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- PDB-1a80: Native 2,5-DIKETO-D-GLUCONIC acid reductase a from CORYNBACTERIUM... -

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Basic information

Entry
Database: PDB / ID: 1a80
TitleNative 2,5-DIKETO-D-GLUCONIC acid reductase a from CORYNBACTERIUM SP. complexed with nadph
Components2,5-DIKETO-D-GLUCONIC ACID REDUCTASE A
KeywordsOXIDOREDUCTASE / ALPHA8/BETA8 BARREL / 2 / 5-DIKETO-D-GLUCONIC ACID / COMMERCIAL VITAMIN C SYNTHESIS
Function / homology
Function and homology information


2,5-didehydrogluconate reductase (2-dehydro-L-gulonate-forming) / L-ascorbic acid biosynthetic process / : / cytoplasm
Similarity search - Function
Aldo-keto reductase family 5C1 / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 2,5-diketo-D-gluconic acid reductase A
Similarity search - Component
Biological speciesCorynebacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKhurana, S. / Powers, D.B. / Anderson, S. / Blaber, M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structure of 2,5-diketo-D-gluconic acid reductase A complexed with NADPH at 2.1-A resolution.
Authors: Khurana, S. / Powers, D.B. / Anderson, S. / Blaber, M.
#1: Journal: Biochem.J. / Year: 1997
Title: Comparative Anatomy of the Aldo-Keto Reductase Superfamily
Authors: Jez, J.M. / Bennett, M.J. / Schlegel, B.P. / Lewis, M. / Penning, T.M.
#2: Journal: Science / Year: 1985
Title: Production of 2-Keto-L-Gulonate, an Intermediate in L-Ascorbate Synthesis, by a Genetically Modified Erwinia Herbicola
Authors: Anderson, S. / Marks, C.B. / Lazarus, R. / Miller, J. / Stafford, K. / Seymour, J. / Light, D. / Rastetter, W.
History
DepositionMar 31, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7662
Polymers30,0201
Non-polymers7451
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.700, 55.800, 74.700
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE A / 2 / 5-DKG REDUCTASE A


Mass: 30020.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Gene: 2 5-DIKETO-D-GLUCONIC ACID / Variant: A / Plasmid: PTRP1-35 / Gene (production host): 2 5-DIKETO-D-GLUCONIC ACID / Production host: Pantoea citrea (bacteria) / Strain (production host): IFO3263 / References: UniProt: P06632
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 50.31 %
Crystal growpH: 7.1 / Details: pH 7.1
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: and 4 degrees centigrade
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118.3 mg/mlenzyme1drop
21.0 Msodium phosphate1reservoir
31.0 Mpotassium phosphate1reservoir
4100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 7, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 14803 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 14.6 Å2 / Rsym value: 0.116 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.421 / % possible all: 75.2
Reflection
*PLUS
Rmerge(I) obs: 0.116
Reflection shell
*PLUS
% possible obs: 75.2 % / Rmerge(I) obs: 0.421

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ADS

1ads


Resolution: 2.1→60 Å / Isotropic thermal model: TRONRUD, 1996 / σ(F): 0 / Stereochemistry target values: TRONRUD, 1987 /
Num. reflection% reflection
all14803 -
obs12891 85 %
Solvent computationSolvent model: TRONRUD, 1987 / Bsol: 365.4 Å2 / ksol: 0.972 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 48 105 2275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191 / Rfactor Rfree: 0.288
Solvent computation
*PLUS
Displacement parameters
*PLUS

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