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- PDB-5izd: Wild-type glyceraldehyde dehydrogenase from Thermoplasma acidophi... -

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Basic information

Entry
Database: PDB / ID: 5izd
TitleWild-type glyceraldehyde dehydrogenase from Thermoplasma acidophilum in complex with NADP
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; 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / D-glyceraldehyde dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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
DepositionMar 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Data collection
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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(+))
E: D-glyceraldehyde dehydrogenase (NADP(+))
F: D-glyceraldehyde dehydrogenase (NADP(+))
G: D-glyceraldehyde dehydrogenase (NADP(+))
H: D-glyceraldehyde dehydrogenase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)456,85214
Polymers452,3928
Non-polymers4,4606
Water24,3741353
1
A: D-glyceraldehyde dehydrogenase (NADP(+))
B: D-glyceraldehyde dehydrogenase (NADP(+))
C: D-glyceraldehyde dehydrogenase (NADP(+))
D: D-glyceraldehyde dehydrogenase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,1708
Polymers226,1964
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27020 Å2
ΔGint-121 kcal/mol
Surface area57910 Å2
MethodPISA
2
E: D-glyceraldehyde dehydrogenase (NADP(+))
F: D-glyceraldehyde dehydrogenase (NADP(+))
G: D-glyceraldehyde dehydrogenase (NADP(+))
H: D-glyceraldehyde dehydrogenase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,6836
Polymers226,1964
Non-polymers1,4872
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25620 Å2
ΔGint-114 kcal/mol
Surface area58300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.289, 152.353, 149.905
Angle α, β, γ (deg.)90.00, 92.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 56548.973 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0809 / Plasmid: pCBRHisC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HK01, D-glyceraldehyde dehydrogenase (NADP+)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1353 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mM glutamic acid (racemic), 20 mM glycine, 20 mM serine (racemic), 20 mM alanine (racemic), 20 mM lysine-HCl (racemic), 50 mM MOPS, 50 mM Sodium HEPES, pH 7.5; 20% Ethylene Glycol, 10% PEG 8000

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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: Jan 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.95→48.1 Å / Num. obs: 310836 / % possible obs: 99.8 % / Redundancy: 6.84 % / Biso Wilson estimate: 37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.38
Reflection shellResolution: 1.95→2.06 Å / Mean I/σ(I) obs: 1.98 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSNovember 3, 2014data reduction
BALBES1.0.0.Nov_16_2011phasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K2W

3k2w


Resolution: 2.05→48.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 9.283 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 13347 5 %RANDOM
Rwork0.16838 ---
obs0.17021 253577 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.134 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å2-0 Å2-1.04 Å2
2---2.5 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.05→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30004 0 186 1353 31543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01930948
X-RAY DIFFRACTIONr_bond_other_d0.0020.0228847
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.94942004
X-RAY DIFFRACTIONr_angle_other_deg1.032.99766267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31453932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76324.3531321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.529155017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.73515154
X-RAY DIFFRACTIONr_chiral_restr0.1030.24587
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02135310
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027002
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_it0.4390.90615710
X-RAY DIFFRACTIONr_mcbond_other0.4390.90615709
X-RAY DIFFRACTIONr_mcangle_it0.7531.35619624
X-RAY DIFFRACTIONr_mcangle_other0.7531.35619625
X-RAY DIFFRACTIONr_scbond_it0.730.99415238
X-RAY DIFFRACTIONr_scbond_other0.7220.99115230
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1631.46622360
X-RAY DIFFRACTIONr_long_range_B_refined6.0928.22535742
X-RAY DIFFRACTIONr_long_range_B_other6.0617.77235185
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 982 -
Rwork0.236 18671 -
obs--99.98 %
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)
10.72710.00220.40830.3314-0.05130.69150.01660.01470.0387-0.02160.00220.0418-0.09440.0977-0.01880.0544-0.01780.01180.3641-0.02860.3139-13.6067.1726.941
20.5666-0.01510.09060.4713-0.11210.5690.0895-0.0426-0.2077-0.06210.02760.20250.1801-0.0356-0.11710.1074-0.0205-0.10660.37220.03510.5215-34.875-25.6458.494
30.5480.2069-0.08470.4922-0.06860.52450.0205-0.1217-0.0540.1323-0.0849-0.0996-0.02950.08470.06450.0491-0.01350.0020.33760.03380.281538.691-7.749101.382
40.57010.2402-0.23140.6836-0.20280.6303-0.09780.1496-0.062-0.06670.05960.00740.0108-0.13220.03820.0249-0.01770.04260.3518-0.02450.259417.781-9.53268.031
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 494
2X-RAY DIFFRACTION1B1 - 492
3X-RAY DIFFRACTION1A601
4X-RAY DIFFRACTION1B601
5X-RAY DIFFRACTION2C1 - 492
6X-RAY DIFFRACTION2D1 - 492
7X-RAY DIFFRACTION2C601
8X-RAY DIFFRACTION2D601
9X-RAY DIFFRACTION3E1 - 492
10X-RAY DIFFRACTION3F1 - 492
11X-RAY DIFFRACTION4G1 - 492
12X-RAY DIFFRACTION4H1 - 492
13X-RAY DIFFRACTION4H601
14X-RAY DIFFRACTION4G601

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