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- PDB-3wfj: The complex structure of D-mandelate dehydrogenase with NADH -

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Basic information

Entry
Database: PDB / ID: 3wfj
TitleThe complex structure of D-mandelate dehydrogenase with NADH
Components2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / Rosmann 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMiyanaga, A. / Fujisawa, S. / Furukawa, N. / Arai, K. / Nakajima, M. / Taguchi, H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: The crystal structure of D-mandelate dehydrogenase reveals its distinct substrate and coenzyme recognition mechanisms from those of 2-ketopantoate reductase.
Authors: Miyanaga, A. / Fujisawa, S. / Furukawa, N. / Arai, K. / Nakajima, M. / Taguchi, H.
History
DepositionJul 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
G: 2-dehydropantoate 2-reductase
H: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,28716
Polymers274,9808
Non-polymers5,3078
Water5,026279
1
A: 2-dehydropantoate 2-reductase
E: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0724
Polymers68,7452
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-33 kcal/mol
Surface area24330 Å2
MethodPISA
2
B: 2-dehydropantoate 2-reductase
G: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0724
Polymers68,7452
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-34 kcal/mol
Surface area24080 Å2
MethodPISA
3
C: 2-dehydropantoate 2-reductase
H: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0724
Polymers68,7452
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-33 kcal/mol
Surface area23370 Å2
MethodPISA
4
D: 2-dehydropantoate 2-reductase
F: 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0724
Polymers68,7452
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-34 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.650, 103.440, 119.740
Angle α, β, γ (deg.)90.00, 90.01, 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
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASNASNAA1 - 3101 - 310
21METMETASNASNBB1 - 3101 - 310
12METMETASNASNAA1 - 3101 - 310
22METMETASNASNCC1 - 3101 - 310
13METMETASNASNAA1 - 3101 - 310
23METMETASNASNDD1 - 3101 - 310
14METMETASNASNAA1 - 3101 - 310
24METMETASNASNEE1 - 3101 - 310
15ALAALAASNASNAA4 - 3104 - 310
25ALAALAASNASNFF4 - 3104 - 310
16METMETASNASNAA1 - 3101 - 310
26METMETASNASNGG1 - 3101 - 310
17ILEILELEULEUAA3 - 3093 - 309
27ILEILELEULEUHH3 - 3093 - 309
18METMETASNASNBB1 - 3101 - 310
28METMETASNASNCC1 - 3101 - 310
19METMETASNASNBB1 - 3101 - 310
29METMETASNASNDD1 - 3101 - 310
110METMETASNASNBB1 - 3101 - 310
210METMETASNASNEE1 - 3101 - 310
111ALAALAASNASNBB4 - 3104 - 310
211ALAALAASNASNFF4 - 3104 - 310
112METMETASNASNBB1 - 3101 - 310
212METMETASNASNGG1 - 3101 - 310
113ILEILELEULEUBB3 - 3093 - 309
213ILEILELEULEUHH3 - 3093 - 309
114METMETASNASNCC1 - 3101 - 310
214METMETASNASNDD1 - 3101 - 310
115METMETASNASNCC1 - 3101 - 310
215METMETASNASNEE1 - 3101 - 310
116ALAALAASNASNCC4 - 3104 - 310
216ALAALAASNASNFF4 - 3104 - 310
117METMETASNASNCC1 - 3101 - 310
217METMETASNASNGG1 - 3101 - 310
118ILEILELEULEUCC3 - 3093 - 309
218ILEILELEULEUHH3 - 3093 - 309
119METMETASNASNDD1 - 3101 - 310
219METMETASNASNEE1 - 3101 - 310
120ALAALAASNASNDD4 - 3104 - 310
220ALAALAASNASNFF4 - 3104 - 310
121METMETASNASNDD1 - 3101 - 310
221METMETASNASNGG1 - 3101 - 310
122ILEILELEULEUDD3 - 3093 - 309
222ILEILELEULEUHH3 - 3093 - 309
123ALAALAASNASNEE4 - 3104 - 310
223ALAALAASNASNFF4 - 3104 - 310
124METMETASNASNEE1 - 3101 - 310
224METMETASNASNGG1 - 3101 - 310
125ILEILELEULEUEE3 - 3093 - 309
225ILEILELEULEUHH3 - 3093 - 309
126ALAALAASNASNFF4 - 3104 - 310
226ALAALAASNASNGG4 - 3104 - 310
127ALAALALEULEUFF4 - 3094 - 309
227ALAALALEULEUHH4 - 3094 - 309
128ILEILELEULEUGG3 - 3093 - 309
228ILEILELEULEUHH3 - 3093 - 309

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
2-dehydropantoate 2-reductase


Mass: 34372.484 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Strain: IAM10071 / Gene: pLG1-0150 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: E3USM3, 2-dehydropantoate 2-reductase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris-HCl (pH 7.0), 0.2M calcium acetate, 20% PEG 3350, 10mM NADH, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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, 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: 2.8→20 Å / Num. all: 69522 / Num. obs: 68132 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.87 Å / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3WFI

3wfi


Resolution: 2.8→19.97 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.791 / SU B: 17.463 / SU ML: 0.359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.466 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30582 3439 5 %RANDOM
Rwork0.23876 ---
all0.24215 66195 --
obs0.24215 64680 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.94 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å2-0 Å20.77 Å2
2---3.26 Å2-0 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17616 0 352 279 18247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01918270
X-RAY DIFFRACTIONr_bond_other_d0.0130.0217686
X-RAY DIFFRACTIONr_angle_refined_deg2.2781.98824689
X-RAY DIFFRACTIONr_angle_other_deg1.773340790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.70152256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.42826.05757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.339153276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7841532
X-RAY DIFFRACTIONr_chiral_restr0.120.22849
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0220256
X-RAY DIFFRACTIONr_gen_planes_other0.0110.023884
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A186150.07
12B186150.07
21A184820.08
22C184820.08
31A177430.1
32D177430.1
41A185590.08
42E185590.08
51A159980.09
52F159980.09
61A181420.09
62G181420.09
71A149040.08
72H149040.08
81B184810.07
82C184810.07
91B177970.08
92D177970.08
101B185870.07
102E185870.07
111B160910.08
112F160910.08
121B181050.09
122G181050.09
131B149780.08
132H149780.08
141C180770.08
142D180770.08
151C186680.07
152E186680.07
161C160280.08
162F160280.08
171C179570.09
172G179570.09
181C149350.08
182H149350.08
191D179700.08
192E179700.08
201D155510.1
202F155510.1
211D174510.09
212G174510.09
221D147480.08
222H147480.08
231E160060.08
232F160060.08
241E184290.08
242G184290.08
251E149520.08
252H149520.08
261F156180.1
262G156180.1
271F145810.09
272H145810.09
281G147740.09
282H147740.09
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 241 -
Rwork0.259 4780 -
obs--97.8 %

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