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- PDB-6muh: Fluoroacetate dehalogenase, room temperature structure solved by ... -

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Basic information

Entry
Database: PDB / ID: 6muh
TitleFluoroacetate dehalogenase, room temperature structure solved by serial 1 degree oscillation crystallography
ComponentsFluoroacetate dehalogenaseHaloacetate dehalogenase
KeywordsHYDROLASE / Dehalogenase / defluorinase
Function / homology
Function and homology information


haloacetate dehalogenase / haloacetate dehalogenase activity
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFinke, A.D. / Wierman, J.L. / Pare-Labrosse, O. / Sarrachini, A. / Besaw, J. / Mehrabi, P. / Gruner, S.M. / Miller, R.J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
CitationJournal: IUCrJ / Year: 2019
Title: Fixed-target serial oscillation crystallography at room temperature.
Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / ...Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / Szebenyi, D.M.E. / Gruner, S.M. / Miller, R.J.D. / Finke, A.D.
History
DepositionOct 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluoroacetate dehalogenase
B: Fluoroacetate dehalogenase


Theoretical massNumber of molelcules
Total (without water)68,1472
Polymers68,1472
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-18 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.600, 79.100, 83.800
Angle α, β, γ (deg.)90.00, 103.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fluoroacetate dehalogenase / Haloacetate dehalogenase


Mass: 34073.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (unknown)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA1163 / Production host: Escherichia coli BL21(DE3) (unknown) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.5 mM defluorinase with a mother liquor of 16-20% PEG 3350, 100mM Tris-Cl pH 8.5, and 200mM CaCl2

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: G3 / Type: CHESS BEAMLINE F3 / Wavelength: 1.2155 Å
DetectorType: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Mar 4, 2018
RadiationMonochromator: W/B4C Multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2155 Å / Relative weight: 1
ReflectionResolution: 1.8→40.826 Å / Num. obs: 48288 / % possible obs: 98.42 % / Redundancy: 6.3 % / CC1/2: 0.993 / Rrim(I) all: 0.188 / Net I/σ(I): 9.33
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 4597 / CC1/2: 0.176 / Rrim(I) all: 0.03651
Serial crystallography sample deliveryDescription: fixed target Si microchips / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Si wafers / Details: oscillation 1 degree per crystal / Motion control: Geobrick LV-IMS-II / Sample dehydration prevention: mylar windows / Sample holding: wells on silicon wafers / Sample unit size: 50 µm / Support base: piezoelectric translation stage on goniometer
Serial crystallography data reductionFrames indexed: 2269 / Frames total: 67055

