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- PDB-5dan: Crystal structure of a novel aldo keto reductase Tm1743 from Ther... -

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Basic information

Entry
Database: PDB / ID: 5dan
TitleCrystal structure of a novel aldo keto reductase Tm1743 from Thermotoga maritima in complex with NADP+
Components2,5-diketo-D-gluconic acid reductase
KeywordsOXIDOREDUCTASE / Aldo keto reductase / Thermostable / NADP
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
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 / Oxidoreductase, aldo/keto reductase family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXu, X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570738 China
National Natural Science Foundation of China31400630 China
Zhejiang Provincial Natural Science Foundation of ChinaLY14C050002 China
CitationJournal: To Be Published
Title: Crystal structure of a novel aldo keto reductase Tm1743 from Thermotoga maritima in complex with NADP+
Authors: Xu, X.
History
DepositionAug 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)32,1462
Polymers31,4031
Non-polymers7431
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-2 kcal/mol
Surface area12090 Å2
Unit cell
Length a, b, c (Å)84.821, 84.821, 93.727
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 2,5-diketo-D-gluconic acid reductase / Oxidoreductase / aldo/keto reductase family


Mass: 31402.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: gene synthesis
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1743, Tmari_1751 / Plasmid: pET-28a(+) / Details (production host): N His6 tag / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9X265, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M Calcium chloride dehydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 20 % v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 25576 / % possible obs: 95.8 % / Redundancy: 10 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 3.3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PYF

1pyf


Resolution: 2→42.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.229 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1285 5 %RANDOM
Rwork0.2047 ---
obs0.2063 24240 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.81 Å2 / Biso mean: 35.755 Å2 / Biso min: 20.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å2-0 Å2
3----2.27 Å2
Refinement stepCycle: final / Resolution: 2→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 48 183 2437
Biso mean--29.26 43.46 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192298
X-RAY DIFFRACTIONr_bond_other_d0.0020.022217
X-RAY DIFFRACTIONr_angle_refined_deg1.6392.0153114
X-RAY DIFFRACTIONr_angle_other_deg1.02735116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9375273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25123.905105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1415424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.771519
X-RAY DIFFRACTIONr_chiral_restr0.0930.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212509
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02495
X-RAY DIFFRACTIONr_mcbond_it1.9243.3361095
X-RAY DIFFRACTIONr_mcbond_other1.9233.3331094
X-RAY DIFFRACTIONr_mcangle_it2.6524.9931367
LS refinement shellResolution: 2.004→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 92 -
Rwork0.162 1817 -
all-1909 -
obs--98.96 %

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