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- PDB-6i9v: Crystal structure of the halohydrin dehalogenase HheG T123G mutant -

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Basic information

Entry
Database: PDB / ID: 6i9v
TitleCrystal structure of the halohydrin dehalogenase HheG T123G mutant
ComponentsPutative oxidoreductase
KeywordsLYASE / halohydrin dehalogenase
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / Putative oxidoreductase / Putative oxidoreductase
Function and homology information
Biological speciesIlumatobacter coccineus YM16-304 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKluenemann, T. / Blankenfeldt, W. / Schallmey, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation1934 Germany
German Research Foundation2223 Germany
CitationJournal: Sci Rep / Year: 2019
Title: Position 123 of halohydrin dehalogenase HheG plays an important role in stability, activity, and enantioselectivity.
Authors: Solarczek, J. / Klunemann, T. / Brandt, F. / Schrepfer, P. / Wolter, M. / Jacob, C.R. / Blankenfeldt, W. / Schallmey, A.
History
DepositionNov 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Putative oxidoreductase
B: Putative oxidoreductase
C: Putative oxidoreductase
D: Putative oxidoreductase
E: Putative oxidoreductase
F: Putative oxidoreductase
G: Putative oxidoreductase
H: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)218,3758
Polymers218,3758
Non-polymers00
Water88349
1
A: Putative oxidoreductase
D: Putative oxidoreductase
E: Putative oxidoreductase
G: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)109,1884
Polymers109,1884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11220 Å2
ΔGint-74 kcal/mol
Surface area34640 Å2
MethodPISA
2
B: Putative oxidoreductase
C: Putative oxidoreductase
F: Putative oxidoreductase
H: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)109,1884
Polymers109,1884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11330 Å2
ΔGint-69 kcal/mol
Surface area34320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.033, 141.320, 172.525
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Putative oxidoreductase


Mass: 27296.926 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ilumatobacter coccineus YM16-304 (bacteria)
Gene: YM304_35350 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M5A5Y8, UniProt: A0A6C7EF96*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium thiocyanate 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.8→172.52 Å / Num. obs: 62219 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.996 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.058 / Rrim(I) all: 0.209 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.8-2.8712.40.9715636245420.9470.2871.0132.7
12.52-172.52120.05696698090.9980.0170.05917

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5o30
Resolution: 2.8→172.52 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 28.54
RfactorNum. reflection% reflection
Rfree0.259 3078 4.97 %
Rwork0.222 --
obs0.2238 61974 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 247.53 Å2 / Biso mean: 75.1397 Å2 / Biso min: 19.62 Å2
Refinement stepCycle: final / Resolution: 2.8→172.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15053 0 0 49 15102
Biso mean---31.42 -
Num. residues----2053
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.84380.34311410.33222654100
2.8438-2.89040.34681390.31612633100
2.8904-2.94020.30831280.2912263399
2.9402-2.99370.30641330.29052675100
