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- PDB-5j77: Mutant glyceraldehyde dehydrogenase (F34M+S405N) from Thermoplasm... -

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Basic information

Entry
Database: PDB / ID: 5j77
TitleMutant glyceraldehyde dehydrogenase (F34M+S405N) from Thermoplasma acidophilum
ComponentsD-glyceraldehyde dehydrogenase (NADP(+))
KeywordsOXIDOREDUCTASE / NADP-DEPENDENT DEHYDROGENASE
Function / homology
Function and homology information


D-glyceraldehyde dehydrogenase (NADP+) / glyceraldehyde dehydrogenase (NADP+) activity / Entner-Doudoroff pathway through 6-phosphogluconate / succinate-semialdehyde dehydrogenase (NAD+) activity / gamma-aminobutyric acid catabolic process / glycolytic process / protein homotetramerization / protein homodimerization activity / cytosol
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: 2.1 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: Structure of wild-type glyceraldehyde dehydrogenase from Thermoplasma acidophilum in complex with NADP
Authors: Iermak, I. / Mesters, J.R. / Steffler, F. / Sieber, V. / Kuta Smatanova, I.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)226,1124
Polymers226,1124
Non-polymers00
Water10,413578
1
A: D-glyceraldehyde dehydrogenase (NADP(+))
B: D-glyceraldehyde dehydrogenase (NADP(+))

A: D-glyceraldehyde dehydrogenase (NADP(+))
B: D-glyceraldehyde dehydrogenase (NADP(+))


Theoretical massNumber of molelcules
Total (without water)226,1124
Polymers226,1124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area23790 Å2
ΔGint-122 kcal/mol
Surface area58060 Å2
MethodPISA
2
C: D-glyceraldehyde dehydrogenase (NADP(+))
D: D-glyceraldehyde dehydrogenase (NADP(+))

C: D-glyceraldehyde dehydrogenase (NADP(+))
D: D-glyceraldehyde dehydrogenase (NADP(+))


Theoretical massNumber of molelcules
Total (without water)226,1124
Polymers226,1124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area23470 Å2
ΔGint-122 kcal/mol
Surface area57970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.071, 158.423, 130.050
Angle α, β, γ (deg.)90.00, 91.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
D-glyceraldehyde dehydrogenase (NADP(+)) / Glyceraldehyde DH


Mass: 56528.020 Da / Num. of mol.: 4 / Mutation: F34N+S405N
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)
Gene: Ta0809 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HK01, D-glyceraldehyde dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.5 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6, 40%(v/v) PEG 200

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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: Mar 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.1→44.63 Å / Num. obs: 126605 / % possible obs: 99.6 % / Redundancy: 3.81 % / Biso Wilson estimate: 32.88 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.13
Reflection shellResolution: 2.1→2.23 Å / Mean I/σ(I) obs: 2.32 / % possible all: 98.7

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Processing

Software
NameVersionClassification
XDSNovember 3, 2014data reduction
XDSNovember 3, 2014data scaling
MOLREP11.2.08phasing
REFMAC5.8.0135refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IZD

5izd


Resolution: 2.1→44.63 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.638 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.175 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22631 6331 5 %RANDOM
Rwork0.17596 ---
obs0.17843 120272 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.093 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å2-0 Å2-1.37 Å2
2---1.87 Å20 Å2
3---0.85 Å2
Refinement stepCycle: 1 / Resolution: 2.1→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15047 0 0 578 15625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01915453
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214412
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.95420984
X-RAY DIFFRACTIONr_angle_other_deg1.042333150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62151988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81324.756675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.968152522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3291569
X-RAY DIFFRACTIONr_chiral_restr0.1030.22304
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117769
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023460
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_it1.142.5157892
X-RAY DIFFRACTIONr_mcbond_other1.1352.5157891
X-RAY DIFFRACTIONr_mcangle_it1.7083.7659864
X-RAY DIFFRACTIONr_mcangle_other1.7083.7669865
X-RAY DIFFRACTIONr_scbond_it1.5052.667560
X-RAY DIFFRACTIONr_scbond_other1.5042.667561
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3143.93211109
X-RAY DIFFRACTIONr_long_range_B_refined4.51320.7217734
X-RAY DIFFRACTIONr_long_range_B_other4.44820.46317520
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 454 -
Rwork0.288 8618 -
obs--97.13 %
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)
10.68480.20360.33230.50190.14980.4592-0.08520.16840.1207-0.07920.0029-0.0074-0.05640.13830.08240.1046-0.0249-0.08760.06030.04740.096517.4411.175-9.037
20.40110.0446-0.14370.7856-0.28570.62330.08080.0909-0.1002-0.0568-0.20790.1308-0.1727-0.11610.12710.35940.1115-0.27550.1458-0.1220.227442.009-32.107-78.942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 492
2X-RAY DIFFRACTION1B1 - 492
3X-RAY DIFFRACTION2C1 - 491
4X-RAY DIFFRACTION2D1 - 489

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