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- PDB-5nyv: Crystal structure determination from picosecond infrared laser ab... -

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Basic information

Entry
Database: PDB / ID: 5nyv
TitleCrystal structure determination from picosecond infrared laser ablated protein crystals by serial synchrotron crystallography
ComponentsFluoroacetate dehalogenaseHaloacetate dehalogenase
KeywordsHYDROLASE / SSX / PIRL / serial crystallography / fixed target
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 ATCC 17001 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchulz, E.C. / Kaub, J. / Busse, F. / Mehrabi, P. / Mueller-Werkmeiser, H. / Pai, E.F. / Robertson, W.D. / Miller, R.J.D.
CitationJournal: J.Appl.Crystallogr. / Year: 2017
Title: Protein crystals IR laser ablated from aqueous solution at high speed retain their diffractive properties: applications in high-speed serial crystallography.
Authors: Schulz, E.C. / Kaub, J. / Busse, F. / Mehrabi, P. / Muller-Werkmeister, H.M. / Pai, E.F. / Robertson, W.D. / Miller, R.J.D.
History
DepositionMay 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell

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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
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-19 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.535, 80.889, 85.633
Angle α, β, γ (deg.)90.00, 102.72, 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 ATCC 17001 (phototrophic)
Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5
Details: 18-20 % (w/v) PEG3350, 200 mM CaCl2, and 100 mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→83.7 Å / Num. obs: 4516925 / % possible obs: 99.7 % / Redundancy: 59.4 % / Net I/σ(I): 4.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2666: ???)refinement
cctbx.xfeldata reduction
cctbx.primedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→83.534 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.08
RfactorNum. reflection% reflection
Rfree0.2193 1995 2.68 %
Rwork0.1926 --
obs0.1933 74331 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→83.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4687 0 0 389 5076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044877
X-RAY DIFFRACTIONf_angle_d0.8336647
X-RAY DIFFRACTIONf_dihedral_angle_d22.9822871
X-RAY DIFFRACTIONf_chiral_restr0.046682
X-RAY DIFFRACTIONf_plane_restr0.005872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.3391400.32494995X-RAY DIFFRACTION96
1.64-1.68440.32541360.29175114X-RAY DIFFRACTION100
1.6844-1.73390.2741370.2535144X-RAY DIFFRACTION100
1.7339-1.78990.25381410.23145162X-RAY DIFFRACTION100
1.7899-1.85390.25991390.21175211X-RAY DIFFRACTION100
1.8539-1.92810.21871560.18915127X-RAY DIFFRACTION100
1.9281-2.01590.21711390.18495192X-RAY DIFFRACTION100
2.0159-2.12220.24861440.22985167X-RAY DIFFRACTION100
2.1222-2.25510.21081440.19295169X-RAY DIFFRACTION100
2.2551-2.42930.21121380.17235166X-RAY DIFFRACTION100
2.4293-2.67370.19131440.16545202X-RAY DIFFRACTION100
2.6737-3.06070.17021410.16055198X-RAY DIFFRACTION100
3.0607-3.85610.17531470.14225199X-RAY DIFFRACTION100
3.8561-83.64750.16421490.13355290X-RAY DIFFRACTION100
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)
10.4349-0.19-0.59561.29230.21520.81740.0106-0.0081-0.00780.05190.011-0.00320.073-0.0292-0.02450.13620.0071-0.00750.11410.07090.092920.0512-79.3858147.4798
22.5841-1.08580.1582.4966-0.93441.8544-0.0271-0.0907-0.1830.04980.02310.12520.0887-0.0172-0.0110.0436-0.01190.02380.1371-0.00430.08066.0627-68.7352144.2735
30.10480.0061-0.01430.26180.07410.15050.0119-0.0552-0.02740.07090.0129-0.02530.05710.00350.02150.03190.0095-0.01020.04450.02780.022920.7876-69.5734144.2761