2.9937-3.05130.3171360.27812617100
3.0513-3.11360.32881430.28342640100
3.1136-3.18130.32311550.26992668100
3.1813-3.25530.29951000.26542648100
3.2553-3.33670.2831330.26262672100
3.3367-3.42690.26531300.2352640100
3.4269-3.52780.2771530.23692675100
3.5278-3.64170.29391630.23162642100
3.6417-3.77180.24751370.21522657100
3.7718-3.92290.27391360.20832682100
3.9229-4.10140.21491200.19192665100
4.1014-4.31770.25181530.19052684100
4.3177-4.58820.18851360.18312685100
4.5882-4.94250.22861620.17762668100
4.9425-5.43990.22731260.19862742100
5.4399-6.22710.26751260.2182734100
6.2271-7.84550.24341520.20912762100
7.8455-172.520.22621760.1955282098
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)
14.81393.26050.23736.12972.09243.18990.2885-0.6641-0.04660.7358-0.1507-0.53430.09540.3559-0.12430.8287-0.4242-0.07850.81320.05210.4257-75.429-28.1962-34.2097
21.47132.02310.20365.26570.26410.02840.3751-0.5874-0.00271.2396-0.62210.58310.4663-0.40940.23291.1292-0.57950.11360.9532-0.06960.5127-89.4288-32.5773-32.0834
30.88-0.0469-0.15483.38571.18611.60490.1285-0.3911-0.01750.5568-0.0898-0.00390.04530.0581-0.03110.4674-0.2581-0.06820.47890.03530.3405-82.6607-38.4901-49.8669
41.38-2.6623-1.89577.51561.86083.95740.18720.4754-0.25550.0199-0.17660.81680.0244-0.85380.00020.4178-0.21840.0050.4853-0.02430.457-89.1507-25.9585-50.5896
58.64724.8545-4.8928.23380.81015.6249-0.295-0.8644-1.07270.52320.1053-2.29361.42792.45340.15990.59770.0844-0.08250.90460.08590.989-59.7932-37.4609-51.135
61.8873-0.24150.63674.03291.54151.5210.10140.00390.49160.14-0.049-0.398-0.27650.385-0.07430.4069-0.2694-0.02470.4850.05720.4255-73.517-25.2507-53.7107
76.3597-0.62570.26391.1878-1.73573.17560.0251-0.00030.3933-0.2420.08530.3051-0.0926-0.2883-0.08350.76280.4191-0.00420.72270.03010.2932-75.472628.8424-48.8731
89.5198-3.0399-0.05611.1362-0.48721.57670.32050.24140.2814-0.1005-0.0451-0.7289-0.07790.0345-0.16630.70990.4125-0.02910.70860.01970.4515-72.318530.9294-52.6814
92.8944-3.9411-0.83877.80021.05210.24640.43450.8408-0.1531-1.1752-0.40060.9172-0.3243-0.6874-0.01050.86550.3739-0.11640.86380.04180.4735-87.013833.7882-54.1345
101.73540.1383-0.05595.43932.8552.67020.03780.2169-0.2210.10420.437-0.7320.10040.388-0.4410.50030.3480.01790.62340.00480.2826-76.564742.8513-38.5861
113.60283.03013.08914.55884.29774.4174-0.02670.33740.0475-0.5197-0.0430.3219-0.1371-0.00170.02350.67260.40110.03020.81960.11520.3722-84.874641.5594-40.886
121.4218-2.0625-0.53513.33210.39790.62360.12430.1361-0.0742-0.2318-0.1375-0.2227-0.0089-0.10270.04480.5690.37690.00630.6159-0.01090.2908-78.940138.0964-31.9214
131.391-1.45330.59991.6062-0.13193.0604-0.05490.30590.562-0.18990.19950.043-0.04190.4394-0.13170.69760.3422-0.09470.7119-0.00750.4371-70.720435.1284-36.8473
143.9752-0.13540.60014.10751.69613.50230.1127-0.001-0.0098-0.16750.2988-0.850.21680.6504-0.41670.61620.4110.01510.7497-0.04660.5533-66.932930.2832-32.6076
150.6053-0.5992-0.2341.59150.20430.37140.00050.03380.1062-0.0005-0.00450.1957-0.0941-0.1272-0.0840.91980.69730.00130.97610.03890.4994-94.662463.9459-15.3206
161.1788-0.9395-0.17381.29950.04160.1544-0.01420.1354-0.08450.0156-0.06910.2339-0.12-0.1470.08250.7040.47910.0230.86690.04760.3867-92.070649.7909-26.1794
171.5645-1.02510.11932.2953-0.06290.6448-0.1329-0.1530.10330.00130.07690.205-0.1254-0.09620.15290.71190.4597-0.02730.70160.0260.3847-85.549554.998-28.3099
182.4824-1.84050.19722.6419-0.48570.31690.0288-0.0093-0.00930.0277-0.0105-0.0740.0133-0.0377-0.00690.58510.41880.02580.72740.05170.2955-83.84346.5539-22.0237
