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- PDB-3b1k: Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase com... -

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Basic information

Entry
Database: PDB / ID: 3b1k
TitleCrystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with CP12 in the absence of copper from Synechococcus elongatus
Components
  • CP12
  • Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
KeywordsOXIDOREDUCTASE/PROTEIN BINDING / alpha/beta fold / OXIDOREDUCTASE-PROTEIN BINDING complex
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / glucose metabolic process / NAD binding / NADP binding / nucleotide binding / metal ion binding
Similarity search - Function
Calvin cycle protein CP12-like / CP12 domain / CP12 domain / CP12 / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain ...Calvin cycle protein CP12-like / CP12 domain / CP12 domain / CP12 / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / CP12 / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.302 Å
AuthorsMatsumura, H. / Kai, A. / Inoue, T.
CitationJournal: Structure / Year: 2011
Title: Structure Basis for the Regulation of Glyceraldehyde-3-Phosphate Dehydrogenase Activity via the Intrinsically Disordered Protein CP12.
Authors: Matsumura, H. / Kai, A. / Maeda, T. / Tamoi, M. / Satoh, A. / Tamura, H. / Hirose, M. / Ogawa, T. / Kizu, N. / Wadano, A. / Inoue, T. / Shigeoka, S.
History
DepositionJul 4, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Structure summary
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
B: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
C: CP12
D: CP12
G: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
H: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
I: CP12
J: CP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,10612
Polymers159,4528
Non-polymers2,6544
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28700 Å2
ΔGint-158 kcal/mol
Surface area45210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.042, 146.887, 161.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glyceraldehyde 3-phosphate dehydrogenase (NADP+) / Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (Phosphorylating)


Mass: 37032.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: gap2, Synpcc7942_1742 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9R6W2, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)
#2: Protein/peptide
CP12


Mass: 2830.917 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 51-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: cp12, Synpcc7942_0361 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6BBK3
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20%(v/v) PEG3350, 0.2M magnesium acetate., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorDate: Nov 16, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 22942 / Num. obs: 22942 / % possible obs: 89 % / Observed criterion σ(I): 5.1 / Rmerge(I) obs: 0.147
Reflection shellResolution: 3.3→3.36 Å / Rmerge(I) obs: 0.35 / % possible all: 85.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D2I

3d2i


Resolution: 3.302→26.062 Å / SU ML: 0.61 / σ(F): 0 / Phase error: 38.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3628 1164 5.08 %RANDOM
Rwork0.2519 ---
obs0.2576 22903 88.89 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.756 Å2 / ksol: 0.273 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4951 Å2-0 Å2-0 Å2
2---11.8301 Å20 Å2
3----3.8657 Å2
Refinement stepCycle: LAST / Resolution: 3.302→26.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11098 0 176 4 11278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111494
X-RAY DIFFRACTIONf_angle_d1.5215668
X-RAY DIFFRACTIONf_dihedral_angle_d21.2734164
X-RAY DIFFRACTIONf_chiral_restr0.0911844
X-RAY DIFFRACTIONf_plane_restr0.0061998
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.302-3.45190.36061250.2811248583
3.4519-3.63350.4551460.2764260787
3.6335-3.86040.37411470.2646270089
3.8604-4.15740.37551390.2509258586
4.1574-4.57380.35381450.2319277291
4.5738-5.23090.32981450.2202273389
5.2309-6.57290.34481550.2531286493
6.5729-26.06270.32831620.2525299393

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