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- PDB-1pz1: Structure of NADPH-dependent family 11 aldo-keto reductase AKR11B... -

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Basic information

Entry
Database: PDB / ID: 1pz1
TitleStructure of NADPH-dependent family 11 aldo-keto reductase AKR11B(holo)
ComponentsGeneral stress protein 69
KeywordsOXIDOREDUCTASE / beta-alpha barrel / aldo-keto reductase / TIM barrel
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / cytosol
Similarity search - Function
: / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase YhdN
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsEhrensberger, A.H. / Wilson, D.K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural and Catalytic Diversity in the Two Family 11 Aldo-keto Reductases
Authors: Ehrensberger, A.H. / Wilson, D.K.
History
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: General stress protein 69
B: General stress protein 69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4024
Polymers75,9152
Non-polymers1,4872
Water7,440413
1
A: General stress protein 69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7012
Polymers37,9581
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: General stress protein 69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7012
Polymers37,9581
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.255, 117.366, 59.787
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit consists of a monomer. Each asymmetric units consists of two biological units.

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Components

#1: Protein General stress protein 69 / GSP69


Mass: 37957.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YHDN / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: P80874
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.74
Details: PEG 8000, sodium acetate, imidazole, pH 7.74, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114.4 mg/mlprotein1drop
25 mMNADP+1drop
325 %PEG80001reservoir
4160 mMsodium acetate1reservoir
5100 mMimidazole1reservoirpH7.74

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97903, 0.88557, 0.97922
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 21, 2003 / Details: double mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979031
20.885571
30.979221
ReflectionResolution: 2.2→100 Å / Num. all: 38524 / Num. obs: 36239 / % possible obs: 94.07 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.49
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 5.02 / % possible all: 88.2
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 37796 / % possible obs: 98.4 % / Num. measured all: 134257
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 88.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1799 -RANDOM
Rwork0.198 ---
all0.198 36232 --
obs0.198 36232 88.9 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5290 0 96 413 5799
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_bond_d0.012
LS refinement shellResolution: 2.2→2.28 Å / % reflection obs: 88.2 %
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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