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- PDB-2r4e: Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydr... -

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Basic information

Entry
Database: PDB / ID: 2r4e
TitleCrystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with DHAP
ComponentsAerobic glycerol-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GlpD / FAD / Flavoprotein / Glycerol metabolism
Function / homology
Function and homology information


glycerol-3-phosphate dehydrogenase / glycerol-3-phosphate dehydrogenase (quinone) activity / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / glycerol catabolic process / FAD binding / electron transfer activity / protein homodimerization activity / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1890 / FAD-dependent glycerol-3-phosphate dehydrogenase signature 2. / Alpha-glycerophosphate oxidase, cap domain / FAD-dependent glycerol-3-phosphate dehydrogenase / Alpha-glycerophosphate oxidase, C-terminal / Alpha-glycerophosphate oxidase, C-terminal domain superfamily / C-terminal domain of alpha-glycerophosphate oxidase / FAD-dependent glycerol-3-phosphate dehydrogenase signature 1. / FAD dependent oxidoreductase / FAD dependent oxidoreductase ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1890 / FAD-dependent glycerol-3-phosphate dehydrogenase signature 2. / Alpha-glycerophosphate oxidase, cap domain / FAD-dependent glycerol-3-phosphate dehydrogenase / Alpha-glycerophosphate oxidase, C-terminal / Alpha-glycerophosphate oxidase, C-terminal domain superfamily / C-terminal domain of alpha-glycerophosphate oxidase / FAD-dependent glycerol-3-phosphate dehydrogenase signature 1. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helicase, Ruva Protein; domain 3 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Helix non-globular / 3-Layer(bba) Sandwich / Special / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / PHOSPHATE ION / Chem-T3A / Aerobic glycerol-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsYeh, J.I. / Du, S. / Chinte, U.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.
Authors: Yeh, J.I. / Chinte, U. / Du, S.
History
DepositionAug 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aerobic glycerol-3-phosphate dehydrogenase
B: Aerobic glycerol-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,23134
Polymers113,6592
Non-polymers5,57232
Water4,738263
1
A: Aerobic glycerol-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,82917
Polymers56,8291
Non-polymers3,00016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aerobic glycerol-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,40217
Polymers56,8291
Non-polymers2,57216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.848, 113.822, 193.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 4 / Auth seq-ID: 5 - 494 / Label seq-ID: 5 - 494

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Sugars , 2 types, 8 molecules AB

#1: Protein Aerobic glycerol-3-phosphate dehydrogenase


Mass: 56829.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glpD, glyD / Production host: Escherichia coli (E. coli) / References: UniProt: P13035, EC: 1.1.99.5
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 7 types, 289 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-T3A / N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC ACID / TAPS (buffer)


Mass: 243.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO6S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M di-Ammonium hydrogen phosphate, 0.1M Taps, 12% w/v PEG 6000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9803 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9803 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 78152 / % possible obs: 99.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.05-2.124.40.58695.9
2.12-2.215.40.46399.6
2.21-2.316.10.4100
2.31-2.436.30.281100
2.43-2.586.30.203100
2.58-2.786.30.137100
2.78-3.066.30.093100
3.06-3.516.30.072100
3.51-4.426.30.052100
4.42-506.10.03599.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.41 Å
Translation2.5 Å41.41 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→10 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.444 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25607 3628 5 %RANDOM
Rwork0.1978 ---
obs0.20074 68832 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.936 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--0.6 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7906 0 363 263 8532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0218447
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1631.99311420
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9545986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19322.821390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.921151378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9121576
X-RAY DIFFRACTIONr_chiral_restr0.1470.21218
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026278
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.23813
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.25503
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2452
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.218
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3211.55059
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05427854
X-RAY DIFFRACTIONr_scbond_it3.06433998
X-RAY DIFFRACTIONr_scangle_it4.4944.53566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3920 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.340.5
medium thermal0.682
LS refinement shellResolution: 2.1→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 268 -
Rwork0.266 4809 -
obs--98.81 %

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