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- PDB-1dpg: GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM LEUCONOSTOC MESENTEROIDES -

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Basic information

Entry
Database: PDB / ID: 1dpg
TitleGLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM LEUCONOSTOC MESENTEROIDES
ComponentsGLUCOSE 6-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE (CHOH(D) - NAD(P)) / OXIDOREDUCTASE / NADP/NAD / GLUCOSE METABOLISM
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase [NAD(P)+] / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt / glucose metabolic process / NADP binding
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
PHOSPHATE ION / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesLeuconostoc mesenteroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsAdams, M.J. / Rowland, P. / Gover, S.
Citation
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.
#1: 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
DepositionDec 4, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX HELIX DETERMINATION METHOD: PROCHECK (I.E. DSSP) IN SUBUNIT A: HELIX_ID: A,BEND AT LYS 21 IS ...HELIX HELIX DETERMINATION METHOD: PROCHECK (I.E. DSSP) IN SUBUNIT A: HELIX_ID: A,BEND AT LYS 21 IS A CONSEQUENCE OF THE CONSERVED PRO 24. HELIX_ID: B,LAST TURN IS 3/10 (CLASS 5). HELIX_ID: D,FIRST TURN IS 3/10 (CLASS 5). HELIX_ID: F,FIRST 2 TURNS ARE 3/10 (CLASS 5). HELIX_ID: H,GLY 231 BRIDGES HELICES H AND I; IT IS NOT HELICAL. HELIX_ID: I,RESIDUES 235 - 239 ARE INFLUENCED BY AN ACTIVE SITE WATER MOLECULE. IN SUBUNIT B: HELIX_ID: A,BEND AT LYS 21 IS A CONSEQUENCE OF THE CONSERVED PRO 24. HELIX_ID: B,LAST TURN IS 3/10 (CLASS 5). HELIX_ID: D,FIRST TURN IS 3/10 (CLASS 5). HELIX_ID: F,FIRST TURN IS 3/10 (CLASS 5). HELIX_ID: H,GLY 231 BRIDGES HELICES H AND I; IT IS NOT HELICAL. HELIX_ID: I,RESIDUES 235 - 239 ARE INFLUENCED BY AN ACTIVE SITE WATER MOLECULE.
Remark 700SHEET SHEET SHEET_ID: COE; DETERMINATION METHOD: PROCHECK (I.E. DSSP, WITH EXTENSION TAKEN WHERE ...SHEET SHEET SHEET_ID: COE; DETERMINATION METHOD: PROCHECK (I.E. DSSP, WITH EXTENSION TAKEN WHERE HYDROGEN BONDING INDICATES THAT THIS IS APPROPRIATE).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,0565
Polymers108,7712
Non-polymers2853
Water10,989610
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-51 kcal/mol
Surface area38170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.710, 105.710, 224.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: CIS PROLINE - PRO A 149 / 2: CIS PROLINE - PRO A 375 / 3: CIS PROLINE - PRO B 375
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.3997, -0.7598, 0.5128), (-0.7814, -0.01, -0.624), (0.4792, -0.6501, -0.5897)
Vector: 8.9714, 111.6337, 162.3932)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. THE ENZYME IS DIMERIC WITH A DIMER IN THE ASYMMETRIC UNIT. THE TRANSFORMATION GIVEN IS FOR BEST (LEAST SQUARES) SUPERPOSITION OF THE C-ALPHA ATOMS OF MONOMER B ONTO THOSE OF MONOMER A, SO APPLYING IT TO THE RESIDUES LISTED FIRST WILL YOELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. THE ROTATION ANGLE IS 178.6 DEGREES AND THE AXIS IS AT 26.9 DEGREES TO THE AB PLANE. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 1 .. B 485 A 1 .. A 485 0.724

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Components

#1: Protein GLUCOSE 6-PHOSPHATE DEHYDROGENASE / G6PD


Mass: 54385.711 Da / Num. of mol.: 2 / Mutation: S61C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leuconostoc mesenteroides (bacteria) / 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.01 % / Description: MERGE OF 7 DATA SETS (SEE JRNL)
Crystal
*PLUS
Density % sol: 64.7 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13.5-6.0 mg/mlprotein1drop
21.8-2.4 Mphosphate1dropNaH2PO4 : K2HPO4 = 7.14
32.8-3.2 Mphosphate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.88, 1.00
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.881
211
ReflectionResolution: 2→27 Å / Num. obs: 92804 / % possible obs: 94 % / Redundancy: 7.5 %
Reflection
*PLUS
Redundancy: 7.5 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
X-PLOR3.1phasing
RefinementResolution: 2→27 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.257 -5 %
Rwork0.206 --
obs0.206 92804 94 %
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 15 610 8305
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.472
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.32
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.288
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.32
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.288

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