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- PDB-5z1z: The apo-structure of D-lactate dehydrogenase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 5z1z
TitleThe apo-structure of D-lactate dehydrogenase from Escherichia coli
ComponentsD-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / NADH binding
Function / homology
Function and homology information


D-lactate dehydrogenase / mixed acid fermentation / D-lactate dehydrogenase (NAD+) activity / NADH binding / NAD binding / response to heat / protein homotetramerization / identical protein binding / cytosol
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 1 / 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 dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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
DI(HYDROXYETHYL)ETHER / D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding / D-lactate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
B: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
C: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
D: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,3736
Polymers146,2434
Non-polymers1302
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.600, 150.490, 62.760
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:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 329 / Label seq-ID: 1 - 329

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding


Mass: 36560.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / BL21-DE3 / Gene: ECBD_2243 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: A0A140N893, UniProt: P52643*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 200 mM magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2014
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: 1.97→48.24 Å / Num. obs: 90771 / % possible obs: 98.6 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.039 / Net I/σ(I): 11.8
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 11859 / CC1/2: 0.597 / Rpim(I) all: 0.325 / % possible all: 88.2

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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: 1.97→48.24 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.91 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.156 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22735 4550 5 %RANDOM
Rwork0.20391 ---
obs0.20509 86162 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.602 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---0.29 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.97→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9745 0 8 148 9901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0199908
X-RAY DIFFRACTIONr_bond_other_d0.0090.029567
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9713379
X-RAY DIFFRACTIONr_angle_other_deg1.479321982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28851248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43924.6450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.537151744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7521554
X-RAY DIFFRACTIONr_chiral_restr0.0990.21526
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211279
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022247
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_it2.4372.4265016
X-RAY DIFFRACTIONr_mcbond_other2.4372.4265015
X-RAY DIFFRACTIONr_mcangle_it3.5663.6246256
X-RAY DIFFRACTIONr_mcangle_other3.5663.6246257
X-RAY DIFFRACTIONr_scbond_it3.2132.8594892
X-RAY DIFFRACTIONr_scbond_other3.2132.8594892
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9094.1517123
X-RAY DIFFRACTIONr_long_range_B_refined6.5319.88510897
X-RAY DIFFRACTIONr_long_range_B_other6.53419.85210861
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)
11A190300.11
12B190300.11
21A191780.1
22C191780.1
31A184880.12
32D184880.12
41B192300.1
42C192300.1
51B187190.11
52D187190.11
61C185700.11
62D185700.11
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 308 -
Rwork0.295 5519 -
obs--84.67 %
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)
10.45980.0811-0.58830.263-0.07530.8132-0.0136-0.1197-0.0412-0.0073-0.0287-0.0493-0.0210.08590.04230.1068-0.0022-0.00880.13350.02310.061297.526618.591323.8747
20.44650.3744-0.31820.3407-0.18950.62870.01540.042-0.0562-0.02080.0139-0.0484-0.1083-0.0309-0.02930.117-0.02140.05020.0854-0.04660.0853112.478827.219-6.1724
31.2173-0.1831-0.9450.25090.06940.80670.0638-0.0472-0.09160.0989-0.0752-0.0358-0.16940.11170.01140.1844-0.12060.08120.079-0.05040.1149119.873760.724913.8394
41.31220.7236-0.37590.4515-0.31440.32980.03020.06730.07730.07970.08340.0742-0.1464-0.1178-0.11360.12410.03670.12120.0714-0.01240.16786.699956.691423.8001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 329
2X-RAY DIFFRACTION2B1 - 329
3X-RAY DIFFRACTION3C1 - 329
4X-RAY DIFFRACTION4D1 - 329

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