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- PDB-4r9o: Crystal Structure of Putative Aldo/Keto Reductase from Salmonella... -

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Basic information

Entry
Database: PDB / ID: 4r9o
TitleCrystal Structure of Putative Aldo/Keto Reductase from Salmonella enterica
ComponentsPutative aldo/keto reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-fold / TIM-barrel
Function / homology
Function and homology information


oxidoreductase activity / cytosol
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
Putative aldo/keto reductase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsKim, Y. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Putative Aldo/Keto Reductase from Salmonella enterica
Authors: Kim, Y. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative aldo/keto reductase
B: Putative aldo/keto reductase
C: Putative aldo/keto reductase


Theoretical massNumber of molelcules
Total (without water)101,9733
Polymers101,9733
Non-polymers00
Water4,378243
1
A: Putative aldo/keto reductase
B: Putative aldo/keto reductase
C: Putative aldo/keto reductase

A: Putative aldo/keto reductase
B: Putative aldo/keto reductase
C: Putative aldo/keto reductase


Theoretical massNumber of molelcules
Total (without water)203,9456
Polymers203,9456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area18790 Å2
ΔGint-27 kcal/mol
Surface area60820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.692, 86.868, 74.162
Angle α, β, γ (deg.)90.00, 102.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative aldo/keto reductase


Mass: 33990.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM1439, ydhF / Plasmid: pMCSG19c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q8ZPN5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 20 %(w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 65800 / Num. obs: 65800 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.118 / Net I/σ(I): 10.2
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.77 / Num. unique all: 3151 / Rsym value: 0.734 / % possible all: 93.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 1OG6

