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- PDB-7dkm: PHGDH covalently linked to oridonin -

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Basic information

Entry
Database: PDB / ID: 7dkm
TitlePHGDH covalently linked to oridonin
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / inhibitor / complex / dehydrogenase / covalent
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 / Chem-ODN / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSun, Q. / Lei, Y.
CitationJournal: Cell.Mol.Life Sci. / Year: 2021
Title: Biophysical and biochemical properties of PHGDH revealed by studies on PHGDH inhibitors.
Authors: Tan, Y. / Zhou, X. / Gong, Y. / Gou, K. / Luo, Y. / Jia, D. / Dai, L. / Zhao, Y. / Sun, Q.
History
DepositionNov 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)69,9689
Polymers67,9422
Non-polymers2,0257
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-61 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.180, 126.470, 59.287
Angle α, β, γ (deg.)90.000, 99.720, 90.000
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 D-3-phosphoglycerate dehydrogenase / 3-PGDH / 2-oxoglutarate reductase / Malate dehydrogenase


Mass: 33971.078 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

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Non-polymers , 6 types, 480 molecules

#2: Chemical ChemComp-ODN / (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one


Mass: 366.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O6 / Feature type: SUBJECT OF INVESTIGATION
#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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Na Formate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97924 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 66526 / % possible obs: 96.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.034 / Rrim(I) all: 0.082 / Χ2: 0.979 / Net I/σ(I): 9.5 / Num. measured all: 354729
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.734.20.82427020.6650.4390.9390.74278.3
1.73-1.764.50.67229030.7970.3430.7590.73185.1
1.76-1.794.90.54932650.8460.2660.6130.77494.8
1.79-1.835.40.49333680.8760.2290.5460.80999.8
1.83-1.875.40.40634750.9160.1880.4490.82399.9
1.87-1.915.40.33534340.9240.1550.3711.00199.7
1.91-1.965.30.28434200.9530.1320.3140.9999.8
1.96-2.025.20.22733860.9710.1060.2511.02399.5
2.02-2.0750.20333140.9760.0970.2261.07496.5
2.07-2.145.60.16234350.9820.0720.1781.07999.8
2.14-2.225.60.13433970.9880.060.1471.06299.7
2.22-2.315.40.12934310.9880.0590.1431.12899.6
2.31-2.415.40.10334360.9920.0470.1141.0499.3
2.41-2.545.10.08933380.9930.0420.0991.02997.2
2.54-2.75.70.08234280.9940.0360.091.0499.1
2.7-2.915.70.07433730.9950.0330.0821.01698.7
2.91-3.25.50.06733650.9940.0310.0740.9997.9
3.2-3.665.70.05933610.9960.0260.0651.07297.4
3.66-4.615.70.05433790.9950.0240.0590.95497.5
4.61-505.70.06633160.9940.0290.0720.97994.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2g76

2g76


Resolution: 1.7→42.95 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1791 / WRfactor Rwork: 0.1401 / FOM work R set: 0.8577 / SU B: 5.047 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1374 / SU Rfree: 0.0864 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.171 3284 4.9 %RANDOM
Rwork0.1358 ---
obs0.1376 63125 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.79 Å2 / Biso mean: 48.191 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å2-0.3 Å2
2--1.76 Å20 Å2
3----2.49 Å2
Refinement stepCycle: final / Resolution: 1.7→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 133 475 5196
Biso mean--49.27 49.86 -
Num. residues----612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134862
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174663
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.6546606
X-RAY DIFFRACTIONr_angle_other_deg1.621.59110862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44722.883222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67515876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7041533
X-RAY DIFFRACTIONr_chiral_restr0.0620.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02894
X-RAY DIFFRACTIONr_rigid_bond_restr0.89539525
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 182 -
Rwork0.25 3806 -
all-3988 -
obs--78.21 %
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)
11.87760.16250.2781.2598-0.15372.98830.02770.18050.3864-0.0965-0.0240.2446-0.4368-0.1898-0.00370.07910.0404-0.00630.03550.03280.11563.329429.67443.1169
22.25260.21320.04280.6406-0.25683.12420.0276-0.1875-0.51410.10940.0327-0.02680.71590.1584-0.06020.21050.0525-0.01290.03070.0420.11878.26445.701327.6475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 502
2X-RAY DIFFRACTION2B5 - 502

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