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- PDB-6pyp: Binary Complex of Human Glycerol 3-Phosphate Dehydrogenase, R269A... -

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Basic information

Entry
Database: PDB / ID: 6pyp
TitleBinary Complex of Human Glycerol 3-Phosphate Dehydrogenase, R269A mutant
ComponentsGlycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
KeywordsOXIDOREDUCTASE / Dehydrogenase
Function / homology
Function and homology information


glycerophosphate shuttle / glycerolipid metabolic process / glycerol-3-phosphate dehydrogenase (quinone) activity / glycerol-3-phosphate dehydrogenase [NAD(P)+] activity / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / NADH oxidation / glycerol-3-phosphate metabolic process / Synthesis of PA ...glycerophosphate shuttle / glycerolipid metabolic process / glycerol-3-phosphate dehydrogenase (quinone) activity / glycerol-3-phosphate dehydrogenase [NAD(P)+] activity / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / NADH oxidation / glycerol-3-phosphate metabolic process / Synthesis of PA / cellular response to cAMP / positive regulation of glycolytic process / gluconeogenesis / NAD binding / cellular response to tumor necrosis factor / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
Glycerol-3-phosphate dehydrogenase, NAD-dependent, eukaryotic / NAD-dependent glycerol-3-phosphate dehydrogenase signature. / Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal / Glycerol-3-phosphate dehydrogenase, NAD-dependent / Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal / NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus / NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...Glycerol-3-phosphate dehydrogenase, NAD-dependent, eukaryotic / NAD-dependent glycerol-3-phosphate dehydrogenase signature. / Glycerol-3-phosphate dehydrogenase, NAD-dependent, C-terminal / Glycerol-3-phosphate dehydrogenase, NAD-dependent / Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal / NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus / NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2,2-bis(hydroxymethyl)propane-1,3-diol / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / PYROPHOSPHATE 2- / Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGulick, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116957 United States
CitationJournal: Acs Catalysis / Year: 2020
Title: Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase.
Authors: Mhashal, A.R. / Romero-Rivera, A. / Mydy, L.S. / Cristobal, J.R. / Gulick, A.M. / Richard, J.P. / Kamerlin, S.C.L.
History
DepositionJul 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
B: Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1547
Polymers75,0452
Non-polymers1,1105
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-32 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.330, 76.560, 64.610
Angle α, β, γ (deg.)90.000, 96.570, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic / GPDH-C


Mass: 37522.434 Da / Num. of mol.: 2 / Mutation: R269A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P21695, glycerol-3-phosphate dehydrogenase (NAD+)

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Non-polymers , 6 types, 388 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-3SY / 2,2-bis(hydroxymethyl)propane-1,3-diol / Pentaerythritol


Mass: 136.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O4
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 23% PEG 20000 175 mM KCl 0.1M Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2017
RadiationMonochromator: APS 23IDB / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→42 Å / Num. obs: 44671 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.071 / Rrim(I) all: 0.103 / Net I/σ(I): 8.6
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 3113 / CC1/2: 0.919 / Rpim(I) all: 0.202 / Rrim(I) all: 0.295

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Starting model was an in-house model of open conformation

Resolution: 1.95→42 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2097 5 %Random
Rwork0.167 ---
obs-44644 99.7 %-
Refinement stepCycle: LAST / Resolution: 1.95→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4998 0 68 383 5449
LS refinement shellResolution: 1.95→2 Å
RfactorNum. reflection% reflection
Rfree0.26 126 5 %
Rwork0.19 2820 -
obs--100 %

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