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- PDB-6e8z: Binary complex of Human glycerol 3-phosphate dehydrogenase with NAD -

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Basic information

Entry
Database: PDB / ID: 6e8z
TitleBinary complex of Human glycerol 3-phosphate dehydrogenase with NAD
ComponentsGlycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


glycerol-3-phosphate shuttle / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate dehydrogenase (NAD+) activity / glycerol-3-phosphate catabolic process / glycerol-3-phosphate metabolic process / Synthesis of PA / cellular response to cAMP / positive regulation of glycolytic process / gluconeogenesis / NAD binding ...glycerol-3-phosphate shuttle / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate dehydrogenase (NAD+) activity / glycerol-3-phosphate catabolic process / 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
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMydy, L.S. / Gulick, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI116998 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116921 United States
CitationJournal: Biochemistry / Year: 2019
Title: Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies.
Authors: Mydy, L.S. / Cristobal, J.R. / Katigbak, R.D. / Bauer, P. / Reyes, A.C. / Kamerlin, S.C.L. / Richard, J.P. / Gulick, A.M.
History
DepositionJul 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)77,06012
Polymers75,2172
Non-polymers1,84310
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-39 kcal/mol
Surface area24830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.580, 78.780, 69.179
Angle α, β, γ (deg.)90.00, 104.32, 90.00
Int Tables number4
Space group name H-MP1211

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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: 37608.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPD1 / Production host: Escherichia coli (E. coli)
References: UniProt: P21695, glycerol-3-phosphate dehydrogenase (NAD+)

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Non-polymers , 5 types, 240 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM potassium chloride, 23% PEG 20000, 0.1 M bis-tris propane pH 7.0, 10 mM NAD; 10 mg/mL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.1→33.96 Å / Num. obs: 37384 / % possible obs: 96.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.056 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.195 / Num. unique obs: 3740 / CC1/2: 0.966 / Rrim(I) all: 0.234 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
MOSFLM7.2.1data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X0X

1x0x


Resolution: 2.1→33.96 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.07 / Phase error: 25.73
RfactorNum. reflection% reflection
Rfree0.2247 3284 4.65 %
Rwork0.169 --
obs0.1717 37372 93.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.92 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5013 0 116 230 5359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125258
X-RAY DIFFRACTIONf_angle_d1.167140
X-RAY DIFFRACTIONf_dihedral_angle_d13.3423086
X-RAY DIFFRACTIONf_chiral_restr0.058832
X-RAY DIFFRACTIONf_plane_restr0.008915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13140.35961190.2512855X-RAY DIFFRACTION91
2.1314-2.16470.3081630.23572929X-RAY DIFFRACTION94
2.1647-2.20020.35591370.23122974X-RAY DIFFRACTION93
2.2002-2.23810.32651120.22052943X-RAY DIFFRACTION93
2.2381-2.27880.26651480.21272891X-RAY DIFFRACTION92
2.2788-2.32260.30911530.20742956X-RAY DIFFRACTION93
2.3226-2.370.28751110.19992846X-RAY DIFFRACTION90
2.37-2.42150.26041490.19222740X-RAY DIFFRACTION88
2.4215-2.47780.27291620.18242823X-RAY DIFFRACTION91
2.4778-2.53980.23231360.17232994X-RAY DIFFRACTION94
2.5398-2.60840.23711680.18542937X-RAY DIFFRACTION94
2.6084-2.68520.27031360.17832969X-RAY DIFFRACTION94
2.6852-2.77180.23531260.18612974X-RAY DIFFRACTION94
2.7718-2.87080.25761500.18022862X-RAY DIFFRACTION92
2.8708-2.98570.26811450.17832785X-RAY DIFFRACTION88
2.9857-3.12150.22181670.17252929X-RAY DIFFRACTION94
3.1215-3.2860.24821590.18193049X-RAY DIFFRACTION96
3.286-3.49170.21791150.17132982X-RAY DIFFRACTION95
3.4917-3.76110.23741350.15263017X-RAY DIFFRACTION95
3.7611-4.13910.14471170.14542903X-RAY DIFFRACTION92
4.1391-4.73690.16731740.12363033X-RAY DIFFRACTION97
4.7369-5.96360.1991040.14372978X-RAY DIFFRACTION93
5.9636-36.11360.18461980.16492975X-RAY DIFFRACTION96

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