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- PDB-1yj8: Initial structural analysis of Plasmodium falciparum Glycerol-3-p... -

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Basic information

Entry
Database: PDB / ID: 1yj8
TitleInitial structural analysis of Plasmodium falciparum Glycerol-3-phosphate dehydrogenase
Componentsglycerol-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / SGPP / Structural Genomics / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium
Function / homology
Function and homology information


Synthesis of PA / glycerol-3-phosphate dehydrogenase [NAD(P)+] activity => GO:0047952 / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate metabolic process / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / NADH oxidation / NAD binding / carbohydrate metabolic process / protein homodimerization activity / cytosol
Similarity search - Function
Glycerol-3-phosphate dehydrogenase, NAD-dependent, eukaryotic / 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 ...Glycerol-3-phosphate dehydrogenase, NAD-dependent, eukaryotic / 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
Glycerol-3-phosphate dehydrogenase [NAD(+)]
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsRobien, M.A. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Initial structural analysis of Plasmodium falciparum Glycerol-3-phosphate dehydrogenase
Authors: Robien, M.A. / Hol, W.G.J. / Medical Structural Genomics of Pathogenic Protozoa
History
DepositionJan 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycerol-3-phosphate dehydrogenase
B: glycerol-3-phosphate dehydrogenase
C: glycerol-3-phosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)126,9323
Polymers126,9323
Non-polymers00
Water18010
1
A: glycerol-3-phosphate dehydrogenase

A: glycerol-3-phosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)84,6222
Polymers84,6222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
2
B: glycerol-3-phosphate dehydrogenase
C: glycerol-3-phosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)84,6222
Polymers84,6222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-19 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.455, 177.455, 232.699
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C
12A
22B
32C
42A
52B
62C
13A
23B
33C
14A
24B
34C
44A
54B
64C

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111TYRTYRGLYGLYAA10 - 2810 - 28
211TYRTYRGLYGLYBB10 - 2810 - 28
311TYRTYRGLYGLYCC10 - 2810 - 28
421ASNASNPHEPHEAA31 - 6231 - 62
521ASNASNPHEPHEBB31 - 6231 - 62
621ASNASNPHEPHECC31 - 6231 - 62
731GLUGLUPROPROAA66 - 8866 - 88
831GLUGLUPROPROBB66 - 8866 - 88
931GLUGLUPROPROCC66 - 8866 - 88
112CYSCYSLYSLYSAA113 - 124113 - 124
212CYSCYSLYSLYSBB113 - 124113 - 124
312CYSCYSLYSLYSCC113 - 124113 - 124
422ILEILEILEILEAA129 - 210129 - 210
522ILEILEILEILEBB129 - 210129 - 210
622ILEILEILEILECC129 - 210129 - 210
113THRTHRSERSERAA216 - 285216 - 285
213THRTHRSERSERBB216 - 285216 - 285
313THRTHRSERSERCC216 - 285216 - 285
114ASNASNLEULEUAA312 - 320312 - 320
214ASNASNLEULEUBB312 - 320312 - 320
314ASNASNLEULEUCC312 - 320312 - 320
424THRTHRGLNGLNAA323 - 372323 - 372
524THRTHRGLNGLNBB323 - 372323 - 372
624THRTHRGLNGLNCC323 - 372323 - 372

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein glycerol-3-phosphate dehydrogenase


Mass: 42310.832 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PFL0780w / Plasmid: pET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star/DE3
References: UniProt: Q8I5P5, glycerol-3-phosphate dehydrogenase (NAD+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10
Details: PEG 400, Potassium phosphate monobasic, CAPS, DTT, pH 10, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL11-310.976
SYNCHROTRONALS 8.2.120.9794, 0.91840, 0.97950
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 11, 2004
ADSC QUANTUM 2102CCDJun 20, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(111) bent monochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
20.97941
30.91841
40.97951
ReflectionResolution: 2.85→50 Å / Num. all: 50738 / Num. obs: 50574 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 69.775 Å2 / Rsym value: 0.132 / Net I/σ(I): 8.4
Reflection shellResolution: 2.85→3 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 7016 / Rsym value: 0.708 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.85→44.54 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.903 / SU B: 13.568 / SU ML: 0.246 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.528 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Hydrogens have been added in the riding positions. The authors state that the electron density of residues in the region of approximately residues 285-313 is quite weak, and hence somewhat ...Details: Hydrogens have been added in the riding positions. The authors state that the electron density of residues in the region of approximately residues 285-313 is quite weak, and hence somewhat uncertain, especially in chains B and C.
RfactorNum. reflection% reflectionSelection details
Rfree0.25576 2557 5.1 %RANDOM
Rwork0.23607 ---
all0.23706 47958 --
obs0.23706 47958 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.225 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.85→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8415 0 0 10 8425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228565
X-RAY DIFFRACTIONr_bond_other_d0.0010.027825
X-RAY DIFFRACTIONr_angle_refined_deg0.9441.95611560
X-RAY DIFFRACTIONr_angle_other_deg0.73318299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.76151062
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.42625.749374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.926151578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4531521
X-RAY DIFFRACTIONr_chiral_restr0.0560.21331
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021623
X-RAY DIFFRACTIONr_nbd_refined0.1880.21790
X-RAY DIFFRACTIONr_nbd_other0.1580.27865
X-RAY DIFFRACTIONr_nbtor_refined0.1710.24203
X-RAY DIFFRACTIONr_nbtor_other0.0810.24739
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.210
X-RAY DIFFRACTIONr_mcbond_it1.01145720
X-RAY DIFFRACTIONr_mcbond_other0.11342172
X-RAY DIFFRACTIONr_mcangle_it1.69468606
X-RAY DIFFRACTIONr_scbond_it1.40663541
X-RAY DIFFRACTIONr_scangle_it2.229102954
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A436tight positional0.020.05
12B436tight positional0.020.05
13C436tight positional0.020.05
21A558tight positional0.020.05
22B558tight positional0.020.05
23C558tight positional0.020.05
31A413tight positional0.020.05
32B413tight positional0.020.05
33C413tight positional0.020.05
41A351tight positional0.020.05
42B351tight positional0.020.05
43C351tight positional0.020.05
11A746loose positional0.595
12B746loose positional0.625
13C746loose positional0.635
21A822loose positional0.55
22B822loose positional0.465
23C822loose positional0.465
31A624loose positional0.585
32B624loose positional0.65
33C624loose positional0.55
41A576loose positional0.725
42B576loose positional0.615
43C576loose positional0.695
11A436tight thermal0.030.5
12B436tight thermal0.030.5
13C436tight thermal0.040.5
21A558tight thermal0.030.5
22B558tight thermal0.030.5
23C558tight thermal0.030.5
31A413tight thermal0.050.5
32B413tight thermal0.030.5
33C413tight thermal0.040.5
41A351tight thermal0.050.5
42B351tight thermal0.030.5
43C351tight thermal0.050.5
11A746loose thermal0.8210
12B746loose thermal1.0310
13C746loose thermal1.1810
21A822loose thermal1.1810
22B822loose thermal1.1410
23C822loose thermal1.2210
31A624loose thermal1.5310
32B624loose thermal0.8910
33C624loose thermal1.4110
41A576loose thermal1.4210
42B576loose thermal0.9610
43C576loose thermal1.5610
LS refinement shellResolution: 2.85→3.004 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.391 364 -
Rwork0.359 6604 -
obs-6604 95.65 %

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