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- PDB-5n6c: Crystal structure of human 3-phosphoglycerate dehydrogenase in co... -

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Basic information

Entry
Database: PDB / ID: 5n6c
TitleCrystal structure of human 3-phosphoglycerate dehydrogenase in complex with NAD and L-Tartrate
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / serine metabolism / enzymology
Function / homology
Function and homology information


gamma-aminobutyric acid metabolic process / threonine metabolic process / 2-oxoglutarate reductase / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / malate dehydrogenase ...gamma-aminobutyric acid metabolic process / threonine metabolic process / 2-oxoglutarate reductase / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / malate dehydrogenase / L-serine biosynthetic process / L-malate dehydrogenase activity / G1 to G0 transition / neural tube development / spinal cord development / glutamine metabolic process / brain development / neuron projection development / NAD binding / regulation of gene expression / electron transfer activity / extracellular exosome / cytosol
Similarity search - Function
D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase, ASB domain / D-3-phosphoglycerate dehydrogenase intervening domain / Allosteric substrate binding domain superfamily / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain ...D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase, ASB domain / D-3-phosphoglycerate dehydrogenase intervening domain / Allosteric substrate binding domain superfamily / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L(+)-TARTARIC ACID / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsUnterlass, J.E. / Basle, A. / Tucker, J. / Cano, C. / Noble, M.E.M. / Curtin, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC2115/A21421 United Kingdom
CitationJournal: Oncotarget / Year: 2017
Title: Structural insights into the enzymatic activity and potential substrate promiscuity of human 3-phosphoglycerate dehydrogenase (PHGDH).
Authors: Unterlass, J.E. / Wood, R.J. / Basle, A. / Tucker, J. / Cano, C. / Noble, M.M.E. / Curtin, N.J.
History
DepositionFeb 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
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
Revision 1.2Feb 20, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-3-phosphoglycerate dehydrogenase
B: D-3-phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7895
Polymers64,3122
Non-polymers1,4773
Water1,33374
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-40 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.523, 109.719, 66.923
Angle α, β, γ (deg.)90.000, 94.400, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 8 - 305 / Label seq-ID: 2 - 299

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

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Components

#1: Protein D-3-phosphoglycerate dehydrogenase / 3-PGDH


Mass: 32155.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHGDH, PGDH3 / Production host: Escherichia coli (E. coli) / References: UniProt: O43175, phosphoglycerate dehydrogenase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5 0.2 M MgCl2 hexahydrate 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→66.73 Å / Num. obs: 27448 / % possible obs: 98.6 % / Redundancy: 3.88 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.048 / Net I/σ(I): 2.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2660 / CC1/2: 0.812 / Rpim(I) all: 0.511 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G76

2g76


Resolution: 2.3→66.73 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.384 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.387 / ESU R Free: 0.251 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 1319 4.8 %RANDOM
Rwork0.2129 ---
obs0.2148 26108 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 179.86 Å2 / Biso mean: 55.104 Å2 / Biso min: 16.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.38 Å20 Å20.08 Å2
2--0.15 Å20 Å2
3----3.5 Å2
Refinement stepCycle: final / Resolution: 2.3→66.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 98 74 4564
Biso mean--33.79 36.03 -
Num. residues----599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0194597
X-RAY DIFFRACTIONr_bond_other_d0.0020.024311
X-RAY DIFFRACTIONr_angle_refined_deg2.2172.0026255
X-RAY DIFFRACTIONr_angle_other_deg1.1762.99910019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.9825.491173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80615787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.541526
X-RAY DIFFRACTIONr_chiral_restr0.1230.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215132
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02828
Refine LS restraints NCS

Ens-ID: 1 / Number: 17298 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 89 -
Rwork0.283 1911 -
all-2000 -
obs--98.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0010.8139-0.88694.4569-0.27685.5624-0.47670.96320.2513-0.97270.3081-0.5416-0.35580.60280.16860.356-0.15520.2750.80370.19151.085640.25854.59129.039
22.97550.35920.00862.27730.08030.85310.001-0.10630.29270.01230.01830.025-0.04260.0097-0.01920.0065-0.01740.04820.2887-0.03030.810824.29850.86554.554
35.8532-2.65532.52359.5068-5.29649.907-0.4916-0.23280.21352.27380.3071-0.0329-2.6979-0.3620.18461.07830.02090.05170.3466-0.10970.757414.94126.85290.197
42.51930.2851-0.0112.5274-0.30210.4375-0.0302-0.2695-0.44710.17830.0323-0.02740.04910.0023-0.00220.035-0.0180.05840.35520.04070.939726.05427.13859.101
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 95
2X-RAY DIFFRACTION2A96 - 306
3X-RAY DIFFRACTION3B8 - 95
4X-RAY DIFFRACTION4B96 - 306

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