09470.07640.00410.07180.01810.041850.743765.4215-94.2608
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 329
2X-RAY DIFFRACTION2B-10 - 329
3X-RAY DIFFRACTION3C0 - 329
4X-RAY DIFFRACTION4D0 - 328
5X-RAY DIFFRACTION5E0 - 329
6X-RAY DIFFRACTION6F-10 - 329

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