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- PDB-1h9b: ACTIVE MUTANT (Q365->C) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM... -

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Basic information

Entry
Database: PDB / ID: 1h9b
TitleACTIVE MUTANT (Q365->C) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM LEUCONOSTOC MESENTEROIDES
ComponentsGLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / 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
Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesLEUCONOSTOC MESENTEROIDES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAdams, M.J. / Naylor, C.E. / Gover, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Nadp+ and Nad+ Binding to the Dual Coenzyme Specific Enzyme Leuconostoc Mesenteroides Glucose 6-Phosphate Dehydrogenase: Different Interdomain Hinge Angles are Seen in Different Binary and Ternary Complexes
Authors: Naylor, C.E. / Gover, S. / Basak, A.K. / Cosgrove, M.S. / Levy, H.R. / Adams, M.J.
#1: Journal: Biochemistry / Year: 2000
Title: An Examination of the Role of Asp-177 in the His-Asp Catalytic Dyad of Leuconostoc Mesenteroides Glucose 6-Phosphate Dehydrogenase: X-Ray Structure and Ph Dependence of Kinetic Parameters of ...Title: An Examination of the Role of Asp-177 in the His-Asp Catalytic Dyad of Leuconostoc Mesenteroides Glucose 6-Phosphate Dehydrogenase: X-Ray Structure and Ph Dependence of Kinetic Parameters of the D177N Mutant Enzyme
Authors: Cosgrove, M.S. / Gover, S. / Naylor, C.E. / Vandeputte-Rutten, L. / Adams, M.J. / Levy, H.R.
#2: Journal: Structure / Year: 1994
Title: The Three-Dimensional Structure of Glucose 6-Phosphate Dehydrogenase from Leuconostoc Mesenteroides Refined at 2 Angstroms Resolution
Authors: Rowland, P. / Basak, A.K. / Gover, S. / Levy, H.R. / Adams, M.J.
#3: 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
DepositionMar 6, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2001Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_strain
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO 2.0A L. MESENTEROIDES ... HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO 2.0A L. MESENTEROIDES STRUCTURE, 1DPG. HELIX_ID: A,BEND AT K21 IS CONSEQUENCE OF CONSERVED P24. HELIX_ID: B,THE LAST TURN IS 3_10 (CLASS 5). HELIX_ID: C,THE FIRST TURN IS 3_10 (CLASS 5). HELIX_ID: D,THE FIRST TURN IS 3_10 (CLASS 5). HELIX_ID: H,GLY 231 BRIDGES H AND I', SO IS NOT HELICAL. HELIX_ID: I',PART OF HELIX I IN 1DPG. RESIDUES 235-239 DISTORTED BY SIDECHAIN INTERACTION OF N239 WITH D235.
Remark 700 SHEET DETERMINATION METHOD: INITIAL AND TERMINAL RESIDUES ARE AS DEFINED BY PROCHECK. REGISTRATION ... SHEET DETERMINATION METHOD: INITIAL AND TERMINAL RESIDUES ARE AS DEFINED BY PROCHECK. REGISTRATION IS AS GIVEN BY HYDROGEN BONDS AND IN THE CASE OF SHEET COE INVOLVES RESIDUES THAT IMMEDIATELY PRECEDE EACH SHEET ELEMENT. THIS IS DONE TO PRESERVE OBSERVED CONSISTENCY WITH NATIVE STRUCTURE 1DPG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4412
Polymers54,3451
Non-polymers961
Water2,504139
1
A: GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules

A: GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8814
Polymers108,6892
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
MethodPQS
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-2048-

HOH

21A-2079-

HOH

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Components

#1: Protein GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE / G6PD


Mass: 54344.660 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEUCONOSTOC MESENTEROIDES (bacteria) / Description: SITE DIRECTED MUTAGENESIS / Gene: G6PD / Plasmid: PLMZ / Gene (production host): G6PD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SU294
References: UniProt: P11411, glucose-6-phosphate dehydrogenase (NADP+)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION GLN365CYS BETA-D-GLUCOSE 6-PHOSPHATE + NADP(+) = D-GLUCONO-DELTA- ...CHAIN A ENGINEERED MUTATION GLN365CYS BETA-D-GLUCOSE 6-PHOSPHATE + NADP(+) = D-GLUCONO-DELTA-LACTONE 6-PHOSPHATE + NADPH.

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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: 3.02 Å3/Da / Density % sol: 56.2 % / Description: RIGID-BODY MINIMISATION USED X-PLOR 3.1
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.8
Details: HANGING DROP VAPOUR DIFFUSION, 2+2 MICROLITER DROPS. THE PROTEIN AT 5MG/ML IN 100MM TRIS-HCL AT PH 7.5 WITH 12.5MM NAD+. DROPS EQUILIBRIATED AGAINST 1.7M UNBUFFERED AMMONIUM SULFATE.
Crystal grow
*PLUS
Temperature: 291 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
2100 mMTris-HCl1drop
312.5 mMNAD+1drop
41.64 Mammonium sulfate1reservoirunbuffered

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1994 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.4→21 Å / Num. obs: 24865 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rsym value: 0.113 / Net I/σ(I): 12.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.418 / % possible all: 93
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 115220 / Rmerge(I) obs: 0.113
Reflection shell
*PLUS
% possible obs: 93 % / Num. unique obs: 3523 / Num. measured obs: 18339 / Rmerge(I) obs: 0.418

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PROTEIN ATOMS OF NADP-BOUND COMPLEX IN THE SAME CRYSTAL FORM, 1H9A.

1h9a


Resolution: 2.4→21 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 0
Details: BULK SOLVENT WAS MODELLED WITH DENSITY 0.321 E/A**3 AND TEMPERATURE FACTOR 26.9 A**2. ALTHOUGH NAD WAS PRESENT IN THE CRYSTALLISATION DROP, NO ELECTRON DENSITY WAS OBSERVED AND IT WAS ...Details: BULK SOLVENT WAS MODELLED WITH DENSITY 0.321 E/A**3 AND TEMPERATURE FACTOR 26.9 A**2. ALTHOUGH NAD WAS PRESENT IN THE CRYSTALLISATION DROP, NO ELECTRON DENSITY WAS OBSERVED AND IT WAS PRESUMED NOT TO HAVE BOUND. THE REFINED MODEL INCLUDES A SULFATE ION WITH OCCUPANCY 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2002 8.1 %RANDOM, USING XPLOR
Rwork0.19 ---
obs0.19 24864 94.1 %-
Displacement parametersBiso mean: 32.8 Å2
Refine analyzeLuzzati d res low obs: 21 Å / Luzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.4→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3837 0 5 139 3981
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_deg1.272
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.73
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.97
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.771.5
X-RAY DIFFRACTIONx_mcangle_it3.882
X-RAY DIFFRACTIONx_scbond_it2.771.5
X-RAY DIFFRACTIONx_scangle_it3.882
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.356 206 5.1 %
Rwork0.283 2180 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3SO4.PARSO4.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.73
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.97
LS refinement shell
*PLUS
Rfactor obs: 0.283

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