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- PDB-4mhb: Structure of a putative reductase from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 4mhb
TitleStructure of a putative reductase from Yersinia pestis
ComponentsPutative aldo/keto reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / alpha and beta protein / TIM beta/alpha barrel
Function / homology
Function and homology information


alcohol dehydrogenase (NADP+) activity / L-ascorbic acid biosynthetic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / aldose reductase (NADPH) activity / oxidoreductase activity / cytosol
Similarity search - Function
Aldo/keto reductase family signature 1. / 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
Putative aldo/keto reductase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Kudritska, M. / Kwon, K. / Rembert, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Structure of a putative reductase from Yersinia pestis
Authors: Anderson, S.M. / Wawrzak, Z. / Kudritska, M. / Kwon, K. / Rembert, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release

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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
D: Putative aldo/keto reductase
E: Putative aldo/keto reductase
F: Putative aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,44448
Polymers204,4106
Non-polymers4,03542
Water30,3011682
1
A: Putative aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8379
Polymers34,0681
Non-polymers7698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6457
Polymers34,0681
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8379
Polymers34,0681
Non-polymers7698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6457
Polymers34,0681
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Putative aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7418
Polymers34,0681
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Putative aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7418
Polymers34,0681
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Putative aldo/keto reductase
hetero molecules

D: Putative aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,48116
Polymers68,1372
Non-polymers1,34514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456x-1/2,-y+1/2,-z+5/41
Buried area3650 Å2
ΔGint-198 kcal/mol
Surface area22820 Å2
MethodPISA
8
F: Putative aldo/keto reductase
hetero molecules

B: Putative aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,38515
Polymers68,1372
Non-polymers1,24913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
Buried area3450 Å2
ΔGint-187 kcal/mol
Surface area22930 Å2
MethodPISA
9
C: Putative aldo/keto reductase
hetero molecules

E: Putative aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,57717
Polymers68,1372
Non-polymers1,44115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_644-y+3/2,x-1/2,z-1/41
Buried area3790 Å2
ΔGint-211 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.746, 128.746, 277.614
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21A-619-

HOH

31D-438-

HOH

41D-598-

HOH

DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein
Putative aldo/keto reductase / Uncharacterized protein


Mass: 34068.250 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: KIM 10+ / Gene: aRA11, y1125, YP_1162, YPO2805 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q7CJX8, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1682 / 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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.3M Ammonium Sulphate, 3.2% Jeffamine ED-2001, 10mM Ethanole, 100mM HEPES, 2% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2012 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 233672 / Num. obs: 232270 / % possible obs: 99.4 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 2.5 / Redundancy: 6.1 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.75-1.816.20.7842.46231261100
1.81-1.896.20.5543.54230681100
1.89-1.976.20.3755.03231271100
1.97-2.076.20.2567.12231881100
2.07-2.26.20.189.86231471100
2.2-2.386.213.312.8423278199.9
2.38-2.616.210.315.523314199.9
2.61-2.996.17.919.123310199.5
2.99-3.7764.927.2123243198.5
3.77-505.6431.0223469196.1

