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- PDB-2x5j: Crystal structure of the Apoform of the D-Erythrose-4-phosphate d... -

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Basic information

Entry
Database: PDB / ID: 2x5j
TitleCrystal structure of the Apoform of the D-Erythrose-4-phosphate dehydrogenase from E. coli
ComponentsD-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / HYDRIDE TRANSFER / ALDEHYDE DEHYDROGENASE / PYRIDOXINE BIOSYNTHESIS
Function / homology
Function and homology information


erythrose-4-phosphate dehydrogenase / erythrose-4-phosphate dehydrogenase activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / cytosol
Similarity search - Function
D-erythrose-4-phosphate dehydrogenase / 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 ...D-erythrose-4-phosphate dehydrogenase / 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
PHOSPHATE ION / D-erythrose-4-phosphate dehydrogenase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMoniot, S. / Didierjean, C. / Boschi-Muller, S. / Branlant, G. / Corbier, C.
CitationJournal: To be Published
Title: Structural Characterization of Erythrose-4- Phosphate Dehydrogenase from Escherichia Coli: Peculiar Features When Compared to Phosphorylating Gapdhs
Authors: Moniot, S. / Didierjean, C. / Boschi-Muller, S. / Branlant, G. / Corbier, C.
History
DepositionFeb 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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
O: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
P: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
Q: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
R: D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7698
Polymers149,3894
Non-polymers3804
Water9,710539
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13930 Å2
ΔGint-100.1 kcal/mol
Surface area46890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.300, 110.700, 138.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.54916, 0.62053, 0.55979), (0.63825, -0.74382, 0.1984), (0.5395, 0.24834, -0.80453)-3.82519, -44.93186, 62.57915
2given(-0.75559, -0.01037, -0.65496), (-0.02785, -0.99846, 0.04794), (-0.65445, 0.05446, 0.75414)103.0701, -12.14119, 38.83133
3given(-0.80232, -0.59043, 0.08754), (-0.58682, 0.75345, -0.29658), (0.10916, -0.28932, -0.95099)67.57433, 36.93527, 84.26688

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Components

#1: Protein
D-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE / E4PDH


Mass: 37347.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH PHOSPHATE ANION / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Variant: HB101 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): TG1
References: UniProt: P0A9B6, erythrose-4-phosphate dehydrogenase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.18 Å3/Da / Density % sol: 43.13 % / Description: NONE
Crystal growDetails: 10 % (W/V) PEG 8000, 100 MM NA/K PHOSPHATE BUFFER PH 6.2, 200 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.3→34.5 Å / Num. obs: 59159 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GD1

2gd1


Resolution: 2.3→34.5 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.315 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.441 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26636 2958 5 %RANDOM
Rwork0.20621 ---
obs0.20921 56201 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.711 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---0.8 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10086 0 20 539 10645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02110461
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.93614239
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7351327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43323.133482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.558151685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7181596
X-RAY DIFFRACTIONr_chiral_restr0.0940.21667
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217932
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8041.56595
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.519210647
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.08233866
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3894.53592
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 214 -
Rwork0.29 4081 -
obs--100 %

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