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- PDB-3b1j: Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase com... -

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Basic information

Entry
Database: PDB / ID: 3b1j
TitleCrystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with CP12 in the presence 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


negative regulation of reductive pentose-phosphate cycle / 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
COPPER (II) ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / CP12 / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 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: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
B: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
C: CP12
D: CP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1808
Polymers79,7264
Non-polymers1,4544
Water3,783210
1
A: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
B: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
C: CP12
D: CP12
hetero molecules

A: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
B: Glyceraldehyde 3-phosphate dehydrogenase (NADP+)
C: CP12
D: CP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,36016
Polymers159,4528
Non-polymers2,9088
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area29720 Å2
ΔGint-209 kcal/mol
Surface area44820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.999, 161.603, 146.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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.: 2
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.: 2 / 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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
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: BL41XU / Wavelength: 1 Å
DetectorDate: Dec 7, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 42240 / Num. obs: 42240 / % possible obs: 99.8 % / Observed criterion σ(I): 0.187 / Rmerge(I) obs: 0.105
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.435 / % possible all: 99.7

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D2I

3d2i


Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.275 2102 RANDOM
Rwork0.23 --
all0.232 42667 -
obs0.232 42064 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5549 0 90 210 5849
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3

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