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- PDB-5x20: The ternary structure of D-mandelate dehydrogenase with NADH and ... -

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Basic information

Entry
Database: PDB / ID: 5x20
TitleThe ternary structure of D-mandelate dehydrogenase with NADH and anilino(oxo)acetate
Components2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / NADH binding
Function / homology
Function and homology information


2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / nucleotide binding
Similarity search - Function
Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain ...Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-oxidanylidene-2-phenylazanyl-ethanoic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesEnterococcus faecium DO (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFurukawa, N. / Miyanaga, A. / Nakajima, M. / Taguchi, H.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: The ternary complex structure of d-mandelate dehydrogenase with NADH and anilino(oxo)acetate.
Authors: Furukawa, N. / Miyanaga, A. / Nakajima, M. / Taguchi, H.
History
DepositionJan 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
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: 2-dehydropantoate 2-reductase
B: 2-dehydropantoate 2-reductase
C: 2-dehydropantoate 2-reductase
D: 2-dehydropantoate 2-reductase
E: 2-dehydropantoate 2-reductase
F: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,76552
Polymers206,2356
Non-polymers7,53046
Water6,161342
1
A: 2-dehydropantoate 2-reductase
B: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,90322
Polymers68,7452
Non-polymers3,15820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-137 kcal/mol
Surface area23650 Å2
MethodPISA
2
C: 2-dehydropantoate 2-reductase
D: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,72720
Polymers68,7452
Non-polymers2,98218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-132 kcal/mol
Surface area23180 Å2
MethodPISA
3
E: 2-dehydropantoate 2-reductase
F: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,13410
Polymers68,7452
Non-polymers1,3898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-64 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.300, 111.950, 108.940
Angle α, β, γ (deg.)90.00, 96.65, 90.00
Int Tables number4
Space group name H-MP1211
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
1010A1 - 312
2010B1 - 312
1020A1 - 311
2020C1 - 311
1030A1 - 312
2030D1 - 312
1040A50 - 310
2040E7 - 310
1050A102 - 311
2050F102 - 311
1060B1 - 311
2060C1 - 311
1070B1 - 312
2070D1 - 312
1080B50 - 310
2080E7 - 310
1090B102 - 311
2090F102 - 311
10100C1 - 310
20100D1 - 310
10110C50 - 310
20110E7 - 310
10120C102 - 310
20120F102 - 310
10130D50 - 310
20130E7 - 310
10140D102 - 311
20140F102 - 311
10150E102 - 310
20150F102 - 310

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
2-dehydropantoate 2-reductase / / Ketopantoate reductase


Mass: 34372.484 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium DO (bacteria) / Gene: panE, HMPREF0351_10295 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q3Y316, 2-dehydropantoate 2-reductase

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Non-polymers , 5 types, 388 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-AOT / 2-oxidanylidene-2-phenylazanyl-ethanoic acid


Mass: 165.146 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H7NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M cacodylate-Na (pH 5.0), 0.17 M ammonium sulfate, 22.5% PEG 8000

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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: May 26, 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: 2.4→43.98 Å / Num. obs: 89403 / % possible obs: 99.6 % / Redundancy: 3.6 % / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 12887 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WFI

3wfi


Resolution: 2.4→29.82 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 12.048 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21831 4479 5 %RANDOM
Rwork0.18413 ---
obs0.18588 84874 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.36 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.4→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12866 0 478 342 13686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01913535
X-RAY DIFFRACTIONr_bond_other_d0.0090.0213005
X-RAY DIFFRACTIONr_angle_refined_deg1.759218262
X-RAY DIFFRACTIONr_angle_other_deg1.5213.00130030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84751657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.53726.161560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.198152422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8341524
X-RAY DIFFRACTIONr_chiral_restr0.090.22102
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214920
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022839
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_it2.3212.6056670
X-RAY DIFFRACTIONr_mcbond_other2.3212.6056669
X-RAY DIFFRACTIONr_mcangle_it3.5753.8858310
X-RAY DIFFRACTIONr_mcangle_other3.5753.8868311
X-RAY DIFFRACTIONr_scbond_it3.1362.9716865
X-RAY DIFFRACTIONr_scbond_other3.1362.9716865
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.884.2959952
X-RAY DIFFRACTIONr_long_range_B_refined6.49820.44415260
X-RAY DIFFRACTIONr_long_range_B_other6.48720.41215159
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)
11A197490.08
12B197490.08
21A193220.09
22C193220.09
31A192360.1
32D192360.1
41A134580.11
42E134580.11
51A101770.12
52F101770.12
61B194240.09
62C194240.09
71B192200.1
72D192200.1
81B134160.11
82E134160.11
91B101170.12
92F101170.12
101C190360.1
102D190360.1
111C134200.11
112E134200.11
121C100470.13
122F100470.13
131D133660.11
132E133660.11
141D100720.12
142F100720.12
151E101040.12
152F101040.12
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 337 -
Rwork0.239 6122 -
obs--98.73 %
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)
10.74070.03630.37690.3420.05270.2331-0.0584-0.00180.03550.01540.00960.01610.00810.00650.04880.0442-0.00130.0190.0519-0.00660.050629.353-26.01924.817
20.418-0.0958-0.03690.14680.01830.4155-0.01410.0968-0.059-0.005-0.05250.00880.0195-0.06530.06660.0617-0.00940.00070.0651-0.0290.047972.86-23.84440.983
30.8060.4279-0.53330.677-0.63160.6352-0.0301-0.1211-0.17520.0187-0.2052-0.2322-0.01920.17610.23530.0260.02370.00940.10370.10070.157325.319-0.05946.302
40.2559-0.2860.02230.78040.14480.37720.0017-0.01410.01090.09930.0579-0.066-0.0502-0.0111-0.05960.080.00830.00990.02920.02480.05776.69816.4410.446
50.83840.3931.08440.39260.37021.4981-0.36450.17940.294-0.1807-0.01110.1396-0.44830.29640.37560.1606-0.0915-0.13250.14820.09910.123469.25413.37230.365
60.1317-0.13060.3060.1347-0.3541.20080.1672-0.0015-0.0379-0.14650.02070.04930.2229-0.1451-0.18790.26160.0309-0.02860.06070.05340.059655.23474.5164-7.4754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 312
2X-RAY DIFFRACTION1A401 - 410
3X-RAY DIFFRACTION2B1 - 311
4X-RAY DIFFRACTION2B401 - 409
5X-RAY DIFFRACTION3C1 - 312
6X-RAY DIFFRACTION3A411
7X-RAY DIFFRACTION3C401 - 413
8X-RAY DIFFRACTION4D7 - 311
9X-RAY DIFFRACTION4D401 - 405
10X-RAY DIFFRACTION5E1 - 312
11X-RAY DIFFRACTION5E401 - 407
12X-RAY DIFFRACTION6F102 - 312
13X-RAY DIFFRACTION6F401

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