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- PDB-5o0v: crystal structure of E. coli GAP-DH by fortuitous crystallization... -

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Basic information

Entry
Database: PDB / ID: 5o0v
Titlecrystal structure of E. coli GAP-DH by fortuitous crystallization as an impurity from a solution of human liver FBPase
ComponentsGlyceraldehyde-3-phosphate dehydrogenase A
KeywordsIMMUNE SYSTEM / oxidoreductase / fortuitous crystallization / impurity
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 / membrane / identical protein binding / cytosol / cytoplasm
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
Glyceraldehyde-3-phosphate dehydrogenase A / Glyceraldehyde-3-phosphate dehydrogenase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsRuf, A. / Benz, J. / Rudolph, M.G.
CitationJournal: To Be Published
Title: fortuitous crystallization of GAP-DH impurity from a solution of human liver FBPase
Authors: Ruf, A. / Benz, J. / Rudolph, M.G.
History
DepositionMay 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 19, 2017Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1May 23, 2018Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref / struct_ref_seq
Item: _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 2.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6303
Polymers35,4461
Non-polymers1842
Water2,540141
1
A: Glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,52212
Polymers141,7854
Non-polymers7378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
Buried area16880 Å2
ΔGint-74 kcal/mol
Surface area44920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.384, 121.384, 157.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase A / GAPDH-A / NAD-dependent glyceraldehyde-3-phosphate dehydrogenase


Mass: 35446.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gapA, b1779, JW1768 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A9B2, UniProt: P0A9B4*PLUS, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-GOL / GLYCEROL / GAPDH-A / NAD-dependent glyceraldehyde-3-phosphate dehydrogenase / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3 / Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: gapA, Z2818, ECs2488 / Production host: Escherichia coli (E. coli)
References: glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 4.06 Å3/Da / Density % sol: 69.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→42.92 Å / Num. obs: 23078 / % possible obs: 99 % / Redundancy: 11.62 % / Net I/σ(I): 12.13
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.08 % / Mean I/σ(I) obs: 1.33 / Num. unique obs: 2213 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(1.11_2558: ???)refinement
DENZOdata reduction
SADABSdata scaling
COMOphasing
RefinementResolution: 2.4→42.916 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.77
RfactorNum. reflection% reflection
Rfree0.1889 1157 5.02 %
Rwork0.1539 --
obs0.1557 23030 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→42.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 0 141 2641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072537
X-RAY DIFFRACTIONf_angle_d0.8533433
X-RAY DIFFRACTIONf_dihedral_angle_d13.0311519
X-RAY DIFFRACTIONf_chiral_restr0.055401
X-RAY DIFFRACTIONf_plane_restr0.005442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.50930.33161140.27382532X-RAY DIFFRACTION92
2.5093-2.64160.27151540.23422694X-RAY DIFFRACTION99
2.6416-2.80710.25951280.20192729X-RAY DIFFRACTION100
2.8071-3.02380.2461550.17862708X-RAY DIFFRACTION100
3.0238-3.3280.19311480.14842748X-RAY DIFFRACTION100
3.328-3.80930.17421700.1322730X-RAY DIFFRACTION100
3.8093-4.79830.14071390.10952799X-RAY DIFFRACTION100
4.7983-42.92260.15021490.14262933X-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)
10.64730.28590.28581.41450.43570.75640.04990.4336-0.2778-0.2372-0.14580.35830.1308-0.26810.03660.3247-0.0637-0.04880.4799-0.14650.386546.344246.896556.3961
20.7241-0.47390.10870.68690.0560.6594-0.02230.1986-0.2353-0.0206-0.10410.13780.21050.02390.07780.2687-0.04110.05310.2413-0.05230.269767.404739.418366.2287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 331 )

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