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- PDB-1h94: COMPLEX OF ACTIVE MUTANT (S215->C) OF GLUCOSE 6-PHOSPHATE DEHYDRO... -

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Basic information

Entry
Database: PDB / ID: 1h94
TitleCOMPLEX OF ACTIVE MUTANT (S215->C) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM L.MESENTEROIDES WITH COENZYME NAD
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesLEUCONOSTOC MESENTEROIDES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionFeb 23, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
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: D,THE FIRST TURN IS 3_10 (CLASS 5). HELIX_ID: F,THE FIRST 2 TURNS ARE 3_10 (CLASS 5). HELIX_ID: H,G231 BRIDGES H & 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: DETERMINATION METHOD: INITIAL AND TERMINAL RESIDUES ARE AS DEFINED BY ... SHEET DETERMINATION METHOD: 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)55,0492
Polymers54,3861
Non-polymers6631
Water1,09961
1
A: GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules

A: GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0984
Polymers108,7712
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5350 Å2
ΔGint-47.5 kcal/mol
Surface area46310 Å2
MethodPQS
Unit cell
Length a, b, c (Å)131.900, 45.200, 93.500
Angle α, β, γ (deg.)90.00, 107.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 54385.711 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEUCONOSTOC MESENTEROIDES (bacteria) / Strain: SU294 / Description: SITE DIRECTED MUTAGENESIS / Gene: G6PD / Plasmid: PLMZ / Gene (production host): G6PD / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P11411, glucose-6-phosphate dehydrogenase (NADP+)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION SER215CYS BETA-D-GLUCOSE 6-PHOSPHATE + NADP(+) = D-GLUCONO-DELTA- ...CHAIN A ENGINEERED MUTATION SER215CYS 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: 2.46 Å3/Da / Density % sol: 42.9 % / Description: RIGID-BODY MINIMISATION USED X-PLOR 3.1
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOUR DIFFUSION, 2+2 MICROLITER DROPS. THE WELL BUFFER: 20% V/V PEG 400 IN 0.1M HEPES-NAOH, PH 7.5 WITH 0.2M CALCIUM CHLORIDE. THE PROTEIN AT 10MG/ML IN 100MM TRIS-HCL WITH 12.5MM NAD+.
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %(v/v)PEG4001reservoir
20.1 MHEPES-NaOH1reservoir
3200 mM1reservoirCaCl2
410 mg/mlprotein1drop
5100 mMTris-HCl1drop
612.5 mMNAD+1drop

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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: May 11, 1995 / 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→20 Å / Num. obs: 16682 / % possible obs: 88.9 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rsym value: 0.101 / Net I/σ(I): 7
Reflection shellResolution: 2.4→2.6 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.48 / % possible all: 81.7
Reflection
*PLUS
Num. measured all: 45041 / Rmerge(I) obs: 0.101
Reflection shell
*PLUS
% possible obs: 81.7 % / Num. unique obs: 1406 / Num. measured obs: 3135 / Rmerge(I) obs: 0.48

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TFFCphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SUBUNIT 'A' OF 1DPG

1dpg


Resolution: 2.5→20 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 0.311 E/A**3 AND TEMPERATURE FACTOR 31.7 A**2. THE OCCUPANCY OF COENZYME NAD HAS BEEN REDUCED TO 0.6 IN ORDER TO MATCH ITS TEMPERATURE FACTORS TO THOSE ...Details: BULK SOLVENT WAS MODELLED WITH DENSITY 0.311 E/A**3 AND TEMPERATURE FACTOR 31.7 A**2. THE OCCUPANCY OF COENZYME NAD HAS BEEN REDUCED TO 0.6 IN ORDER TO MATCH ITS TEMPERATURE FACTORS TO THOSE OF ATOMS IN THE NEIGHBOURING PROTEIN RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 810 4.9 %RANDOM, USING XPLOR
Rwork0.213 ---
obs0.213 16513 89.1 %-
Displacement parametersBiso mean: 29 Å2
Refine analyzeLuzzati d res low obs: 20 Å / Luzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3840 0 44 61 3945
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_deg1.257
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.93
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.07
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.771.5
X-RAY DIFFRACTIONx_mcangle_it5.452
X-RAY DIFFRACTIONx_scbond_it3.771.5
X-RAY DIFFRACTIONx_scangle_it5.452
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.366 46 5.1 %
Rwork0.322 904 -
obs--78.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3NAD.PARNAD.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.93
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.07
LS refinement shell
*PLUS
Rfactor obs: 0.322

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