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- PDB-2qe0: Thioacylenzyme Intermediate of GAPN from S. Mutans, New Data Inte... -

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Basic information

Entry
Database: PDB / ID: 2qe0
TitleThioacylenzyme Intermediate of GAPN from S. Mutans, New Data Integration and Refinement.
ComponentsNADP-dependent glyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / ALDH / GAPN / TERNARY COMPLEX
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) 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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal ...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, 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
GLYCERALDEHYDE-3-PHOSPHATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsCorbier, C. / Didierjean, C. / Bricogne, G. / Branlant, G. / D'Ambrosio, K. / Vonrhein, C.
CitationJournal: Biochemistry / Year: 2006
Title: The First Crystal Structure of a Thioacylenzyme Intermediate in the ALDH Family: New Coenzyme Conformation and Relevance to Catalysis
Authors: D'Ambrosio, K. / Pailot, A. / Talfournier, F. / Didierjean, C. / Benedetti, E. / Aubry, A. / Branlant, G. / Corbier, C.
History
DepositionJun 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,52712
Polymers204,8744
Non-polymers3,6548
Water24,9331384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23440 Å2
ΔGint-116 kcal/mol
Surface area57480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)142.470, 155.210, 113.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe asymmetric unit consists of the biological assembly which is a tetramer

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Components

#1: Protein
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase / Non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase / Glyceraldehyde-3-phosphate ...Non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase / Glyceraldehyde-3-phosphate dehydrogenase [NADP+] / Triosephosphate dehydrogenase


Mass: 51218.402 Da / Num. of mol.: 4 / Mutation: E250A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: gapN / Plasmid: PBLUESCRIPT SK / Production host: Escherichia coli (E. coli) / Strain (production host): DH5
References: UniProt: Q59931, glyceraldehyde-3-phosphate dehydrogenase (NADP+)
#2: Chemical
ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE / Glyceraldehyde 3-phosphate


Mass: 170.058 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1384 / 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: 3.05 Å3/Da / Density % sol: 59.67 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9804 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 21, 2002
RadiationMonochromator: Silicon single crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 2.19→19.78 Å / Num. obs: 124421 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 7.1 % / Biso Wilson estimate: 36.03 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 17.4
Reflection shellResolution: 2.19→2.33 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.9 / Num. unique all: 17938 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER-TNT2.1.1refinement
MAR345dtbdata collection
XDSdata reduction
SCALAdata scaling
MOLREP9.4.09phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ESD

2esd


Resolution: 2.19→19.78 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 12452 10.01 %RANDOM
Rwork0.1843 ---
obs0.1889 124377 96.52 %-
Displacement parametersBiso mean: 32.32 Å2
Baniso -1Baniso -2Baniso -3
1-4.85464586 Å20 Å20 Å2
2---7.58909516 Å20 Å2
3---2.7344493 Å2
Refine analyzeLuzzati coordinate error obs: 0.2604 Å
Refinement stepCycle: LAST / Resolution: 2.19→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14368 0 232 1384 15984
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.011148762
X-RAY DIFFRACTIONt_angle_deg1.285201042
X-RAY DIFFRACTIONt_dihedral_angle_d19.80729920
X-RAY DIFFRACTIONt_trig_c_planes0.0114042
X-RAY DIFFRACTIONt_gen_planes0.01821325
X-RAY DIFFRACTIONt_it1.2911487620
X-RAY DIFFRACTIONt_nbd0.0711585
LS refinement shellResolution: 2.19→2.32 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2713 1711 10.32 %
Rwork0.2187 14871 -
all22.42 16582 -
obs--96.52 %

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