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- PDB-5m4x: Mutant glyceraldehyde dehydrogenase (F34M+Y399C+S405N) from Therm... -

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Basic information

Entry
Database: PDB / ID: 5m4x
TitleMutant glyceraldehyde dehydrogenase (F34M+Y399C+S405N) from Thermoplasma acidophilum
ComponentsD-glyceraldehyde dehydrogenase (NADP(+))
KeywordsOXIDOREDUCTASE / NAD(P)-dependent dehydrogenase
Function / homology
Function and homology information


D-glyceraldehyde dehydrogenase (NADP+) / glyceraldehyde dehydrogenase (NADP+) activity / Entner-Doudoroff pathway through 6-phosphogluconate / glycolytic process / protein homotetramerization / protein homodimerization activity
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-glyceraldehyde dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.56 Å
AuthorsIermak, I. / Mesters, J.R. / Kuta Smatanova, I.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Academy of SciencesDAAD-16-09 Czech Republic
CitationJournal: To Be Published
Title: Mutant glyceraldehyde dehydrogenase (F34M+Y399C+S405N) from Thermoplasma acidophilum
Authors: Iermak, I. / Mesters, J.R. / Steffler, F. / Sieber, V. / Kuta Smatanova, I.
History
DepositionOct 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-glyceraldehyde dehydrogenase (NADP(+))
B: D-glyceraldehyde dehydrogenase (NADP(+))
C: D-glyceraldehyde dehydrogenase (NADP(+))
D: D-glyceraldehyde dehydrogenase (NADP(+))


Theoretical massNumber of molelcules
Total (without water)225,8724
Polymers225,8724
Non-polymers00
Water0
1
A: D-glyceraldehyde dehydrogenase (NADP(+))
B: D-glyceraldehyde dehydrogenase (NADP(+))


Theoretical massNumber of molelcules
Total (without water)112,9362
Polymers112,9362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-36 kcal/mol
Surface area36510 Å2
MethodPISA
2
C: D-glyceraldehyde dehydrogenase (NADP(+))
D: D-glyceraldehyde dehydrogenase (NADP(+))


Theoretical massNumber of molelcules
Total (without water)112,9362
Polymers112,9362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-38 kcal/mol
Surface area36520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.292, 120.292, 344.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 1 - 494 / Label seq-ID: 1 - 494

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-glyceraldehyde dehydrogenase (NADP(+)) / Glyceraldehyde DH


Mass: 56467.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (acidophilic)
Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
Gene: Ta0809 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9HK01, D-glyceraldehyde dehydrogenase (NADP+)

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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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine pH 9.0, 10% PEG 20 000, 2% dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 3.56→48.73 Å / Num. obs: 31219 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 12.87 % / Biso Wilson estimate: 95.155 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.195 / Net I/σ(I): 14.14
Reflection shellResolution: 3.56→3.77 Å / Mean I/σ(I) obs: 1.97 / CC1/2: 0.747 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSOctober 15, 2015data reduction
PHASER2.5.7phasing
XDSOctober 15, 2015data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IZD

5izd


Resolution: 3.56→48.73 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.876 / SU B: 62.458 / SU ML: 0.846 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.792
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3192 1093 3.5 %RANDOM
Rwork0.3118 ---
obs0.3121 30126 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 123.4 Å2 / Biso mean: 53.865 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å2-0 Å2-0 Å2
2--2.4 Å2-0 Å2
3----4.79 Å2
Refinement stepCycle: final / Resolution: 3.56→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13897 0 0 0 13897
Num. residues----1862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914560
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213622
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.95419762
X-RAY DIFFRACTIONr_angle_other_deg1.005331264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35151854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09324.531618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.899152358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4851566
X-RAY DIFFRACTIONr_chiral_restr0.1040.22192
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02116644
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023270
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A298700.05
12B298700.05
21A299020.04
22C299020.04
31A299800.04
32D299800.04
41B302920.04
42C302920.04
51B299540.04
52D299540.04
61C299120.02
62D299120.02
LS refinement shellResolution: 3.559→3.651 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 77 -
Rwork0.404 2131 -
all-2208 -
obs--97.48 %

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