41.2785-0.9596-0.59431.68720.84152.9473-0.001-0.05210.01830.09840.0433-0.14890.05410.2192-0.03820.11870.0104-0.04820.15910.01270.063627.8058-69.727152.5756
51.1680.26860.78420.32570.30271.16320.0098-0.056-0.07540.018-0.01060.00820.0544-0.0428-0.02380.01070.00350.01090.03640.01350.026312.8802-69.7153139.2634
62.8213-0.5395-0.26522.2935-0.96384.1179-0.00390.16180.1239-0.21360.03890.3266-0.0735-0.3134-0.02580.04940.0294-0.03180.09430.00740.09614.7616-58.9836126.7137
70.0392-0.02550.0320.0434-0.01690.6615-0.0062-0.08510.00710.05920.01340.0447-0.0118-0.06760.01290.03660.02060.0170.083-0.00540.039510.4449-59.2037143.8299
80.311-0.09850.00520.3857-0.0010.60.0008-0.03010.05780.020.0075-0.0091-0.06280.0066-0.01540.0108-0.0010.00520.0075-0.00890.022122.4369-54.9576137.6741
91.40810.934-0.79952.99320.20914.75090.0401-0.05430.07160.062-0.03820.0662-0.1183-0.04710.01140.0728-0.04450.02240.1038-0.03580.067230.9357-56.8492118.7645
100.30120.12930.04520.40640.04840.178-0.00350.0127-0.0201-0.0250.01170.01530.0127-0.00570.01380.023-0.0054-0.00640.0024-0.00330.030317.888-64.931118.6044
112.99640.22852.18990.43720.37272.16940.02040.021-0.0779-0.01470.0148-0.03160.0650.032-0.02610.0681-00.00040.0310.00530.058322.3247-76.3342122.532
120.8368-0.1795-0.40841.4755-0.76271.08580.0063-0.02680.0023-0.0158-0.0319-0.11590.02140.07670.05580.06990.0465-0.01970.074-0.00710.130131.9134-76.0892132.1385
130.43840.2310.20190.41730.09090.3720.0256-0.0053-0.0788-0.01350.00160.01440.0589-0.0059-0.0230.0499-0.0124-0.00690.00820.00280.054215.4074-77.3711130.2857
140.1420.15450.06810.5320.14790.1406-0.0184-0.01250.0290.0034-0.00160.0135-0.0337-0.0083-0.01190.03270.0225-0.0101-0.0129-0.00710.039115.0092-57.0033126.9897
150.4623-0.72011.06351.1224-1.65862.4528-0.027-0.00170.03580.0234-0.004-0.0254-0.05320.00460.02030.10170.009-0.01640.028-0.01340.090623.2711-44.8029139.9635
161.3297-0.4822-0.0540.44630.0050.00320.01840.11610.0017-0.0376-0.0153-0.06150.01220.0754-0.00690.02970.00620.00760.1003-0.02830.107434.9906-59.2588134.261
172.0314-0.5657-0.82391.204-0.16521.7196-0.00530.10270.0018-0.12940.0201-0.2205-0.06980.2043-0.01870.0895-0.0411-0.00410.1258-0.04110.143633.8955-50.6748134.0885
180.5253-0.54320.06891.15410.31830.315-0.0313-0.06970.10440.06930.0178-0.1439-0.01830.0416-0.00930.0346-0.0064-0.00590.0941-0.03740.114133.2804-53.9882139.2624
190.51040.1472-0.05090.64350.70450.8932-0.0071-0.0537-0.02470.0550.0055-0.09330.03750.08950.00050.05150.0399-0.03310.10920.00090.125833.878-69.4975140.8477
201.41230.68810.09382.68240.49084.4213-0.0082-0.0868-0.03140.11640.0261-0.13870.10580.1729-0.01830.11290.0002-0.05260.1566-0.01750.073832.109-60.7942151.3058
213.0919-0.5559-0.32730.3857-0.04084.9276-0.0614-0.1164-0.1668-0.0520.02960.08070.3132-0.28390.02770.1838-0.0333-0.03410.2216-0.0730.115314.3864-72.860683.1074
225.01730.65172.10252.7789-0.08323.45250.04280.1028-0.1385-0.0905-0.01560.06450.1414-0.0624-0.03160.17660.01880.05770.1332-0.03190.113832.5859-74.51985.1754
230.1184-0.0106-0.09830.2427-0.03220.1488-0.00690.0806-0.0079-0.0817-0.00160.0140.0201-0.03890.0030.0712-0.03740.00390.1371-0.01670.032921.8386-64.648186.6303
241.89930.7167-1.30561.1018-0.53813.44670.01840.12230.13350.02970.04710.1035-0.176-0.2429-0.06650.1244-0.0008-0.00910.16920.01950.038617.2945-58.309679.1136
250.2125-0.27710.23880.7841-0.29211.18810.01740.0332-0.0413-0.0218-0.01540.03860.0897-0.0232-0.01540.0993-0.03390.01580.0795-0.03380.050627.0634-71.396591.567
264.72081.50232.72146.17084.32219.22250.06340.0058-0.24570.26480.1391-0.50650.23250.3183-0.20080.13860.02330.01680.13270.01420.137840.2798-72.6902103.99
270.1673-0.01420.15820.1327-0.12981.46130.0210.06460.0043-0.0556-0.0106-0.01430.06160.0374-0.00030.0795-0.00630.02170.0987-0.01480.03336.2268-64.797189.0288
