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- PDB-6abi: The apo-structure of D-lactate dehydrogenase from Fusobacterium n... -

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Basic information

Entry
Database: PDB / ID: 6abi
TitleThe apo-structure of D-lactate dehydrogenase from Fusobacterium nucleatum
ComponentsD-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / NADH binding
Function / homology
Function and homology information


D-lactate dehydrogenase / D-lactate dehydrogenase 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 dehydrogenase, NAD-binding domain conserved site 1 / 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, 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 dehydrogenase, NAD-binding domain conserved site 1 / 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, 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
D-lactate dehydrogenase
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: 3WWY
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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,08318
Polymers81,5782
Non-polymers1,50516
Water5,441302
1
A: D-lactate dehydrogenase
B: D-lactate dehydrogenase
hetero molecules

A: D-lactate dehydrogenase
B: D-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,16636
Polymers163,1554
Non-polymers3,01132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area25470 Å2
ΔGint-323 kcal/mol
Surface area49220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.290, 116.290, 234.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 2 - 334 / Label seq-ID: 25 - 357

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

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Components

#1: Protein D-lactate dehydrogenase /


Mass: 40788.836 Da / Num. of mol.: 2
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) / Variant (production host): Rosetta2 (DE3) / References: UniProt: Q8RG11, D-lactate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 4.86 Å3/Da / Density % sol: 74.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MES-Na (pH 6.0) and 1.26 M ammonium sulfate

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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 20, 2012
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: 2.1→37.03 Å / Num. obs: 94385 / % possible obs: 100 % / Redundancy: 14.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.046 / Net I/σ(I): 9.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 13597 / CC1/2: 0.908 / Rpim(I) all: 0.229 / % possible all: 100

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Processing

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

1j49


Resolution: 2.1→37.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.142 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21665 4714 5 %RANDOM
Rwork0.18643 ---
obs0.18793 89290 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.673 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→37.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5281 0 88 302 5671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.025433
X-RAY DIFFRACTIONr_bond_other_d0.0070.025319
X-RAY DIFFRACTIONr_angle_refined_deg2.1021.9847314
X-RAY DIFFRACTIONr_angle_other_deg1.375312228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9425.08250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.198151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.6241526
X-RAY DIFFRACTIONr_chiral_restr0.1380.2846
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026024
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021190
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_it2.3992.222653
X-RAY DIFFRACTIONr_mcbond_other2.3972.2192652
X-RAY DIFFRACTIONr_mcangle_it3.353.3093311
X-RAY DIFFRACTIONr_mcangle_other3.353.3113312
X-RAY DIFFRACTIONr_scbond_it4.1222.7772780
X-RAY DIFFRACTIONr_scbond_other4.1222.7772780
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2353.9514004
X-RAY DIFFRACTIONr_long_range_B_refined7.66318.9696400
X-RAY DIFFRACTIONr_long_range_B_other7.66218.9736401
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19857 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 379 -
Rwork0.26 6502 -
obs--99.81 %
Refinement TLS params.

L23: -0.0473 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°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)
10.2863-0.0677-0.12870.0310.47790.0081-0.0403-0.04560.00330.01550.017-0.0467-0.011-0.02360.0155-0.01410.00880.06980.01770.085210.993234.614214.5496
20.0109-0.0355-0.01770.23790.34480.0232-0.0004-0.0001-0.0159-0.0031-0.0245-0.0557-0.0155-0.02020.088-0.00040.00030.00690.02110.068224.607849.2455-13.1564
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 334
2X-RAY DIFFRACTION2B2 - 334

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