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- PDB-2g76: Crystal structure of human 3-phosphoglycerate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 2g76
TitleCrystal structure of human 3-phosphoglycerate dehydrogenase
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / phosphoglycerate dehydrogenase deficiency / serine metabolism / 2-hydroxyacid dehydrogenases / Structural Genomics / Structural Genomics Consortium / SGC
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
D-MALATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTurnbull, A.P. / Salah, E. / Savitsky, P. / Gileadi, O. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human 3-phosphoglycerate dehydrogenase
Authors: Turnbull, A.P. / Salah, E. / Savitsky, P. / Gileadi, O. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Sundstrom, M. / Oppermann, U.
History
DepositionFeb 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
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.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)73,8006
Polymers72,2052
Non-polymers1,5954
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-39 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.084, 124.113, 59.502
Angle α, β, γ (deg.)90.00, 100.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
12A
22B

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGGLYGLYAA6 - 10027 - 121
211ARGARGGLYGLYBB6 - 10027 - 121
321ALAALAVALVALAA290 - 306311 - 327
421ALAALAVALVALBB290 - 306311 - 327
112ASNASNGLUGLUAA101 - 289122 - 310
212ASNASNGLUGLUBB101 - 289122 - 310

NCS ensembles :
ID
1
2

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Components

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


Mass: 36102.418 Da / Num. of mol.: 2 / Fragment: residues 3-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHGDH, PGDH3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)R3 / References: UniProt: O43175, phosphoglycerate dehydrogenase
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#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.: 278 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M MMT, 30 % PEG1k, 5mM NAD+, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99806 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 9, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99806 Å / Relative weight: 1
ReflectionResolution: 1.7→36.2 Å / Num. all: 66626 / Num. obs: 66626 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.76 Å / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YGY, 1PSD

1ygy

1psd


Resolution: 1.7→36.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.638 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21644 3371 5.1 %RANDOM
Rwork0.18098 ---
obs0.1828 63219 98.6 %-
all-63219 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.461 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.08 Å2
2--2 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4413 0 106 278 4797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224638
X-RAY DIFFRACTIONr_bond_other_d0.0030.023057
X-RAY DIFFRACTIONr_angle_refined_deg1.4532.0096314
X-RAY DIFFRACTIONr_angle_other_deg0.93237550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9425.205171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98315794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3961528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02810
X-RAY DIFFRACTIONr_nbd_refined0.2210.2912
X-RAY DIFFRACTIONr_nbd_other0.1990.23269
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22271
X-RAY DIFFRACTIONr_nbtor_other0.0850.22433
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0460.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7091.53140
X-RAY DIFFRACTIONr_mcbond_other0.1861.51247
X-RAY DIFFRACTIONr_mcangle_it1.01424843
X-RAY DIFFRACTIONr_scbond_it1.75931712
X-RAY DIFFRACTIONr_scangle_it2.6374.51460
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1658medium positional0.230.5
21103medium positional0.120.5
1574loose positional0.375
21275loose positional0.545
1658medium thermal0.622
21103medium thermal0.632
1574loose thermal0.8710
21275loose thermal1.110
LS refinement shellResolution: 1.697→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 203 -
Rwork0.229 4353 -
obs--91.84 %
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)
12.6041-1.34832.42233.3899-2.04237.6322-0.2391-0.26320.29810.33540.35450.223-1.2142-0.8573-0.11530.21020.15430.06450.00060.06490.0796-5.36845.27811.6769
21.4582-0.09650.19380.7801-0.26991.95890.05510.1753-0.0487-0.109-0.05910.01810.14890.06880.004-0.14250.04450.0072-0.0922-0.0021-0.11417.975417.17193.8216
32.83360.6273-0.88164.7920.10962.7131-0.0732-0.1354-0.46970.2717-0.044-0.13050.92080.05420.11720.34230.0951-0.0113-0.09580.02030.072813.0254-12.62928.1536
41.2883-0.02930.05110.556-0.27712.3539-0.0447-0.1771-0.01120.06870.07060.04110.0231-0.1127-0.0259-0.15020.04160.0038-0.10640.0094-0.10623.980317.267227.645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 10027 - 121
2X-RAY DIFFRACTION1AA290 - 306311 - 327
3X-RAY DIFFRACTION2AA101 - 289122 - 310
4X-RAY DIFFRACTION3BB6 - 10027 - 121
5X-RAY DIFFRACTION3BB290 - 306311 - 327
6X-RAY DIFFRACTION4BB101 - 289122 - 310

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