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FSX
Resolution: 1.8→40.826 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.98
RfactorNum. reflection% reflection
Rfree0.1813 2413 5 %
Rwork0.1518 --
obs0.1533 48271 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→40.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4712 0 0 211 4923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074924
X-RAY DIFFRACTIONf_angle_d0.966713
X-RAY DIFFRACTIONf_dihedral_angle_d16.0053978
X-RAY DIFFRACTIONf_chiral_restr0.051688
X-RAY DIFFRACTIONf_plane_restr0.006884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83680.41761330.3852520X-RAY DIFFRACTION93
1.8368-1.87670.32311380.32212629X-RAY DIFFRACTION97
1.8767-1.92040.30061400.2762678X-RAY DIFFRACTION97
1.9204-1.96840.31381410.24692682X-RAY DIFFRACTION98
1.9684-2.02160.26931400.23432660X-RAY DIFFRACTION98
2.0216-2.08110.26071440.22242740X-RAY DIFFRACTION99
2.0811-2.14830.26651400.19772653X-RAY DIFFRACTION99
2.1483-2.2250.19511420.17142699X-RAY DIFFRACTION99
2.225-2.31410.21741440.16652736X-RAY DIFFRACTION99
2.3141-2.41940.1861430.15132715X-RAY DIFFRACTION99
2.4194-2.5470.20411420.15562697X-RAY DIFFRACTION99
2.547-2.70650.2031430.14992714X-RAY DIFFRACTION99
2.7065-2.91540.20431430.15252725X-RAY DIFFRACTION99
2.9154-3.20870.14551460.13882767X-RAY DIFFRACTION100
3.2087-3.67280.15791430.11652706X-RAY DIFFRACTION99
3.6728-4.62630.10951460.10432775X-RAY DIFFRACTION99
4.6263-40.83660.14911450.12612762X-RAY DIFFRACTION99
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)
11.8434-0.1826-0.21573.25860.77524.3817-0.0293-0.3939-0.12140.30970.0491-0.07870.42380.1151-0.03830.22040.02750.00280.23150.05140.1913-13.9274-72.7836102.8325
21.59450.1229-0.15072.30430.64947.39750.0464-0.13150.01920.0187-0.02330.1539-0.0777-0.4254-0.02460.11780.01670.010.2126-0.01020.2446-23.1513-64.0595.0776
32.4776-0.01670.13833.53910.54435.52060.0303-0.2620.22830.1902-0.0201-0.0977-0.16340.0143-0.00960.15450.00080.00280.1841-0.01560.1941-11.6208-58.294296.5973
40.9795-0.4059-0.77320.82651.15663.9710.04210.05960.1281-0.02790.1732-0.1073-0.0990.4213-0.21670.23260.00160.00140.19950.0130.2461-8.6484-59.948377.5797
54.0493-1.46152.4372.2147-0.93874.59580.01780.1869-0.1468-0.05830.0429-0.16120.43760.2954-0.0930.240.03130.02580.1596-0.00410.2683-9.2901-77.95683.6558
61.69681.00030.63432.45321.39972.1216-0.02370.02470.1853-0.0603-0.03010.1428-0.213-0.07040.04210.18110.03880.00550.15980.01050.201-18.6251-60.611183.643
76.384-4.292-1.33467.63370.52553.36410.109-0.01240.2608-0.2144-0.0681-0.4332-0.23570.5725-0.08150.2436-0.0621-0.00770.3089-0.04160.3244-1.9522-54.196694.0968
82.8708-1.7054-1.29365.14452.17692.5261-0.0175-0.4427-0.03140.56470.2887-0.49470.30250.7275-0.23760.20250.0415-0.04940.42640.00530.30330.1993-67.564499.9673
93.60580.21-1.35661.4856-0.31944.7310.02330.59-0.133-0.2759-0.02220.09640.2701-0.4742-0.01420.2772-0.0386-0.00970.3525-0.05030.1957-11.367-67.873241.0846
102.68311.3459-1.10673.1491-1.83128.33390.03250.0163-0.20420.0458-0.1161-0.09630.46550.41770.09350.19860.04380.02980.2233-0.02840.23121.0327-69.679448.8844
116.27530.354-1.92891.8038-0.19664.39140.06850.30840.3663-0.05610.0446-0.0321-0.3062-0.0462-0.11750.234-0.02460.00680.21630.00170.2014-2.9848-57.261349.3631
122.85080.035-2.20920.21970.73124.31180.11150.15110.23410.0340.12890.0289-0.3891-0.0164-0.25090.2262-0.0092-0.01130.1827-0.00250.1719-6.9441-59.656367.9584
138.4093-2.46494.13681.6077-1.41065.5623-0.117-0.12-0.24890.02620.24450.12690.2547-0.4183-0.15430.2615-0.08140.03580.25040.00460.2327-19.2692-71.229459.3535
142.25950.5688-0.48272.2511-1.67462.626-0.0062-0.18450.12570.0342-0.0574-0.1893-0.19950.16170.09070.2428-0.01130.03010.2211-0.06970.1803-0.8668-60.261757.4374
156.943.33190.26155.10931.29632.04290.2339-0.0120.5981-0.0547-0.19740.323-0.4138-0.3891-0.02280.33940.07280.03950.33010.05280.3231-13.2532-50.965350.4122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 104 )
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 164 )
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 208 )
6X-RAY DIFFRACTION6chain 'A' and (resid 209 through 235 )
7X-RAY DIFFRACTION7chain 'A' and (resid 236 through 276 )
8X-RAY DIFFRACTION8chain 'A' and (resid 277 through 300 )
9X-RAY DIFFRACTION9chain 'B' and (resid 4 through 63 )
10X-RAY DIFFRACTION10chain 'B' and (resid 64 through 104 )
11X-RAY DIFFRACTION11chain 'B' and (resid 105 through 137 )
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 164 )
13X-RAY DIFFRACTION13chain 'B' and (resid 165 through 208 )
14X-RAY DIFFRACTION14chain 'B' and (resid 209 through 249 )
15X-RAY DIFFRACTION15chain 'B' and (resid 250 through 300 )

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