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- PDB-6abj: The apo-structure of D-lactate dehydrogenase from Pseudomonas aer... -

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Basic information

Entry
Database: PDB / ID: 6abj
TitleThe apo-structure of D-lactate dehydrogenase from Pseudomonas aeruginosa
ComponentsD-lactate dehydrogenase (Fermentative)
KeywordsOXIDOREDUCTASE / 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
ACETATE ION / D-lactate dehydrogenase (Fermentative)
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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
DepositionJul 21, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 19, 2018ID: 3WWZ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 27, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Mar 12, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7844
Polymers75,6662
Non-polymers1182
Water4,252236
1
A: D-lactate dehydrogenase (Fermentative)
B: D-lactate dehydrogenase (Fermentative)
hetero molecules

A: D-lactate dehydrogenase (Fermentative)
B: D-lactate dehydrogenase (Fermentative)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,5678
Polymers151,3314
Non-polymers2364
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area15430 Å2
ΔGint-54 kcal/mol
Surface area46180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.100, 186.840, 90.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-618-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 326 / Label seq-ID: 17 - 342

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein D-lactate dehydrogenase (Fermentative)


Mass: 37832.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (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) / Variant (production host): Rosetta2 (DE3) / References: UniProt: Q9I530
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM sodium acetate (pH 5.5), 8% PEG3350, and 50 mM magnesium chloride.

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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: Nov 1, 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: 1.86→52.26 Å / Num. obs: 68606 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.04 / Net I/σ(I): 12.3
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 9844 / CC1/2: 0.774 / Rpim(I) all: 0.349 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
ADSCdata collection
SCALAdata scaling
ARP/wARPmodel building
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J49

1j49


Resolution: 1.86→52.26 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.426 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22691 3466 5.1 %RANDOM
Rwork0.1984 ---
obs0.19985 65029 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.809 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.86→52.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5041 0 8 236 5285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195162
X-RAY DIFFRACTIONr_bond_other_d0.0060.024928
X-RAY DIFFRACTIONr_angle_refined_deg1.721.9517018
X-RAY DIFFRACTIONr_angle_other_deg1.206311226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69523.068251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60115791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5951547
X-RAY DIFFRACTIONr_chiral_restr0.1140.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026020
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021275
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_it2.3582.3912633
X-RAY DIFFRACTIONr_mcbond_other2.3422.3892630
X-RAY DIFFRACTIONr_mcangle_it3.2423.5693287
X-RAY DIFFRACTIONr_mcangle_other3.2423.5693288
X-RAY DIFFRACTIONr_scbond_it3.082.7782529
X-RAY DIFFRACTIONr_scbond_other3.0792.7792530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7394.0483732
X-RAY DIFFRACTIONr_long_range_B_refined6.72519.965846
X-RAY DIFFRACTIONr_long_range_B_other6.72419.9625847
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19061 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.858→1.906 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 238 -
Rwork0.317 4597 -
obs--96.43 %
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)
10.0199-0.04850.14090.2083-0.38881.0368-0.0187-0.0323-0.01870.11270.1038-0.0179-0.1467-0.2587-0.08510.11560.0139-0.00660.10720.02550.0944-20.3777-10.1021-17.6143
20.31930.18250.06160.57870.24330.11820.02860.1359-0.04050.12670.0446-0.12020.0951-0.024-0.07320.1444-0.1001-0.08030.15890.02870.0744-13.4697-36.487-39.025
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 327
2X-RAY DIFFRACTION2B1 - 329

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