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- PDB-5ur0: Crystallographic structure of glyceraldehyde-3-phosphate dehydrog... -

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Basic information

Entry
Database: PDB / ID: 5ur0
TitleCrystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Naegleria gruberi / glyceraldehyde-3-phosphate dehydrogenase
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRIETHYLENE GLYCOL / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesNaegleria gruberi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMachado, A.T.P. / Silva, M. / Iulek, J.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)573607/2008-7 Brazil
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Structural studies of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi, the first one from phylum Percolozoa.
Authors: Machado, A.T.P. / Silva, M. / Iulek, J.
History
DepositionFeb 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,28413
Polymers154,3884
Non-polymers2,8969
Water23,0771281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20790 Å2
ΔGint-181 kcal/mol
Surface area42290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.743, 94.552, 90.932
Angle α, β, γ (deg.)90.00, 99.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase


Mass: 38597.004 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria gruberi (eukaryote) / Gene: NAEGRDRAFT_53883 / Production host: Escherichia coli (E. coli)
References: UniProt: D2W142, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1281 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 2.5% (m/V) PEG 1000, 50 mM acetate buffer (pH 4.8), 25.7% (m/V) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45861 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45861 Å / Relative weight: 1
ReflectionResolution: 1.94→89.536 Å / Num. obs: 102380 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 24.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.26
Reflection shellResolution: 1.94→2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.28 / CC1/2: 0.787 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSVERSION May 1, 2016 BUILT=20160617data processing
XSCALEVERSION May 1, 2016 BUILT=20160617data scaling
PHASER2.5.5phasing
Coot0.7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E6A, edited

