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- PDB-2x5k: Structure of an active site mutant of the D-Erythrose-4-Phosphate... -

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Basic information

Entry
Database: PDB / ID: 2x5k
TitleStructure of an active site mutant of the D-Erythrose-4-Phosphate Dehydrogenase from E. coli
ComponentsD-ERYTHROSE-4-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / S-LOOP / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / D-erythrose-4-phosphate dehydrogenase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 10, 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

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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)151,17325
Polymers149,1974
Non-polymers1,97621
Water17,222956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17820 Å2
ΔGint-91.4 kcal/mol
Surface area48280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.810, 134.810, 246.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.47356, -0.21362, -0.85446), (-0.1865, -0.92382, 0.33433), (-0.86079, 0.31768, 0.39765)-43.21506, 85.67675, -46.8022
2given(0.46797, 0.17125, 0.86699), (0.16203, -0.98104, 0.10632), (0.86876, 0.09072, -0.48685)12.3546, 86.14532, -38.02863
3given(-0.99947, 0.02307, -0.02307), (0.03067, 0.90536, -0.42354), (0.01112, -0.42403, -0.90558)-34.35789, -9.61372, -44.48878

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Components

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Protein , 1 types, 4 molecules OPQR

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


Mass: 37299.199 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Variant: TG1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): DS111
References: UniProt: P0A9B6, erythrose-4-phosphate dehydrogenase

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Non-polymers , 7 types, 977 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 956 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN O, CYS 155 TO ALA ENGINEERED RESIDUE IN CHAIN O, CYS 159 TO SER ...ENGINEERED RESIDUE IN CHAIN O, CYS 155 TO ALA ENGINEERED RESIDUE IN CHAIN O, CYS 159 TO SER ENGINEERED RESIDUE IN CHAIN P, CYS 155 TO ALA ENGINEERED RESIDUE IN CHAIN P, CYS 159 TO SER ENGINEERED RESIDUE IN CHAIN Q, CYS 155 TO ALA ENGINEERED RESIDUE IN CHAIN Q, CYS 159 TO SER ENGINEERED RESIDUE IN CHAIN R, CYS 155 TO ALA ENGINEERED RESIDUE IN CHAIN R, CYS 159 TO SER

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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: 3.45 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growDetails: 24 % (W/V) PEG 1000, 100 MM TRIS-HCL BUFFER PH 8.5, 3 MM ERYTHROSE-4-PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.37→56 Å / Num. obs: 91660 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28.1
Reflection shellResolution: 2.37→2.5 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 4.5 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X5J

2x5j


Resolution: 2.37→55.97 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 11.112 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20699 4579 5 %RANDOM
Rwork0.16444 ---
obs0.16656 87182 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.37→55.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10354 0 126 956 11436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02110806
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.93914669
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82351369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09723.28503
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.093151731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1441598
X-RAY DIFFRACTIONr_chiral_restr0.1330.21700
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218182
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_it1.1651.56746
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.172210896
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.60934060
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7174.53768
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: 2.367→2.429 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 269 -
Rwork0.367 5414 -
obs--84.81 %
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)
10.8645-0.07910.30810.4507-0.06070.2323-0.02480.04260.1092-0.02860.015-0.0151-0.01830.04680.00990.0539-0.0003-0.02650.1070.030.0473-19.23852.094-55.288
20.544-0.17380.3690.2279-0.21320.80720.07960.061-0.0918-0.0013-0.0303-0.00430.12540.0163-0.04920.06560.0221-0.05780.0708-0.03170.06342.17323.723-34.465
30.93310.47240.270.65140.22190.99180.0138-0.10890.13670.0092-0.090.0093-0.1891-0.21650.07610.07950.0843-0.050.1317-0.06620.0752-12.89460.191-16.7
40.9760.61380.56411.07920.58380.43040.1247-0.28480.07370.1106-0.20730.12220.1052-0.17750.08260.0392-0.06520.01690.2751-0.02290.0241-35.43426.598-23.2
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1O0 - 334
2X-RAY DIFFRACTION2P0 - 334
3X-RAY DIFFRACTION3Q0 - 333
4X-RAY DIFFRACTION4R0 - 333

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