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- PDB-1m9h: Corynebacterium 2,5-DKGR A and Phe 22 replaced with Tyr (F22Y), L... -

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Basic information

Entry
Database: PDB / ID: 1m9h
TitleCorynebacterium 2,5-DKGR A and Phe 22 replaced with Tyr (F22Y), Lys 232 replaced with Gly (K232G), Arg 238 replaced with His (R238H)and Ala 272 replaced with Gly (A272G)in presence of NADH cofactor
Components2,5-diketo-D-gluconic acid reductase A
KeywordsOXIDOREDUCTASE / TIM-barrel
Function / homology
Function and homology information


2,5-didehydrogluconate reductase (2-dehydro-L-gulonate-forming) / L-ascorbic acid biosynthetic process / oxidoreductase activity / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2,5-diketo-D-gluconic acid reductase A
Similarity search - Component
Biological speciesCorynebacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSanli, G. / Blaber, M.
CitationJournal: Protein Sci. / Year: 2004
Title: Structural alteration of cofactor specificity in Corynebacterium 2,5-diketo-D-gluconic acid reductase
Authors: Sanli, G. / Banta, S. / Anderson, S. / Blaber, M.
History
DepositionJul 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _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 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)30,8223
Polymers30,0621
Non-polymers7592
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: 2,5-diketo-D-gluconic acid reductase A
hetero molecules

A: 2,5-diketo-D-gluconic acid reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6446
Polymers60,1252
Non-polymers1,5194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4360 Å2
ΔGint-53 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.950, 55.240, 51.540
Angle α, β, γ (deg.)90.00, 111.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2,5-diketo-D-gluconic acid reductase A / 2 / 5-DKG reductase A / 2 / 5-DKGR A / 25DKGR-A / AKR5C


Mass: 30062.465 Da / Num. of mol.: 1 / Mutation: F22Y, K232G, R238H, A272G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli)
References: UniProt: P06632, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: lithium sulfate monohydrate, hepes-sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
225 mMTris-HCl1droppH7.5
31.5 Mlithium sulfate1reservoir
40.1 Msodium HEPES1reservoirpH7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
1,21
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
ROTATING ANODERIGAKU RUH2R21.5418
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IIC1IMAGE PLATEApr 4, 2002Osmic Blue confocal mirrors
MARRESEARCH2CCDApr 11, 2002Osmic Blue confocal mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1osmic mirrorsSINGLE WAVELENGTHMx-ray1
2osmic mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 20178 / Num. obs: 17803 / % possible obs: 88.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 16.6
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.2 / % possible all: 83.3
Reflection
*PLUS
Lowest resolution: 27 Å / Num. obs: 18364 / % possible obs: 92.9 % / Num. measured all: 242073
Reflection shell
*PLUS
% possible obs: 83.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A80

1a80


Resolution: 2→40 Å / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / Stereochemistry target values: TRONRUD
RfactorNum. reflectionSelection details
Rfree0.261 561 Random
Rwork0.213 --
all0.214 20178 -
obs0.214 17803 -
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 0 49 146 2301
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.5
X-RAY DIFFRACTIONt_bond_d0.008
X-RAY DIFFRACTIONt_dihedral_angle_d14.9
LS refinement shellResolution: 2→2.05 Å /
RfactorNum. reflection
Rfree0.52 46
Rwork0.31 -
obs-1102
Refinement
*PLUS
Lowest resolution: 27 Å / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg14.9

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