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- PDB-6i9w: Crystal structure of the halohydrin dehalogenase HheG T123G mutant -

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Basic information

Entry
Database: PDB / ID: 6i9w
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 / (R,R)-2,3-BUTANEDIOL / Putative oxidoreductase / Putative oxidoreductase
Function and homology information
Biological speciesIlumatobacter coccineus YM16-304 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,06413
Polymers109,4724
Non-polymers5929
Water15,043835
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13320 Å2
ΔGint-107 kcal/mol
Surface area35140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.613, 107.422, 67.244
Angle α, β, γ (deg.)90.000, 90.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative oxidoreductase


Mass: 27368.002 Da / Num. of mol.: 4
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: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 835 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris/HCl pH 8.5 25% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.953714 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953714 Å / Relative weight: 1
ReflectionResolution: 1.55→107.42 Å / Num. obs: 135686 / % possible obs: 99.3 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Net I/σ(I): 15.6 / Num. measured all: 907391 / Scaling rejects: 436
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.586.70.4964469066560.8840.2050.5373.198.6
8.49-107.427.10.024621487110.010.02653.799.9

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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

5o30


Resolution: 1.55→53.711 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 15.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.159 6863 5.06 %
Rwork0.138 128770 -
obs0.1391 135633 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.24 Å2 / Biso mean: 25.4128 Å2 / Biso min: 8.71 Å2
Refinement stepCycle: final / Resolution: 1.55→53.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7622 0 84 835 8541
Biso mean--38.48 31.18 -
Num. residues----1032
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.56760.21942420.2144428199
1.5676-1.58610.19852100.207421397
1.5861-1.60540.19492200.1985427299
1.6054-1.62570.22412500.1953418898
1.6257-1.64710.21542360.1906426699
1.6471-1.66970.19942020.1834425798
1.6697-1.69350.19912340.1739425799
1.6935-1.71880.21482240.175423798
1.7188-1.74570.20162130.168427399
1.7457-1.77430.19082160.1621430699
1.7743-1.80490.15662750.1519420698
1.8049-1.83770.15732260.1474427299
1.8377-1.87310.16341980.1411432399
1.8731-1.91130.15542510.1382425999
1.9113-1.95290.16472410.1411427199
1.9529-1.99830.15911960.138429999
1.9983-2.04830.162410.1406426799
2.0483-2.10370.17692210.1363431199
2.1037-2.16560.14162370.1311427199
2.1656-2.23550.15451880.125434799
2.2355-2.31540.13452330.12024314100
2.3154-2.40810.142440.12314291100
2.4081-2.51770.16372280.12544331100
2.5177-2.65040.16921880.12184371100
2.6504-2.81640.13672560.13074313100
2.8164-3.03390.1612350.13434330100
3.0339-3.33910.15531970.1354381100
3.3391-3.82220.14042480.12344321100
3.8222-4.81510.13532580.1134335100
4.8151-53.7110.17222550.15364407100
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)
13.2156-0.31780.42671.18970.99012.41660.12440.24240.1477-0.26770.0053-0.4394-0.1310.1871-0.05430.1230.02250.07150.1398-0.01840.22058.0732-24.4219-5.8543
20.8576-0.6241-0.07241.43440.18790.33890.12470.14280.0302-0.2326-0.0996-0.1452-0.04280.0236-0.02350.12420.0170.02230.13030.00460.1036-6.8047-16.7993-5.386
31.52040.32650.10471.58610.74221.0598-0.00180.04380.1994-0.15990.0954-0.3319-0.19240.2159-0.04990.1098-0.03370.01630.13580.00430.17172.184-11.44418.0234
41.7010.5578-0.07752.14490.031.66140.04990.04520.1245-0.145-0.03180.32280.0042-0.0603-0.00470.11810.0217-0.04780.13950.01290.2047-38.18738.4599-2.0572
55.28270.4356-0.49571.5893-2.42873.71860.22190.7348-0.5099-0.7663-0.09280.58620.5901-0.3735-0.0520.29670.0006-0.16590.2897-0.01590.3677-46.41511.6719-9.5845
62.956-1.6551-0.68462.5610.07241.21180.20040.4710.0789-0.554-0.20070.13670.1655-0.05410.00620.27020.05-0.05410.20120.02990.1629-32.57959.309-12.8088
70.6685-0.5015-0.0111.26540.05110.19080.07830.09170.0009-0.2015-0.09030.1015-0.007-0.01640.01550.12820.0183-0.01840.12690.00240.1091-23.3948-4.9042-3.9796
81.4165-0.2939-0.82051.5376-1.02181.4358-0.10540.1076-0.0506-0.41050.07260.20970.1477-0.10950.02640.11290.0119-0.0290.1098-0.00470.0942-29.7593-2.8162.5678
97.62674.09873.94943.6730.86934.06110.060.6005-0.4507-0.93440.35560.2480.6715-0.3073-0.3250.4569-0.1262-0.10410.3580.01060.5639-42.3801-21.58553.8233
100.88180.04890.2521.9738-0.09150.6480.0202-0.0563-0.04080.01670.02060.32110.0152-0.123-0.04080.0926-0.00650.00490.1343-0.00010.1477-32.763-2.55759.8075
111.7783-0.56390.32952.40520.28752.08410.0206-0.3178-0.2390.3235-0.0155-0.10920.23630.04010.00350.2161-0.0031-0.08330.20690.06670.16763.0391-30.589831.3207
120.6063-0.2653-0.08780.9536-0.07980.75380.0036-0.1081-0.05370.2257-0.0162-0.04050.05840.0040.00980.1505-0.0241-0.03150.13120.02070.0974-9.174-20.734325.7132
132.4242-0.73720.1131.219-0.52772.1908-0.0633-0.34780.20510.55460.07770.2843-0.3236-0.1197-0.01560.36120.00860.14880.2412-0.07410.2307-35.779510.067833.018
140.466-0.30290.17581.1749-0.01060.5356-0.0119-0.13290.0550.2881-0.01370.0982-0.0398-0.04140.01680.1633-0.02280.03550.1499-0.0240.1023-24.18940.75826.2295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 61 )A4 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 207 )A62 - 207
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 262 )A208 - 262
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 38 )B4 - 38
5X-RAY DIFFRACTION5chain 'B' and (resid 39 through 61 )B39 - 61
6X-RAY DIFFRACTION6chain 'B' and (resid 62 through 91 )B62 - 91
7X-RAY DIFFRACTION7chain 'B' and (resid 92 through 182 )B92 - 182
8X-RAY DIFFRACTION8chain 'B' and (resid 183 through 206 )B183 - 206
9X-RAY DIFFRACTION9chain 'B' and (resid 207 through 222 )B207 - 222
10X-RAY DIFFRACTION10chain 'B' and (resid 223 through 262 )B223 - 262
11X-RAY DIFFRACTION11chain 'C' and (resid 6 through 76 )C6 - 76
12X-RAY DIFFRACTION12chain 'C' and (resid 77 through 262 )C77 - 262
13X-RAY DIFFRACTION13chain 'D' and (resid 6 through 76 )D6 - 76
14X-RAY DIFFRACTION14chain 'D' and (resid 77 through 262 )D77 - 262

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