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- PDB-5fb3: Structure of glycerophosphate dehydrogenase in complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 5fb3
TitleStructure of glycerophosphate dehydrogenase in complex with NADPH
ComponentsGlycerol-1-phosphate dehydrogenase [NAD(P)+]
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


glycerol-1-phosphate dehydrogenase [NAD(P)+] activity / sn-glycerol-1-phosphate dehydrogenase / glycerophospholipid metabolic process / phospholipid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Glycerol-1-phosphate dehydrogenase, archaea / Glycerol-1-phosphate dehydrogenase / Iron-containing alcohol dehydrogenase / Glycerol dehydrogenase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Glycerol-1-phosphate dehydrogenase, archaea / Glycerol-1-phosphate dehydrogenase / Iron-containing alcohol dehydrogenase / Glycerol dehydrogenase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / PYROPHOSPHATE / Glycerol-1-phosphate dehydrogenase [NAD(P)+]
Similarity search - Component
Biological speciesPyrobaculum calidifontis JCM 11548 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.45 Å
AuthorsSakuraba, H. / Hayashi, J. / Yamamoto, K. / Yoneda, K. / Ohshima, T.
CitationJournal: Proteins / Year: 2016
Title: Unique coenzyme binding mode of hyperthermophilic archaeal sn-glycerol-1-phosphate dehydrogenase from Pyrobaculum calidifontis
Authors: Hayashi, J. / Yamamoto, K. / Yoneda, K. / Ohshima, T. / Sakuraba, H.
History
DepositionDec 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
B: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
C: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
D: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
E: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
F: Glycerol-1-phosphate dehydrogenase [NAD(P)+]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,21728
Polymers222,2586
Non-polymers3,95922
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22510 Å2
ΔGint-449 kcal/mol
Surface area73390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.182, 123.335, 166.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glycerol-1-phosphate dehydrogenase [NAD(P)+] / Glycerophosphate dehydrogenase / G1PDH / Enantiomeric glycerophosphate synthase / sn-glycerol-1- ...Glycerophosphate dehydrogenase / G1PDH / Enantiomeric glycerophosphate synthase / sn-glycerol-1-phosphate dehydrogenase


Mass: 37042.953 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis JCM 11548 (archaea)
Strain: JCM 11548 / Gene: egsA, Pcal_0566 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A3MTM6, sn-glycerol-1-phosphate dehydrogenase

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Non-polymers , 5 types, 187 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#5: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 12, 2015
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 78117 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Χ2: 0.75 / Net I/av σ(I): 25.771 / Net I/σ(I): 7.2 / Num. measured all: 520646
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.496.50.67638690.8980.2880.7360.473100
2.49-2.546.50.55138720.9170.2340.5990.486100
2.54-2.596.30.49338260.930.2140.5380.498100
2.59-2.646.90.4538810.9580.1840.4870.551100
2.64-2.770.39138600.9670.1580.4220.517100
2.7-2.7670.32438740.9730.1310.350.505100
2.76-2.8370.28338530.9790.1150.3050.537100
2.83-2.970.21938680.990.0890.2370.535100
2.9-2.996.90.18538590.9890.0760.20.577100
2.99-3.096.80.16439090.9910.0680.1770.684100
3.09-3.26.70.13238760.9940.0550.1440.719100
3.2-3.326.60.09838690.9950.0410.1060.748100
3.32-3.486.10.08538930.9960.0370.0930.834100
3.48-3.666.40.07439120.9970.0320.080.954100
3.66-3.896.30.06539020.9970.0280.071.071100
3.89-4.1970.05939190.9980.0240.0641.10299.9
4.19-4.6170.05439410.9980.0220.0591.17399.8
4.61-5.286.80.0539520.9980.020.0541.077100
5.28-6.656.10.04340070.9980.0190.0470.99100
6.65-506.50.03241750.9980.0140.0350.97199.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
BUCCANEERmodel building
RefinementMethod to determine structure: SIRAS / Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.703 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.63 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 3854 4.9 %RANDOM
Rwork0.2071 ---
obs0.2098 74184 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.28 Å2 / Biso mean: 63.236 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å2-0 Å20 Å2
2--2.55 Å20 Å2
3----4.03 Å2
Refinement stepCycle: final / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15470 0 219 165 15854
Biso mean--63.94 49.73 -
Num. residues----2008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01915979
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215905
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.99821656
X-RAY DIFFRACTIONr_angle_other_deg0.751336605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.29852005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01822.689610
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.367152840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.34415133
X-RAY DIFFRACTIONr_chiral_restr0.0630.22528
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02117501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023408
X-RAY DIFFRACTIONr_mcbond_it3.0996.0858029
X-RAY DIFFRACTIONr_mcbond_other3.0996.0858028
X-RAY DIFFRACTIONr_mcangle_it4.8669.11810022
LS refinement shellResolution: 2.447→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 296 -
Rwork0.297 5140 -
all-5436 -
obs--94.57 %

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