190.86560.06190.2383.6232-0.14831.0872-0.0312-0.2515-0.0693-0.05280.09620.5494-0.1259-0.5634-0.1450.63740.51590.01210.96440.13740.4556-94.661443.6612-12.9405
201.82630.9634-0.0491.7736-0.20340.4843-0.06340.1224-0.1197-0.08520.0698-0.00870.0350.02130.05810.3525-0.24960.02130.36110.03590.41-93.4389-60.3336-75.8911
219.40242.56215.4335.59642.33693.28920.43-1.87330.20861.5641-1.14221.20310.4216-0.97080.68280.6874-0.41040.0860.7222-0.01780.6311-104.6669-63.1558-71.5108
220.30080.42060.27040.98620.76090.84580.0654-0.2041-0.18430.3445-0.25570.19710.1244-0.04530.16560.4858-0.30290.01640.47570.03960.4455-91.4763-59.5937-63.383
230.48990.54710.03671.96120.26480.88350.0139-0.1121-0.08540.2525-0.1073-0.04190.0278-0.0110.01510.3431-0.2675-0.00540.40770.04990.406-88.2794-48.0465-63.4026
248.2485-2.04915.6274.97572.03797.2679-0.168-0.4684-0.91990.53970.12532.03491.0793-2.10930.02950.4193-0.13520.05070.8880.00970.9763-111.8613-37.4497-68.7832
251.84730.239-0.19161.28290.34120.4526-0.06340.08550.0301-0.0955-0.04060.19540.0129-0.06340.01350.32-0.2439-0.02890.34950.08710.4095-92.0892-43.6588-76.359
265.2627-0.4237-1.63484.4558-0.8951.8597-0.16860.30320.2347-0.29810.2409-0.359-0.08530.1019-0.00630.6647-0.4548-0.05220.71590.07720.4419-82.5525-39.6628-99.5893
270.7920.8134-0.30151.6801-0.20890.6834-0.26150.4210.1559-0.5010.2282-0.0515-0.17420.1060.00740.522-0.3406-0.02750.58430.11250.4547-80.3689-32.7486-87.0445
283.2032-1.65883.12093.5362-2.34924.00890.0462-0.1647-0.13390.07880.09280.0637-0.0123-0.0712-0.02841.06470.63230.00730.99730.0720.4402-80.437441.77813.2036
290.3917-0.05930.58660.6582-0.36790.99720.0321-0.3952-0.20520.34110.3390.18820.168-0.3487-0.24231.05140.5112-0.06261.15070.26250.6437-78.980227.96527.4584
301.1405-0.69860.34982.2044-0.60681.0410.0366-0.2358-0.13830.21840.1632-0.14080.0405-0.04070.10180.74690.4907-0.0950.80490.08370.4016-75.867639.32-4.0091
311.52150.2864-0.09231.38341.56962.53410.11190.0070.8705-0.1195-0.0257-0.1566-0.58120.1413-0.08451.0664-0.3785-0.05960.49880.0740.9885-71.3533-0.0969-63.7814
321.16740.31170.24961.60130.12390.51830.01420.04910.547-0.28190.09150.0973-0.18350.0688-0.04570.6751-0.3578-0.15770.55160.16070.7012-75.4912-11.9916-75.5579
332.32471.50110.58362.13340.5762.2493-0.33790.14340.46-0.3910.1490.1604-0.46950.04550.14540.4829-0.2322-0.10670.39140.07980.558-78.9491-17.6071-68.6081
347.302-3.48795.34927.6601-5.03025.0173-0.0510.00322.2413-0.04190.19021.6005-2.4783-1.3175-0.13421.12170.16390.00040.9546-0.07311.4305-100.9939-9.4868-62.8874
356.6381-0.78721.10671.77050.10171.5624-0.1051-0.40470.75360.4452-0.13550.1017-0.4780.12830.25780.5737-0.197-0.00250.34590.01930.5018-80.8084-17.3349-57.7249
361.4574-0.36180.07090.17130.2981.22840.1523-0.1271-0.93240.04840.11190.34590.63340.1614-0.2531.85690.6778-0.22940.93120.08671.1624-67.48772.3736-24.6436
370.406-0.1603-0.22840.1360.15320.1832-0.3445-0.4791-0.43140.57570.1465-0.31290.11580.20490.17391.38040.7294-0.12831.04750.02031.1107-58.10087.804-17.5594
381.7168-0.89290.57150.8704-0.08240.68470.2256-0.13-0.58260.27520.21550.29840.0534-0.2735-0.40361.30940.5785-0.10240.91350.17290.865-73.25315.3524-8.0028
390.4255-0.20550.21310.8380.27571.23980.32720.68660.5587-0.2028-0.1313-0.10020.0146-0.498-0.19791.04110.4649-0.07860.76170.09740.5678-76.433920.2335-17.7839
400.0815-0.45120.57433.7028-2.59984.33830.1292-0.1636-0.61910.0762-0.0287-0.09310.31510.484-0.07670.92180.4412-0.23040.7077-0.00390.6334-68.944624.3818-14.4974