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1101refinement
PDB_EXTRACT3.11data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→36.4 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7531 / SU ML: 0.15 / σ(F): 1.34 / σ(I): 2.5 / Phase error: 29.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 10112 5 %random
Rwork0.1779 ---
obs0.1791 231535 99.1 %-
all-233685 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.31 Å2 / Biso mean: 27.75 Å2 / Biso min: 10.36 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13451 0 210 1682 15343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01613961
X-RAY DIFFRACTIONf_angle_d1.43518940
X-RAY DIFFRACTIONf_chiral_restr0.1142048
X-RAY DIFFRACTIONf_plane_restr0.0082441
X-RAY DIFFRACTIONf_dihedral_angle_d13.5435060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.75-1.810.298111470.2638721875972294399.2
1.81-1.880.261311530.2316726576472304299.8
1.88-1.970.231811550.2082730876942304799.7
1.97-2.070.210411580.183729576772311099.6
2.07-2.20.206811540.1671731076952312799.8
2.2-2.370.197911590.1631728476702318699.6
2.37-2.610.20511640.1675730576902327099.7
2.61-2.990.20311660.1688730176862328699.4
2.99-3.770.185911550.1692728276672319298.3
3.77-36.40.185611600.1739731276982335095.8
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)
11.60261.81090.05042.5113-1.21028.28810.1237-0.1822-0.09750.0318-0.1412-0.2530.0974-0.01610.05190.10790.0077-0.06670.20660.01560.247162.050930.2205152.8335
20.80590.12270.23871.0856-0.461.22560.0627-0.0487-0.03280.0967-0.0305-0.115-0.02260.0759-0.02520.1159-0.0085-0.0310.13790.00040.169361.188441.6207151.6448
31.50550.32980.46271.8005-0.6732.86850.0945-0.1987-0.17990.1699-0.025-0.08830.0881-0.1612-0.0440.1492-0.0101-0.03350.14160.00930.186150.928921.9749152.4138
40.61730.456-0.1662.4494-0.14270.19530.03960.078-0.04260.32180.0886-0.0230.05520.0021-0.12990.23880.0044-0.03580.23130.01670.193643.087635.122150.0057
51.5642-1.2285-0.24291.33230.63042.11080.1421-0.1639-0.22280.0461-0.03420.11280.0733-0.0964-0.07990.2892-0.05950.02390.2460.11850.282394.55122.3208136.4522
60.49670.2227-0.22160.7611-0.23510.9228-0.0501-0.2103-0.30.0638-0.0125-0.06880.31270.1640.08340.19020.03440.01360.2240.12330.2221105.86052.9918135.0993
71.1997-0.1888-0.35781.6119-0.71782.5330.0064-0.2873-0.15310.2632-0.00480.1528-0.08360.0286-0.00070.1243-0.02270.00410.19960.05130.165386.285513.3659135.9154
86.25371.4143-2.27012.0064-0.70861.74260.0522-0.330.1173-0.1588-0.00860.1753-0.139-0.1035-0.05750.17080.003-0.020.13750.01790.127189.861522.2459130.4471
92.0557-1.50170.63624.9687-0.13260.2248-0.0138-0.6877-0.46610.96260.22250.3962-0.286-0.1357-0.10620.20930.00430.04630.41450.06960.1676113.703619.5153138.0109
102.3314-1.41550.29363.1045-1.68148.15910.14770.19160.0591-0.19630.0237-0.2297-0.15270.2793-0.13410.1353-0.01060.09140.24510.0070.2478126.34634.0498108.1961
110.9221-0.3376-0.15610.8013-0.25831.00730.11760.00650.0379-0.1272-0.0227-0.13330.00350.1591-0.00240.08880.01490.0430.16140.01760.1465125.480122.64109.4799
121.4698-0.2145-0.37531.1732-0.49162.16930.15290.11210.2516-0.228-0.0117-0.1367-0.204-0.0602-0.10180.18340.0160.06780.13140.01360.1649115.274542.3107108.7807
132.36391.122-0.18586.5993-1.02161.65610.1325-0.24140.1543-0.1947-0.04120.123-0.2732-0.1519-0.09010.1520.03530.04530.24750.00450.1481106.370238.8327114.2484
145.453-5.0548-6.54994.89036.01378.1190.51351.00770.4856-0.6283-0.2129-0.1016-0.4891-0.5511-0.28850.2803-0.0208-0.03380.32040.06340.2503108.927215.0195106.5595
153.02121.45492.64361.03890.74464.89530.0507-0.1151-0.06290.08050.14510.1888-0.0131-0.2058-0.15530.29150.06060.14060.25770.02130.2971134.048636.1416154.4949
160.7393-0.0633-0.18060.95120.66762.06020.053-0.009-0.03610.19570.02220.1680.0615-0.2555-0.01170.2022-0.0050.08850.18350.02420.2301134.255823.8216155.397
170.71120.4131-0.05921.37870.39160.98050.0282-0.01620.07920.20330.03680.0712-0.06210.007-0.06040.22640.02130.06470.16890.01220.1986146.272440.5703150.9163
186.13223.1485-4.8482.0511-3.37526.4450.26-0.51410.24720.4246-0.16120.1108-0.40680.5331-0.19410.28070.02960.01210.1765-0.04680.2326152.028316.5888154.137
191.2406-1.10391.65982.2889-1.1362.31010.258-0.14620.27-0.04940.0771-0.0394-0.12270.3109-0.30050.3377-0.13660.08630.3219-0.14680.3067100.538459.0891138.0695
200.41990.09610.15380.83090.42690.86730.1092-0.12750.2076-0.12020.0843-0.0167-0.490.06990.2640.204-0.04240.0550.1669-0.10380.195688.230758.836138.9587
210.878-0.3275-0.06021.12370.23840.99850.1202-0.26220.141-0.01510.0195-0.0972-0.07860.1825-0.06380.1463-0.06710.03720.2634-0.08090.1624104.962146.8236134.5594
220.5001-1.6159-1.61125.5674.72665.85950.0124-0.2246-0.05640.4073-0.0258-0.00730.45730.31-0.13250.11-0.0097-0.04080.1942-0.02430.179781.034641.0111137.626
232.6371-1.0661-1.73541.6947-0.24488.86690.0266-0.01520.101-0.1122-0.07810.1984-0.044-0.26840.03950.24490.0539-0.15340.3415-0.05160.301369.744428.2992106.5716
240.50750.23370.27630.35980.30360.95670.01520.05380.1174-0.241-0.01780.207-0.203-0.28750.0660.28380.0815-0.12310.2659-0.03280.256870.924940.0959108.2343
251.4014-0.21580.5050.91330.2713.35450.07120.1524-0.0511-0.3119-0.0350.1185-0.09880.0396-0.02210.19240.0101-0.06870.1302-0.01480.153681.3520.5232106.6832
260.4785-0.0983-0.36321.77930.26050.2938-0.0198-0.07080.0051-0.52620.14810.0646-0.0725-0.0698-0.13180.31590.0242-0.0640.2886-0.01630.190488.910533.3991110.5964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 38 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 173 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 261 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 262 through 297 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 15 through 38 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 39 through 173 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 174 through 261 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 262 through 283 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 284 through 297 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 15 through 38 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 39 through 173 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 174 through 261 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 262 through 283 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 284 through 297 )C0
15X-RAY DIFFRACTION15chain 'D' and (resid 15 through 38 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 39 through 152 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 153 through 283 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 284 through 297 )D0
19X-RAY DIFFRACTION19chain 'E' and (resid 15 through 38 )E0
20X-RAY DIFFRACTION20chain 'E' and (resid 39 through 152 )E0
21X-RAY DIFFRACTION21chain 'E' and (resid 153 through 283 )E0
22X-RAY DIFFRACTION22chain 'E' and (resid 284 through 297 )E0
23X-RAY DIFFRACTION23chain 'F' and (resid 15 through 38 )F0
24X-RAY DIFFRACTION24chain 'F' and (resid 39 through 173 )F0
25X-RAY DIFFRACTION25chain 'F' and (resid 174 through 261 )F0
26X-RAY DIFFRACTION26chain 'F' and (resid 262 through 297 )F0

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