3e6a


Resolution: 1.94→29.854 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / Phase error: 21.19
RfactorNum. reflection% reflection
Rfree0.1984 1988 1.94 %
Rwork0.1536 --
obs0.1545 102371 99.16 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 1.94→29.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10201 0 190 1281 11672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110742
X-RAY DIFFRACTIONf_angle_d1.30214695
X-RAY DIFFRACTIONf_dihedral_angle_d12.4923961
X-RAY DIFFRACTIONf_chiral_restr0.0521707
X-RAY DIFFRACTIONf_plane_restr0.0061933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.98850.28971340.25086944X-RAY DIFFRACTION97
1.9885-2.04230.31161440.23656919X-RAY DIFFRACTION96
2.0423-2.10230.26891440.21647169X-RAY DIFFRACTION99
2.1023-2.17020.25571370.19177148X-RAY DIFFRACTION100
2.1702-2.24770.21621380.17887196X-RAY DIFFRACTION100
2.2477-2.33770.21281450.16847188X-RAY DIFFRACTION100
2.3377-2.4440.21351420.16927170X-RAY DIFFRACTION100
2.444-2.57280.23241420.17067162X-RAY DIFFRACTION100
2.5728-2.73390.23431420.17087204X-RAY DIFFRACTION100
2.7339-2.94480.22221490.16537181X-RAY DIFFRACTION100
2.9448-3.24090.20051350.15397240X-RAY DIFFRACTION100
3.2409-3.70910.20611520.13217216X-RAY DIFFRACTION100
3.7091-4.67010.14051440.10957290X-RAY DIFFRACTION100
4.6701-29.85780.13891400.137356X-RAY DIFFRACTION100
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)
11.3061-0.09260.32250.7748-0.20861.35440.00460.17750.0379-0.187-0.0479-0.0549-0.01140.19190.04490.26820.0097-0.00070.21420.00270.19076.349530.9528-4.5532
22.95922.4268-0.48613.91331.23511.4841-0.09660.17410.3068-0.20230.08640.2649-0.2679-0.03760.01170.18260.0165-0.01810.15310.03140.16352.201839.478317.8473
31.83030.29180.91351.51950.3391.40130.0027-0.0065-0.0176-0.17350.00370.358-0.0122-0.3040.0290.15170.0016-0.02490.19670.02410.1953-13.122429.64210.7363
45.99260.24920.67051.3182-0.13192.3688-0.01470.0235-0.5054-0.18750.07330.18360.2384-0.2412-0.0530.2279-0.0178-0.02820.1338-0.00440.2679-7.941715.09139.5521
52.8191-0.4585-0.77631.0416-0.23861.9603-0.0431-0.1184-0.1492-0.17240.01710.1220.17360.03270.05290.1622-0.0171-0.04150.0805-0.01710.193-6.851223.61684.4601
62.82560.3103-1.38492.2068-0.12094.61990.0384-0.37450.0570.3187-0.0434-0.1443-0.14680.28360.00470.2332-0.0163-0.00010.2407-0.00790.15725.691831.672852.8637
72.745-0.48770.38481.7078-1.51854.3128-0.0188-0.2066-0.19540.1625-0.02460.03330.13810.05540.01760.2284-0.01960.05360.12220.00160.1984-10.105223.222750.9031
84.3579-1.9821-0.20021.57950.19930.246-0.1542-0.2959-0.25350.18310.18760.27150.0634-0.0442-0.02030.19130.00340.03590.22970.0590.2237-7.907324.270328.5511
92.48590.0321-0.31421.34480.09181.0281-0.01550.00550.14080.10930.02610.2902-0.0934-0.1539-0.00420.16750.01750.03470.18560.02350.212-13.774438.338129.7737
101.50180.24680.79811.12490.17373.2534-0.0410.04470.07860.1549-0.00680.12-0.1294-0.00980.03850.1520.02560.04420.08970.01470.2006-12.589735.511837.2816
113.32640.29660.05893.6108-0.42292.277-0.0058-0.02060.12980.1028-0.0166-0.0848-0.207-0.05080.0270.18790.00930.02410.1279-0.02060.166711.044156.020427.5915
125.5314-3.12393.33755.9427-0.47977.39470.0545-0.04690.23150.17280.08990.05610.11720.0254-0.08860.28050.00230.04170.1743-0.01890.21233.636862.727428.3751
132.1897-0.0293-0.03633.0782-0.49182.9436-0.05140.48390.5111-0.2328-0.0658-0.4103-0.28410.20910.08570.2586-0.070.0590.27240.04240.373826.20561.459721.9748
142.61450.57411.38151.07510.85591.3731-0.02160.01150.2069-0.00220.072-0.198-0.11890.2327-0.04440.1686-0.02660.01140.2518-0.01330.254229.003938.531424.2042
151.0105-0.19910.09640.92210.38471.0391-0.0451-0.17410.08950.14090.1053-0.2803-0.03660.2014-0.03940.1631-0.0131-0.03940.2694-0.03180.247830.368340.466937.2573
164.0211-1.00150.21694.554-0.91882.88940.0422-0.0307-0.2734-0.0762-0.00110.10260.1519-0.0431-0.0330.1872-0.0216-0.0420.1321-0.01350.1611.13442.83222.1338
176.07762.2847-2.56313.004-0.86453.9166-0.01710.0133-0.1218-0.37720.07630.2382-0.1570.0256-0.06680.3806-0.0297-0.05270.1833-0.02110.22694.0189-3.809719.915
182.79711.4583-0.50053.136-0.64061.03860.0559-0.1958-0.22110.1277-0.0172-0.12930.16060.0446-0.03470.19440.0268-0.0540.21150.030.178227.02772.20631.3863
192.45740.4769-1.63381.641.04462.2777-0.0667-0.396-0.22960.25890.003-0.09720.18110.25680.0790.16870.0184-0.01990.22030.03350.161917.778823.882635.8337
201.2221-0.45980.23471.0404-0.12830.61540.01170.05530.0655-0.0506-0.0373-0.2740.05140.20640.01290.14710.00790.01840.240.01970.230233.544617.273321.2009
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:171)
2X-RAY DIFFRACTION2(chain A and resid 172:208)
3X-RAY DIFFRACTION3(chain A and resid 209:251)
4X-RAY DIFFRACTION4(chain A and resid 252:298)
5X-RAY DIFFRACTION5(chain A and resid 299:333)
6X-RAY DIFFRACTION6(chain B and resid 0:74)
7X-RAY DIFFRACTION7(chain B and resid 75:155)
8X-RAY DIFFRACTION8(chain B and resid 156:214)
9X-RAY DIFFRACTION9(chain B and resid 215:299)
10X-RAY DIFFRACTION10(chain B and resid 300:333)
11X-RAY DIFFRACTION11(chain C and resid 0:54)
12X-RAY DIFFRACTION12(chain C and resid 55:75)
13X-RAY DIFFRACTION13(chain C and resid 76:145)
14X-RAY DIFFRACTION14(chain C and resid 146:217)
15X-RAY DIFFRACTION15(chain C and resid 218:333)
16X-RAY DIFFRACTION16(chain D and resid 0:54)
17X-RAY DIFFRACTION17(chain D and resid 55:75)
18X-RAY DIFFRACTION18(chain D and resid 76:171)
19X-RAY DIFFRACTION19(chain D and resid 172:208)
20X-RAY DIFFRACTION20(chain D and resid 209:333)

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