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- PDB-6cia: Crystal structure of aldo-keto reductase from Klebsiella pneumoni... -

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Basic information

Entry
Database: PDB / ID: 6cia
TitleCrystal structure of aldo-keto reductase from Klebsiella pneumoniae in complex with NADPH.
ComponentsAldo/keto reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


D-threo-aldose 1-dehydrogenase activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Similarity search - Function
NADP-dependent oxidoreductase domain / 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 / Putative an aldehyde reductase / Aldo/keto reductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLipowska, J. / Leung, E.S. / Shabalin, I.G. / Grabowski, M. / Almo, S.C. / Satchell, K.J. / Joachimiak, A. / Lewinski, K. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: Crystal structure of of aldo-keto reductase from Klebsiella pneumoniae in complex with NADPH.
Authors: Lipowska, J. / Leung, E.S. / Shabalin, I.G. / Grabowski, M. / Almo, S.C. / Satchell, K.J. / Joachimiak, A. / Lewinski, K. / Minor, W.
History
DepositionFeb 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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: Aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5142
Polymers31,7681
Non-polymers7451
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-5 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.626, 83.626, 72.834
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Aldo/keto reductase / General stress protein 69


Mass: 31768.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: yhdN_4, yhdN, B1727_06910, B4U21_09420, BN49_2327, CAK82_20800, CQB04_18905, CR230_19100, CTI52_15935, CTI54_15930, PMK1_03573, SAMEA3531778_00013
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL
References: UniProt: W9BFN4, UniProt: A6T7Q7*PLUS, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


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


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 ul of 11 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the Top 96 #90 (0.2 uL 0.1 M Tris: HCl, pH 8.5, 25 % ...Details: 0.2 ul of 11 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the Top 96 #90 (0.2 uL 0.1 M Tris: HCl, pH 8.5, 25 % (w/v) PEG 3350) and 0.1 uL 30%v/v Ethanol (Additive Screen #82) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2017 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13360 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 33.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.03 / Rrim(I) all: 0.088 / Rsym value: 0.083 / Net I/av σ(I): 30.9 / Net I/σ(I): 30.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7 % / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 649 / CC1/2: 0.838 / Rpim(I) all: 0.438 / Rrim(I) all: 1.178 / Rsym value: 1.092 / % possible all: 100

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Processing

Software
NameVersionClassification
MD2data collection
HKL-3000data scaling
SCALEPACKdata scaling
HKL-3000data reduction
HKL-3000phasing
MOLREPphasing
REFMAC5.8.0189refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WGH

4wgh


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / SU B: 15.302 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.49 / ESU R Free: 0.257 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22957 612 5.1 %RANDOM
Rwork0.16727 ---
obs0.17052 11434 89.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.872 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.18 Å20 Å2
2---0.35 Å2-0 Å2
3---1.14 Å2
Refinement stepCycle: 1 / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 48 150 2413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192343
X-RAY DIFFRACTIONr_bond_other_d0.0020.022166
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9513199
X-RAY DIFFRACTIONr_angle_other_deg0.96834993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8795290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68923.119109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3515384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9791523
X-RAY DIFFRACTIONr_chiral_restr0.0710.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022697
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7491.5571143
X-RAY DIFFRACTIONr_mcbond_other1.7351.5561142
X-RAY DIFFRACTIONr_mcangle_it2.6052.3281429
X-RAY DIFFRACTIONr_mcangle_other2.6052.3291430
X-RAY DIFFRACTIONr_scbond_it3.0051.981200
X-RAY DIFFRACTIONr_scbond_other2.971.9791198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4232.8561767
X-RAY DIFFRACTIONr_long_range_B_refined6.39919.5962595
X-RAY DIFFRACTIONr_long_range_B_other6.319.2412564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.303→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 23 -
Rwork0.214 414 -
obs--44.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2573-0.86470.032510.8686-1.21614.78390.1226-0.00510.2551-0.36290.01090.23780.1044-0.4942-0.13340.06590.0480.00530.14320.01510.041934.6286.63236.816
22.4261-0.5718-0.78842.89910.8044.26670.0902-0.09270.2666-0.38850.0237-0.5843-0.24050.1944-0.1140.190.00880.07640.015-0.00590.130146.3349.43433.398
36.0474-0.4993-0.06193.80070.34692.64920.2210.2934-0.3394-0.9747-0.0972-0.21220.4771-0.2213-0.12380.51210.02390.03130.0446-0.00170.038940.516-4.93923.453
44.1744-1.5565-1.66044.0240.44952.41120.30160.3783-0.2147-0.9621-0.33920.94950.3088-1.0350.03760.5473-0.0512-0.19930.6398-0.08420.242725.5-0.39725.629
51.9048-0.5235-0.70635.53421.42283.91920.13630.2315-0.1732-0.517-0.27980.79960.4019-0.94670.14350.2973-0.0763-0.14770.3802-0.02090.154422.801-0.33529.988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 31
2X-RAY DIFFRACTION2A32 - 139
3X-RAY DIFFRACTION3A140 - 176
4X-RAY DIFFRACTION4A177 - 218
5X-RAY DIFFRACTION5A219 - 284

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