1og6


Resolution: 1.949→37.391 Å / SU ML: 0.26 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3331 5.07 %random
Rwork0.186 ---
obs0.188 65745 96.53 %-
all-65745 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.4 Å2
Refinement stepCycle: LAST / Resolution: 1.949→37.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7021 0 0 243 7264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077419
X-RAY DIFFRACTIONf_angle_d1.06110093
X-RAY DIFFRACTIONf_dihedral_angle_d15.1582768
X-RAY DIFFRACTIONf_chiral_restr0.041126
X-RAY DIFFRACTIONf_plane_restr0.0051318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9487-1.97650.30151230.26442296241985
1.9765-2.0060.29091540.26272517267195
2.006-2.03730.33421320.25492599273197
2.0373-2.07070.29591300.24472660279098
2.0707-2.10640.26421400.23262580272098
2.1064-2.14470.25681310.2262636276798
2.1447-2.1860.29511430.22642632277598
2.186-2.23060.31181300.22762643277398
2.2306-2.27910.28621520.21422605275798
2.2791-2.33210.26771440.20742623276798
2.3321-2.39040.26371410.20192630277198
2.3904-2.4550.25131430.20342614275798
2.455-2.52730.25771490.21042607275698
2.5273-2.60880.2541410.21152621286298
2.6088-2.7020.28521360.21342659279598
2.702-2.81020.27091610.2142607276898
2.8102-2.9380.24151400.19352627276798
2.938-3.09290.21591410.19732649279098
3.0929-3.28650.28671250.20222621274697
3.2865-3.54010.21581410.18212657279098
3.5401-3.8960.19511190.15652629274896
3.896-4.4590.17051330.152606273996
4.459-5.61480.17441300.14292573270394
5.6148-37.39740.18421520.16092523277591
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)
11.8430.46940.26741.73310.42791.0364-0.05850.0472-0.0681-0.03560.01860.13420.1266-0.25210.03120.2368-0.0459-0.00220.3331-0.03510.2677-32.2606-46.053119.2154
21.76391.2579-0.2992.9196-0.8352.20080.0204-0.18610.2213-0.0195-0.02730.1611-0.0656-0.2495-0.00890.18920.04340.00410.262-0.02350.1978-27.7559-28.144318.8509
35.1880.4683-2.27382.2394-0.34632.6613-0.0251-0.36850.44730.23560.08740.0565-0.0085-0.1319-0.03190.25460.0178-0.03480.3216-0.02320.2118-22.5241-30.696728.713
40.3896-0.3263-0.0641.81240.84560.77570.0354-0.0028-0.0237-0.165-0.0315-0.0978-0.07-0.1297-0.0020.218-0.0101-0.01380.2460.0180.2895-12.7306-41.152717.1942
54.79020.83051.80982.75382.60386.72170.16630.342-0.6724-0.28560.0839-0.22030.1241-0.0807-0.25090.34840.00290.04480.2635-0.03750.3291-14.5763-57.93793.142
65.2938-1.348-0.04323.1052-0.74661.7382-0.27950.3351-0.6729-0.34360.16640.46780.4467-0.31250.05740.4036-0.11310.05250.3395-0.03630.3727-21.6732-55.16714.8829
76.4447-2.74581.40781.17-0.76628.3526-0.20260.3595-0.24540.1422-0.3078-0.23150.36610.34040.44970.339-0.0048-0.00010.2244-0.060.3685-5.5614-57.68048.8431
82.88930.50090.03432.47-0.82941.7452-0.01210.051-0.1568-0.17950.14640.27510.2405-0.2955-0.13970.297-0.092-0.00950.3401-0.00450.3322-26.9986-53.6437-20.0496
93.2093-0.06970.471.6199-0.36112.3683-0.05340.1416-0.3675-0.21430.0270.00390.35460.0250.02810.3491-0.02530.01340.2006-0.01760.3245-9.5655-59.0106-19.3433
103.98641.10930.96864.0130.70863.9176-0.04220.521-0.2206-0.45420.0448-0.40360.46590.0441-0.03580.353-0.00480.05180.25580.0060.1815-9.0228-53.1501-29.1332
111.5405-0.5174-0.67040.38670.43141.7376-0.0846-0.10920.13030.12840.11530.03350.2149-0.0824-0.05920.2629-0.00970.00820.24160.0210.3216-13.389-39.5127-17.441
122.7404-1.47960.97814.1515-1.10134.44990.0132-0.28741.07230.50630.0330.3648-0.0776-0.4243-0.05930.3020.01490.01120.342-0.08180.5788-27.8938-32.25010.9851
134.3875-1.3642-1.7115.48161.44.8756-0.0303-0.1687-0.565-0.3963-0.03360.9785-0.1131-0.38910.00660.2365-0.0002-0.04220.35470.06770.4158-30.726-33.9588-10.296
141.5553-0.37880.35445.31560.57111.53180.0632-0.2529-0.1270.3338-0.17690.6495-0.1106-0.40540.08210.2661-0.01660.010.4339-0.04380.3725-30.0528-40.3773-15.3656
150.6452-0.4743-1.49957.7397-0.70556.1180.0229-0.05030.23250.3483-0.25370.1796-0.57330.04550.13620.22870.01260.03440.33070.02510.3476-24.3897-25.219-9.458
161.59261.54930.17282.25140.39960.41750.12690.76450.0446-0.54330.5372-0.5558-0.24490.3983-0.54380.4109-0.00880.04290.3641-0.02850.48174.05-7.2893-29.6662
172.3144-0.53850.12553.20150.03991.44120.05280.01660.35620.1516-0.0401-0.186-0.380.0122-0.01540.38720.0152-0.01890.2350.00010.3759-3.46273.646-15.5683
182.84150.3064-0.22263.3098-0.3611.3690.01440.18360.4856-0.2479-0.00570.1417-0.3074-0.271-0.03470.39790.0654-0.02320.26890.02320.4042-10.30772.6294-20.8447
191.5320.8617-1.44382.45340.28232.80410.0020.09890.2261-0.1117-0.00730.3719-0.0437-0.3659-0.0140.25230.0988-0.01940.32570.01830.3915-21.0859-10.8983-17.2796
202.72811.9088-1.10865.7251-0.74191.8509-0.0924-0.01760.1672-0.44550.1176-0.01080.0033-0.1367-0.03270.22880.0364-0.00590.25540.00050.2916-12.2901-11.6216-22.6102
213.4229-0.0696-0.75365.0917-0.99083.4013-0.05540.38860.0038-0.35480.1840.3411-0.2942-0.3861-0.16850.26820.0249-0.00480.28430.00350.2255-12.8349-14.4977-29.0596
221.78061.02480.51711.25850.46471.63640.0672-0.05950.13630.135-0.0186-0.2049-0.09760.0178-0.02450.26490.0210.00350.2103-0.02670.35070.6094-19.1628-20.2836
232.99570.90730.17071.84990.17723.61870.3082-0.2218-0.4890.3314-0.0935-0.5335-0.1699-0.122-0.17710.3568-0.0193-0.06020.34590.0250.428212.2065-8.59160.8216
243.3569-0.62210.6751.5672-0.28622.65750.0676-0.16950.697-0.0804-0.1158-0.0704-0.4373-0.00020.04570.3249-0.01920.01530.2382-0.02620.412710.5336-6.7614-12.9502
255.8269-2.3610.20782.2965-1.25732.51480.16920.32691.2377-0.01010.08-0.6857-0.6740.1842-0.22490.584-0.1362-0.05570.38160.07850.774112.942-0.0967-13.5609
263.1383-0.8545-5.3130.75070.86129.7617-0.322-0.3665-1.52520.0242-0.4005-0.4294-0.02220.24560.60180.2827-0.0323-0.01360.3270.02110.507418.0525-18.3103-6.5892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 135 )
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 161 )
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 220 )
5X-RAY DIFFRACTION5chain 'A' and (resid 221 through 251 )
6X-RAY DIFFRACTION6chain 'A' and (resid 252 through 277 )
7X-RAY DIFFRACTION7chain 'A' and (resid 278 through 293 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 84 )
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 135 )
10X-RAY DIFFRACTION10chain 'B' and (resid 136 through 161 )
11X-RAY DIFFRACTION11chain 'B' and (resid 162 through 220 )
12X-RAY DIFFRACTION12chain 'B' and (resid 221 through 236 )
13X-RAY DIFFRACTION13chain 'B' and (resid 237 through 251 )
14X-RAY DIFFRACTION14chain 'B' and (resid 252 through 277 )
15X-RAY DIFFRACTION15chain 'B' and (resid 278 through 293 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 15 )
17X-RAY DIFFRACTION17chain 'C' and (resid 16 through 54 )
18X-RAY DIFFRACTION18chain 'C' and (resid 55 through 84 )
19X-RAY DIFFRACTION19chain 'C' and (resid 85 through 116 )
20X-RAY DIFFRACTION20chain 'C' and (resid 117 through 135 )
21X-RAY DIFFRACTION21chain 'C' and (resid 136 through 161 )
22X-RAY DIFFRACTION22chain 'C' and (resid 162 through 212 )
23X-RAY DIFFRACTION23chain 'C' and (resid 213 through 237 )
24X-RAY DIFFRACTION24chain 'C' and (resid 238 through 265 )
25X-RAY DIFFRACTION25chain 'C' and (resid 266 through 281 )
26X-RAY DIFFRACTION26chain 'C' and (resid 282 through 295 )

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