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- PDB-1hw6: CRYSTAL STRUCTURE OF APO-2,5-DIKETO-D-GLUCONATE REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1hw6
TitleCRYSTAL STRUCTURE OF APO-2,5-DIKETO-D-GLUCONATE REDUCTASE
Components2,5-DIKETO-D-GLUCONIC ACID REDUCTASE
KeywordsOXIDOREDUCTASE / aldo-keto reductase / TIM barrel
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
2,5-diketo-D-gluconic acid reductase A
Similarity search - Component
Biological speciesCorynebacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSanli, G. / Blaber, M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structural assembly of the active site in an aldo-keto reductase by NADPH cofactor.
Authors: Sanli, G. / Blaber, M.
History
DepositionJan 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2715
Polymers30,1521
Non-polymers1204
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.03, 53.94, 89.75
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE / APO-2 / 5-DIKETO-D-GLUCONATE REDUCTASE


Mass: 30151.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P06632, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.2M MgCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113 mg/mlprotein1drop
225 mMTris-HCl1drop
330 %(w/v)PEG40001reservoir
40.2 M1reservoirMgCl2
50.1 MTris1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 2000 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→27 Å / Num. all: 19905 / Num. obs: 126729 / % possible obs: 94.5 % / Observed criterion σ(I): 3 / Redundancy: 6.4 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.24 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.2 / % possible all: 82.8
Reflection
*PLUS
Num. obs: 19905 / Num. measured all: 126729
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 82.8 %

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Processing

Software
NameVersionClassification
MRCHKmodel building
TNT5Erefinement
DENZOdata reduction
MRCHKphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A80

1a80


Resolution: 1.9→27 Å / Isotropic thermal model: TRONRUD / Stereochemistry target values: TRONRUD
RfactorNum. reflection% reflection
all0.206 20962 -
obs-19905 82.8 %
Refinement stepCycle: LAST / Resolution: 1.9→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 4 267 2202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.33
X-RAY DIFFRACTIONt_bond_d0.007
X-RAY DIFFRACTIONt_dihedral_angle_d14.92
X-RAY DIFFRACTIONt_trig_c_planes0.005
X-RAY DIFFRACTIONt_gen_planes0.01
X-RAY DIFFRACTIONt_nbd0.012
LS refinement shellResolution: 1.9→1.93 Å
RfactorNum. reflection% reflection
Rfree0.42 133 -
Rwork0.35 --
obs-1385 82.8 %
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.33
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg14.92

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