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- PDB-2dpg: COMPLEX OF INACTIVE MUTANT (H240->N) OF GLUCOSE 6-PHOSPHATE DEHYD... -

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Basic information

Entry
Database: PDB / ID: 2dpg
TitleCOMPLEX OF INACTIVE MUTANT (H240->N) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM LEUCONOSTOC MESENTEROIDES WITH NADP+
ComponentsGLUCOSE 6-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CHOH(D) - NAD(P) / NADP/NAD / GLUCOSE METABOLISM
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase [NAD(P)+] / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt, oxidative branch / glucose metabolic process / NADP binding / cytosol
Similarity search - Function
Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesLeuconostoc mesenteroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID-BODY, DIFFERENCE FOURIER / Resolution: 2.5 Å
AuthorsAdams, M.J. / Naylor, C.E. / Paludin, S. / Gover, S.
Citation
Journal: Biochemistry / Year: 1998
Title: On the mechanism of the reaction catalyzed by glucose 6-phosphate dehydrogenase.
Authors: Cosgrove, M.S. / Naylor, C. / Paludan, S. / Adams, M.J. / Levy, H.R.
#1: Journal: Structure / Year: 1994
Title: The Three-Dimensional Structure of Glucose 6-Phosphate Dehydrogenase from Leuconostoc Mesenteroides Refined at 2.0 A Resolution
Authors: Rowland, P. / Basak, A.K. / Gover, S. / Levy, H.R. / Adams, M.J.
#2: Journal: Protein Sci. / Year: 1993
Title: Site-Directed Mutagenesis to Facilitate X-Ray Structural Studies of Leuconostoc Mesenteroides Glucose 6-Phosphate Dehydrogenase
Authors: Adams, M.J. / Basak, A.K. / Gover, S. / Rowland, P. / Levy, H.R.
History
DepositionApr 17, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Nov 3, 2021Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOSE 6-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0892
Polymers54,3461
Non-polymers7431
Water1,33374
1
A: GLUCOSE 6-PHOSPHATE DEHYDROGENASE
hetero molecules

A: GLUCOSE 6-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,1784
Polymers108,6912
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area5910 Å2
ΔGint-30 kcal/mol
Surface area38700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)136.700, 136.700, 121.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1137-

HOH

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Components

#1: Protein GLUCOSE 6-PHOSPHATE DEHYDROGENASE / G6PD


Mass: 54345.602 Da / Num. of mol.: 1 / Mutation: H240N
Source method: isolated from a genetically manipulated source
Details: THE MUTANT IS INACTIVE, LACKING THE CATALYTIC BASE. THE STRUCTURE CONTAINS A PARTIAL NADP BOUND TO NUCLEOTIDE BINDING DOMAIN.
Source: (gene. exp.) Leuconostoc mesenteroides (bacteria) / Gene: PLMZ/H240N / Plasmid: PUC-19/HIS240ASNPLMZ / Gene (production host): PLMZ/H240N / Production host: Escherichia coli (E. coli) / Strain (production host): SU294
References: UniProt: P11411, glucose-6-phosphate dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.98 Å3/Da / Density % sol: 60 %
Description: MERGE OF 2.5 ANGSTROM SRS DATA (EXPT 1) WITH 3.5 ANGSTROM IN-HOUSE DATA (EXPT 2). FOR DETAILS, SEE JRNL REFERENCE.
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOR DIFFUSION. 2+2 MICROLITER DROPS. IN THE WELL 2.27M UNBUFFERED AMMONIUM SULFATE. THE PROTEIN AT 4.8MG/ML IN 0.1M TRIS-HCL AT PH 7.5 WITH 0.5MM NADP+ AND 25MM G6P., vapor ...Details: HANGING DROP VAPOR DIFFUSION. 2+2 MICROLITER DROPS. IN THE WELL 2.27M UNBUFFERED AMMONIUM SULFATE. THE PROTEIN AT 4.8MG/ML IN 0.1M TRIS-HCL AT PH 7.5 WITH 0.5MM NADP+ AND 25MM G6P., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.27 Mammonium sulfate1reservoir
24.8 mg/mlenzyme1drop
325 mMTris-HCl1drop
40.500 mMNADP+1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.876
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.876 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 16263 / % possible obs: 68.4 % / Observed criterion σ(I): -3 / Redundancy: 1.3 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.1
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.411 / % possible all: 0.548
Reflection
*PLUS
Num. measured all: 21142
Reflection shell
*PLUS
Rmerge(I) obs: 0.125

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: RIGID-BODY, DIFFERENCE FOURIER
Starting model: INCOMPLETE REFINED STRUCTURE OF NATIVE PROTEIN CONTAINING NADP

Resolution: 2.5→25 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Cross valid method: FREE R / σ(F): 0
Details: FOR DETAILS OF THE BULK SOLVENT MODELLING, SEE JRNL REFERENCE.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 789 4.8 %RANDOM
Rwork0.173 ---
obs0.173 16244 68.4 %-
Displacement parametersBiso mean: 30.8 Å2
Refine analyzeLuzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3838 0 31 74 3943
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.42
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.51.5
X-RAY DIFFRACTIONx_mcangle_it2.642
X-RAY DIFFRACTIONx_scbond_it2.51.5
X-RAY DIFFRACTIONx_scangle_it2.642
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.35 60 4.7 %
Rwork0.282 1220 -
obs--55 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION32-5-ABP.PAR2-5-ABP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.11
LS refinement shell
*PLUS
Rfactor Rfree: 0.35

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