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- PDB-2g82: High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-... -

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Basic information

Entry
Database: PDB / ID: 2g82
TitleHigh Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GAPDH / G3PDH / GLYCOLYSIS / NAD / ROSSMANN FOLD
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 / cytosol
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRIETHYLENE GLYCOL / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsJenkins, J.L. / Buencamino, R. / Tanner, J.J.
CitationJournal: To be Published
Title: High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis
Authors: Jenkins, J.L. / Buencamino, R. / Tanner, J.J.
History
DepositionMar 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Nov 12, 2014Group: Non-polymer description
Revision 1.4Aug 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.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.ptnr1_symmetry / _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.ptnr2_symmetry / _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
O: Glyceraldehyde-3-phosphate dehydrogenase
P: Glyceraldehyde-3-phosphate dehydrogenase
Q: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
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)293,66323
Polymers287,7868
Non-polymers5,87715
Water28,5721586
1
O: Glyceraldehyde-3-phosphate dehydrogenase
P: Glyceraldehyde-3-phosphate dehydrogenase
Q: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,79111
Polymers143,8934
Non-polymers2,8987
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
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)146,87212
Polymers143,8934
Non-polymers2,9798
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)141.549, 147.403, 147.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules OPQRABCD

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


Mass: 35973.273 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: gap / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): W3CG
References: UniProt: P00361, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

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Non-polymers , 6 types, 1601 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1586 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 23% PEG 300, 0.1 M Hepes, 15% isopropanol, and 5% glycerol, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→99 Å / Num. obs: 390958 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 18.3
Reflection shellResolution: 1.65→1.69 Å / Rmerge(I) obs: 0.397 / % possible all: 85

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CER

1cer


Resolution: 1.65→65.94 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.364 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.172 18372 5 %RANDOM
Rwork0.158 ---
all0.159 345630 --
obs-364002 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.833 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.65→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19752 0 389 1586 21727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02120846
X-RAY DIFFRACTIONr_bond_other_d0.0020.0219193
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.97828491
X-RAY DIFFRACTIONr_angle_other_deg0.8023.00144246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48752696
X-RAY DIFFRACTIONr_chiral_restr0.0730.23416
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0223294
X-RAY DIFFRACTIONr_gen_planes_other0.0060.024040
X-RAY DIFFRACTIONr_nbd_refined0.1910.25695
X-RAY DIFFRACTIONr_nbd_other0.2480.224707
X-RAY DIFFRACTIONr_nbtor_other0.1160.215153
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.21362
X-RAY DIFFRACTIONr_metal_ion_refined0.1160.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.216
X-RAY DIFFRACTIONr_mcbond_it0.3981.513288
X-RAY DIFFRACTIONr_mcangle_it0.742221337
X-RAY DIFFRACTIONr_scbond_it1.36637558
X-RAY DIFFRACTIONr_scangle_it2.2914.57154
LS refinement shellResolution: 1.646→1.689 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.22 1109
Rwork0.199 21196
obs-22305
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)
10.37510.0161-0.07360.9609-0.60340.93320.0238-0.05280.06760.2486-0.1269-0.1989-0.30650.16440.10310.1121-0.057-0.05170.0638-0.00160.100918.79766.008113.198
20.36870.0398-0.0220.6259-0.21850.64080.01390.076-0.0363-0.120.01050.07050.0319-0.1074-0.02440.02820.0176-0.01880.0735-0.02180.0482-6.59850.05489.907
30.530.092-0.17980.3564-0.13170.5263-0.0397-0.0054-0.0989-0.0297-0.0239-0.07080.10650.08130.06360.01590.02520.01110.0467-0.00180.077617.50227.497113.034
40.28740.0557-0.09360.7204-0.26660.70610.028-0.03010.03420.13060.01270.1348-0.1132-0.1169-0.04070.02810.02180.02840.0669-0.01740.0677-12.47445.396128.124
50.5703-0.0998-0.05320.44440.18680.9780.01960.02920.1487-0.08270.0109-0.0132-0.2891-0.0992-0.03050.14320.0128-0.00930.05330.00860.0963-14.45460.487184.273
60.6164-0.0152-0.00680.97620.38820.8631-0.0338-0.17740.02580.23150.1044-0.19940.06330.1982-0.07060.09670.0141-0.06450.1773-0.03860.10712.86143.292204.218
70.5996-0.1519-0.23660.39660.23140.7496-0.0821-0.0334-0.14410.01830.03940.03590.1580.0420.04270.0517-0.00790.00710.03480.01190.082-11.20222.502179.296
80.6470.0558-0.03270.4340.0790.8154-0.03390.12120.0709-0.09160.05-0.1217-0.15510.2768-0.01610.0795-0.08380.02560.1894-0.00980.11317.2943.759165.856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1O1 - 330
2X-RAY DIFFRACTION2P1 - 330
3X-RAY DIFFRACTION3Q1 - 330
4X-RAY DIFFRACTION4R1 - 330
5X-RAY DIFFRACTION5A1 - 330
6X-RAY DIFFRACTION6B1 - 330
7X-RAY DIFFRACTION7C1 - 330
8X-RAY DIFFRACTION8D1 - 330

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