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- PDB-5t79: X-Ray Crystal Structure of a Novel Aldo-keto Reductases for the B... -

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Basic information

Entry
Database: PDB / ID: 5t79
TitleX-Ray Crystal Structure of a Novel Aldo-keto Reductases for the Biocatalytic Conversion of 3-hydroxybutanal to 1,3-butanediol
ComponentsAldo-keto Reductase, OXIDOREDUCTASE
KeywordsTRANSLATION / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / NADP-dependent oxidoreductase
Function / homology
Function and homology information


methylglyoxal catabolic process / nucleotide binding / metal ion binding
Similarity search - Function
Potassium channel, voltage-dependent, beta subunit, KCNAB-related / NADP-dependent oxidoreductase domain / 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 / Oxidoreductase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Yakunin, A.F. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Appl. Environ. Microbiol. / Year: 2017
Title: Structural and biochemical studies of novel aldo-keto reductases for the biocatalytic conversion of 3-hydroxybutanal to 1,3-butanediol.
Authors: Kim, T. / Flick, R. / Brunzelle, J. / Singer, A. / Evdokimova, E. / Brown, G. / Joo, J.C. / Minasov, G.A. / Anderson, W.F. / Mahadevan, R. / Savchenko, A. / Yakunin, A.F.
History
DepositionSep 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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: Aldo-keto Reductase, OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4045
Polymers37,4311
Non-polymers9734
Water8,071448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-38 kcal/mol
Surface area13630 Å2
2
A: Aldo-keto Reductase, OXIDOREDUCTASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)307,22840
Polymers299,4448
Non-polymers7,78432
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
crystal symmetry operation5_757-x+2,y,-z+21
crystal symmetry operation6_577x,-y+2,-z+21
crystal symmetry operation7_557y,x,-z+21
crystal symmetry operation8_777-y+2,-x+2,-z+21
Buried area33750 Å2
ΔGint-344 kcal/mol
Surface area89510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.387, 94.387, 91.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

#1: Protein Aldo-keto Reductase, OXIDOREDUCTASE /


Mass: 37430.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: STM2406 / Plasmid: P15TVLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8ZNA1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.5M NH4Sulfate, 12% Sucrose, 0.1M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97917 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2012 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 35207 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 21.73 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 25.4
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ERP
Resolution: 1.86→29.85 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.108
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1999 5.74 %RANDOM
Rwork0.164 ---
obs0.166 34852 98.4 %-
Displacement parametersBiso mean: 25.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.2126 Å20 Å20 Å2
2--0.2126 Å20 Å2
3----0.4252 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.86→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 59 448 3006
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012761HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.953790HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1290SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes431HARMONIC5
X-RAY DIFFRACTIONt_it2761HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.85
X-RAY DIFFRACTIONt_other_torsion2.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion340SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3496SEMIHARMONIC4
LS refinement shellResolution: 1.86→1.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.256 154 5.74 %
Rwork0.257 2527 -
all0.257 2681 -
obs--89.15 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.158-1.10935.55735.18653.32753.2594-0.08050.6798-0.3128-0.1365-0.10740.42840.13840.0540.18790.0364-0.0301-0.0650.0302-0.05060.03997.588560.68996.3062
21.2317-0.0246-0.42110.57480.00411.1049-0.00320.0073-0.0931-0.0381-0.00320.00310.1380.04320.0065-0.01230.0256-0.0151-0.05790.0111-0.0426108.27167.7621106.666
32.1293.7650.69642.0271-0.09190.55960.06230.03610.0277-0.0522-0.05540.08330.0316-0.1837-0.00690.04910.04030.01790.0613-0.003-0.0137105.91273.486995.4434
40.68960.323-0.04090.92410.20930.40920.0318-0.00660.04980.001-0.0145-0.0318-0.0314-0.0446-0.01730.01060.0156-0.0061-0.00090.02370.0065109.68282.5806109.032
51.068-1.58581.42084.2075-0.50731.69820.03990.00350.02160.4499-0.0173-0.25-0.07780.0272-0.02260.0106-0.0094-0.0101-0.0504-0.0033-0.0767113.70590.621123.821
62.0435-0.38540.43731.774-0.63691.77380.0159-0.18270.1120.2470.01160.0747-0.1442-0.0262-0.0275-0.0198-0.00720.0065-0.05550.0009-0.0764106.44783.2281122.936
71.5835-0.7122-0.4582.76790.55650.47550.0032-0.1764-0.09670.0943-0.0015-0.18680.00360.0202-0.0017-0.0510.0056-0.016-0.05990.0494-0.0853114.02268.1423123.263
81.9908-1.7485-4.475505.42894.84140.00280.2288-0.1266-0.1823-0.06930.0005-0.00120.18730.06660.07050.0154-0.00560.09070.06120.1875131.41558.9998110.421
93.90370.5330.90240.439-0.582400.0225-0.1452-0.2393-0.00020.0074-0.0618-0.17130.3852-0.0298-0.02390.00670.0151-0.01270.07010.2245131.5454.0831119.766
101.5494-0.3652-0.10141.6992-0.15691.38440.0249-0.1598-0.3924-0.0576-0.0348-0.15460.16530.02550.01-0.07750.0029-0.0076-0.12010.07910.0073114.69554.7836118.98
113.1741.475-2.64781.486-2.86056.41860.06590.2616-0.32-0.2396-0.0985-0.15960.36340.00770.0327-0.02280.0398-0.0039-0.092-0.0120.0631111.90555.9147106.944
124.5658-0.361-2.53762.39052.58662.17390.0155-0.6153-0.39460.3527-0.30250.3403-0.0257-0.08680.287-0.0164-0.0265-0.0034-0.0610.16620.0663111.65449.5403125.216
130-3.77880.10490.18461.96041.7740.0425-0.3046-0.0420.13390.0731-0.35120.17810.0725-0.11560.00090.0402-0.07130.00070.19870.105124.5452.5534128.531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - A|8}
2X-RAY DIFFRACTION2{A|9 - A|75}
3X-RAY DIFFRACTION3{A|76 - A|84}
4X-RAY DIFFRACTION4{A|85 - A|142}
5X-RAY DIFFRACTION5{A|143 - A|151}
6X-RAY DIFFRACTION6{A|152 - A|185}
7X-RAY DIFFRACTION7{A|186 - A|230}
8X-RAY DIFFRACTION8{A|231 - A|255}
9X-RAY DIFFRACTION9{A|256 - A|265}
10X-RAY DIFFRACTION10{A|266 - A|297}
11X-RAY DIFFRACTION11{A|298 - A|312}
12X-RAY DIFFRACTION12{A|313 - A|321}
13X-RAY DIFFRACTION13{A|322 - A|330}

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