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- PDB-6e90: Ternary complex of human glycerol 3-phosphate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 6.0E+90
TitleTernary complex of human glycerol 3-phosphate dehydrogenase
ComponentsGlycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
KeywordsOXIDOREDUCTASE
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
1,3-DIHYDROXYACETONEPHOSPHATE / 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: 2.05 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
C: Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
D: Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,27115
Polymers150,4344
Non-polymers2,83711
Water11,422634
1
A: Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
C: Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9678
Polymers75,2172
Non-polymers1,7506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-65 kcal/mol
Surface area23710 Å2
MethodPISA
2
B: Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
hetero molecules

D: Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3047
Polymers75,2172
Non-polymers1,0875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5660 Å2
ΔGint-57 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.940, 79.560, 85.060
Angle α, β, γ (deg.)63.87, 86.60, 83.61
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 37608.551 Da / Num. of mol.: 4
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 , 6 types, 645 molecules

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


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M calcium chloride, 5% MPD, 20% PEG 8000, 50 mM bis-Tris propane pH 7.0, 2 mM NAD, 1 mM dihydroxyacetone phosphate; 10 mg/mL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→71.11 Å / Num. obs: 80815 / % possible obs: 93.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 20.64 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.199 / Net I/σ(I): 5.2
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3 % / Rmerge(I) obs: 0.753 / Num. unique obs: 7975 / CC1/2: 0.379 / Rrim(I) all: 0.916 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2650)refinement
MOSFLM7.2.1data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E8Z, 1X0X

6e8z

1x0x


Resolution: 2.05→71.11 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.55
RfactorNum. reflection% reflection
Rfree0.2261 7710 4.84 %
Rwork0.177 --
obs0.1793 80813 92.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.16 Å2
Refinement stepCycle: LAST / Resolution: 2.05→71.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9926 0 180 637 10743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210292
X-RAY DIFFRACTIONf_angle_d1.15814006
X-RAY DIFFRACTIONf_dihedral_angle_d11.2656025
X-RAY DIFFRACTIONf_chiral_restr0.061659
X-RAY DIFFRACTIONf_plane_restr0.0071793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07330.2622320.23384855X-RAY DIFFRACTION89
2.0733-2.09770.27032640.21334954X-RAY DIFFRACTION90
2.0977-2.12330.27592560.22484903X-RAY DIFFRACTION89
2.1233-2.15020.29872590.22814925X-RAY DIFFRACTION90
2.1502-2.17840.25982560.21975038X-RAY DIFFRACTION90
2.1784-2.20830.29232860.21874788X-RAY DIFFRACTION90
2.2083-2.23980.28332980.21494978X-RAY DIFFRACTION91
2.2398-2.27330.28732620.20814997X-RAY DIFFRACTION91
2.2733-2.30880.26552850.21044895X-RAY DIFFRACTION91
2.3088-2.34670.22442000.19485085X-RAY DIFFRACTION90
2.3467-2.38710.28152030.19494973X-RAY DIFFRACTION91
2.3871-2.43050.2542550.1985029X-RAY DIFFRACTION91
2.4305-2.47730.23662450.1875188X-RAY DIFFRACTION93
2.4773-2.52790.26912670.18485070X-RAY DIFFRACTION94
2.5279-2.58280.24092840.19035110X-RAY DIFFRACTION93
2.5828-2.64290.22962790.19035090X-RAY DIFFRACTION93
2.6429-2.7090.25642520.18655074X-RAY DIFFRACTION93
2.709-2.78230.2312740.18495085X-RAY DIFFRACTION94
2.7823-2.86410.26052900.20315120X-RAY DIFFRACTION93
2.8641-2.95660.262350.195197X-RAY DIFFRACTION94
2.9566-3.06220.21311930.16595201X-RAY DIFFRACTION94
3.0622-3.18490.21512360.17235119X-RAY DIFFRACTION94
3.1849-3.32980.21222700.17125195X-RAY DIFFRACTION94
3.3298-3.50540.22112760.16045044X-RAY DIFFRACTION93
3.5054-3.7250.20132530.14345158X-RAY DIFFRACTION93
3.725-4.01260.17072290.14295071X-RAY DIFFRACTION92
4.0126-4.41630.18042640.13215098X-RAY DIFFRACTION93
4.4163-5.05530.16362470.13435051X-RAY DIFFRACTION92
5.0553-6.36860.21192930.17954969X-RAY DIFFRACTION91
6.3686-76.41440.20242670.18625299X-RAY DIFFRACTION96

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