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- PDB-7cvp: The Crystal Structure of human PHGDH from Biortus. -

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Basic information

Entry
Database: PDB / ID: 7cvp
TitleThe Crystal Structure of human PHGDH from Biortus.
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / catalytic activity / electron transfer activity / oxidoreductase activity
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 domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, F. / Lv, Z. / Cheng, W. / Lin, D. / Miao, Q. / Huang, Y.
CitationJournal: To Be Published
Title: The Crystal Structure of human PHGDH from Biortus.
Authors: Wang, F. / Lv, Z. / Cheng, W. / Lin, D. / Miao, Q. / Huang, Y.
History
DepositionAug 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: D-3-phosphoglycerate dehydrogenase
B: D-3-phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1784
Polymers70,8512
Non-polymers1,3272
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-29 kcal/mol
Surface area21850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.101, 121.638, 59.372
Angle α, β, γ (deg.)90.000, 99.974, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D-3-phosphoglycerate dehydrogenase / 3-PGDH / 2-oxoglutarate reductase / Malate dehydrogenase


Mass: 35425.648 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-oxoglutarate reductase, malate dehydrogenase
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris pH6.5, 25% PEG3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→42.486 Å / Num. obs: 19518 / % possible obs: 93.7 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.4
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2202 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CWA

6cwa


Resolution: 2.5→42.486 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.833 / WRfactor Rfree: 0.32 / WRfactor Rwork: 0.261 / SU B: 14.262 / SU ML: 0.313 / Average fsc free: 0.8052 / Average fsc work: 0.8308 / Cross valid method: FREE R-VALUE / ESU R: 0.658 / ESU R Free: 0.369
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3196 944 4.837 %
Rwork0.2607 18572 -
all0.263 --
obs-19516 93.584 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.884 Å2
Baniso -1Baniso -2Baniso -3
1--4.55 Å20 Å2-1.675 Å2
2--10.676 Å20 Å2
3----5.215 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3567 0 88 16 3671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133707
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173385
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.6435037
X-RAY DIFFRACTIONr_angle_other_deg1.1141.5747841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9415487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21722.39159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56815577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg141524
X-RAY DIFFRACTIONr_chiral_restr0.0450.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
X-RAY DIFFRACTIONr_nbd_refined0.1880.2763
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.23285
X-RAY DIFFRACTIONr_nbtor_refined0.1430.21725
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21757
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2102
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1410.23
X-RAY DIFFRACTIONr_nbd_other0.1630.221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.22
X-RAY DIFFRACTIONr_mcbond_it1.4033.811975
X-RAY DIFFRACTIONr_mcbond_other1.4033.8081974
X-RAY DIFFRACTIONr_mcangle_it2.3535.6832453
X-RAY DIFFRACTIONr_mcangle_other2.3535.6852454
X-RAY DIFFRACTIONr_scbond_it1.0663.7771732
X-RAY DIFFRACTIONr_scbond_other1.0663.7771733
X-RAY DIFFRACTIONr_scangle_it1.7785.6662584
X-RAY DIFFRACTIONr_scangle_other1.7775.6672585
X-RAY DIFFRACTIONr_lrange_it3.97944.7523848
X-RAY DIFFRACTIONr_lrange_other3.97844.7543849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.332770.311349X-RAY DIFFRACTION93.4469
2.565-2.6350.297660.2971359X-RAY DIFFRACTION96.089
2.635-2.7110.379720.2931345X-RAY DIFFRACTION95.8728
2.711-2.7950.405640.2711272X-RAY DIFFRACTION96.5318
2.795-2.8860.289720.2631266X-RAY DIFFRACTION95.7767
2.886-2.9870.321510.2441193X-RAY DIFFRACTION95.472
2.987-3.10.296640.2161181X-RAY DIFFRACTION95.6956
3.1-3.2260.259560.2431120X-RAY DIFFRACTION95.0687
3.226-3.3690.296590.2641021X-RAY DIFFRACTION92.8633
3.369-3.5330.321510.2461051X-RAY DIFFRACTION95.5768
3.533-3.7230.289470.228955X-RAY DIFFRACTION94.3503
3.723-3.9480.347470.233924X-RAY DIFFRACTION93.7259
3.948-4.2190.294310.223843X-RAY DIFFRACTION92.1941
4.219-4.5550.322340.219749X-RAY DIFFRACTION88.0765
4.555-4.9870.266310.247691X-RAY DIFFRACTION87.5152
4.987-5.5710.38320.327636X-RAY DIFFRACTION88.8298
5.571-6.4240.438290.37565X-RAY DIFFRACTION90.8257
6.424-7.8460.33270.32474X-RAY DIFFRACTION89.1459
7.846-11.0050.304240.242363X-RAY DIFFRACTION86.9663
11.005-42.4860.305100.305215X-RAY DIFFRACTION87.8906

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