410.78051.2888-0.64772.9709-1.25142.3236-0.07920.2341-0.7572-0.16170.3282-0.08110.7552-0.3378-0.24981.18170.3763-0.01790.89270.06140.5458-79.268213.9694-22.2907
423.044-0.2124-1.51870.01760.10340.76-0.1949-0.248-1.52880.520.25060.73271.2449-0.6206-0.06681.5296-0.27220.03771.41790.09521.4424-96.30189.1606-23.6581
433.2590.84530.5710.4525-0.50951.9610.10390.0126-0.518-0.33980.17550.04270.6431-0.1112-0.27370.98660.3529-0.13730.6360.06430.6769-76.386219.5006-28.668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 76 )A6 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 91 )A77 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 182 )A92 - 182
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 195 )A183 - 195
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 220 )A196 - 220
6X-RAY DIFFRACTION6chain 'A' and (resid 221 through 262 )A221 - 262
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 19 )B6 - 19
8X-RAY DIFFRACTION8chain 'B' and (resid 20 through 76 )B20 - 76
9X-RAY DIFFRACTION9chain 'B' and (resid 77 through 91 )B77 - 91
10X-RAY DIFFRACTION10chain 'B' and (resid 92 through 113 )B92 - 113
11X-RAY DIFFRACTION11chain 'B' and (resid 114 through 142 )B114 - 142
12X-RAY DIFFRACTION12chain 'B' and (resid 143 through 182 )B143 - 182
13X-RAY DIFFRACTION13chain 'B' and (resid 183 through 212 )B183 - 212
14X-RAY DIFFRACTION14chain 'B' and (resid 213 through 262 )B213 - 262
15X-RAY DIFFRACTION15chain 'C' and (resid 6 through 91 )C6 - 91
16X-RAY DIFFRACTION16chain 'C' and (resid 92 through 113 )C92 - 113
17X-RAY DIFFRACTION17chain 'C' and (resid 114 through 142 )C114 - 142
18X-RAY DIFFRACTION18chain 'C' and (resid 143 through 186 )C143 - 186
19X-RAY DIFFRACTION19chain 'C' and (resid 187 through 262 )C187 - 262
20X-RAY DIFFRACTION20chain 'D' and (resid 6 through 37 )D6 - 37
21X-RAY DIFFRACTION21chain 'D' and (resid 38 through 61 )D38 - 61
22X-RAY DIFFRACTION22chain 'D' and (resid 62 through 113 )D62 - 113
23X-RAY DIFFRACTION23chain 'D' and (resid 114 through 206 )D114 - 206
24X-RAY DIFFRACTION24chain 'D' and (resid 207 through 221 )D207 - 221
25X-RAY DIFFRACTION25chain 'D' and (resid 222 through 262 )D222 - 262
26X-RAY DIFFRACTION26chain 'E' and (resid 6 through 61 )E6 - 61
27X-RAY DIFFRACTION27chain 'E' and (resid 62 through 262 )E62 - 262
28X-RAY DIFFRACTION28chain 'F' and (resid 6 through 61 )F6 - 61
29X-RAY DIFFRACTION29chain 'F' and (resid 62 through 141 )F62 - 141
30X-RAY DIFFRACTION30chain 'F' and (resid 142 through 262 )F142 - 262
31X-RAY DIFFRACTION31chain 'G' and (resid 6 through 90 )G6 - 90
32X-RAY DIFFRACTION32chain 'G' and (resid 91 through 142 )G91 - 142
33X-RAY DIFFRACTION33chain 'G' and (resid 143 through 206 )G143 - 206
34X-RAY DIFFRACTION34chain 'G' and (resid 207 through 222 )G207 - 222
35X-RAY DIFFRACTION35chain 'G' and (resid 223 through 262 )G223 - 262
36X-RAY DIFFRACTION36chain 'H' and (resid 6 through 76 )H6 - 76
37X-RAY DIFFRACTION37chain 'H' and (resid 77 through 100 )H77 - 100
38X-RAY DIFFRACTION38chain 'H' and (resid 101 through 142 )H101 - 142
39X-RAY DIFFRACTION39chain 'H' and (resid 143 through 162 )H143 - 162
40X-RAY DIFFRACTION40chain 'H' and (resid 163 through 186 )H163 - 186
41X-RAY DIFFRACTION41chain 'H' and (resid 187 through 207 )H187 - 207
42X-RAY DIFFRACTION42chain 'H' and (resid 208 through 222 )H208 - 222
43X-RAY DIFFRACTION43chain 'H' and (resid 223 through 262 )H223 - 262

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