280.4911-0.0297-0.05680.26810.00490.62180.01190.06190.0382-0.0314-0.006-0.0235-0.05310.0228-0.01180.0602-0.02930.01150.0712-0.00940.025830.6216-54.869592.7885
291.7-0.03970.22162.59630.14572.73590.003-0.04560.19080.04780.0050.0769-0.2166-0.05790.00280.13280.0045-0.00190.0677-0.03560.078329.3333-51.0797109.2537
300.79540.5075-0.03393.2641.58451.5309-0.02140.07030.095-0.16210.01220.0762-0.1111-0.05010.01810.11310.00060.01850.03340.00360.050620.8718-54.548113.8669
310.4889-0.04420.12321.0220.00130.3709-0.0031-0.0375-0.07620.05340.03040.02590.0638-0.0035-0.01090.060.0070.00530.0414-0.0010.034726.1715-69.105112.1445
322.1239-1.33660.8413.4221-1.92682.4841-0.0012-0.0424-0.09540.03630.02210.08610.0736-0.0531-0.02340.0809-0.03580.00380.08920.02530.066913.5909-70.2276106.6352
331.5997-0.3311-0.18971.83231.20332.05970.02980.00840.0075-0.0284-0.00960.0442-0.053-0.08720.00740.0636-0.0249-0.01510.11860.00280.05919.3793-64.833997.6751
340.66310.04260.38811.84740.17982.37830.05180.0162-0.1782-0.0295-0.01260.06550.1534-0.0508-0.02420.1317-0.04790.02580.0638-0.02870.088920.8222-76.7100.8808
350.44140.3067-0.09980.7155-0.23970.4519-0.0074-0.02240.03770.0437-0.0082-0.0293-0.06580.0397-0.00580.0581-0.03340.00020.0603-0.03250.044135.5323-59.84104.5931
361.7248-0.0627-0.30760.6196-0.02570.6910.0124-0.07580.02240.0462-0.0248-0.0122-0.03930.02480.00740.1367-0.00460.03440.09220.01730.108726.1402-47.799494.2927
370.87920.29560.77381.56680.93881.02650.0574-0.3274-0.08690.3193-0.05320.07180.0537-0.0517-0.00520.2654-0.00110.01750.26610.01010.261420.9039-46.4609104.1629
382.05540.160.06790.2976-0.11960.23170.0019-0.00050.24680.01380.02130.0472-0.1469-0.0547-0.00360.1702-0.04610.04160.1130.02720.151426.9374-43.473995.1467
391.79450.39820.68291.2424-0.03933.0414-0.00140.0150.1222-0.0404-0.01410.1284-0.1359-0.16220.00950.04110.01760.01240.13650.02580.104612.1489-55.503494.1406
401.79411.0509-0.40471.9635-0.77242.91040.0250.11550.1692-0.0330.04130.1344-0.1214-0.1643-0.06350.19940.0367-0.03970.21460.06170.104718.1666-49.800983.4832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:13)
2X-RAY DIFFRACTION2(chain A and resid 14:23)
3X-RAY DIFFRACTION3(chain A and resid 24:48)
4X-RAY DIFFRACTION4(chain A and resid 49:59)
5X-RAY DIFFRACTION5(chain A and resid 60:74)
6X-RAY DIFFRACTION6(chain A and resid 75:81)
7X-RAY DIFFRACTION7(chain A and resid 82:103)
8X-RAY DIFFRACTION8(chain A and resid 104:144)
9X-RAY DIFFRACTION9(chain A and resid 145:152)
10X-RAY DIFFRACTION10(chain A and resid 153:169)
11X-RAY DIFFRACTION11(chain A and resid 170:182)
12X-RAY DIFFRACTION12(chain A and resid 183:199)
13X-RAY DIFFRACTION13(chain A and resid 200:211)
14X-RAY DIFFRACTION14(chain A and resid 212:233)
15X-RAY DIFFRACTION15(chain A and resid 234:244)
16X-RAY DIFFRACTION16(chain A and resid 245:256)
17X-RAY DIFFRACTION17(chain A and resid 257:264)
18X-RAY DIFFRACTION18(chain A and resid 265:280)
19X-RAY DIFFRACTION19(chain A and resid 281:291)
20X-RAY DIFFRACTION20(chain A and resid 292:299)
21X-RAY DIFFRACTION21(chain B and resid 2:13)
22X-RAY DIFFRACTION22(chain B and resid 14:22)
23X-RAY DIFFRACTION23(chain B and resid 23:48)
24X-RAY DIFFRACTION24(chain B and resid 49:60)
25X-RAY DIFFRACTION25(chain B and resid 61:74)
26X-RAY DIFFRACTION26(chain B and resid 75:79)
27X-RAY DIFFRACTION27(chain B and resid 80:103)
28X-RAY DIFFRACTION28(chain B and resid 104:139)
29X-RAY DIFFRACTION29(chain B and resid 140:145)
30X-RAY DIFFRACTION30(chain B and resid 146:154)
31X-RAY DIFFRACTION31(chain B and resid 155:170)
32X-RAY DIFFRACTION32(chain B and resid 171:183)
33X-RAY DIFFRACTION33(chain B and resid 184:202)
34X-RAY DIFFRACTION34(chain B and resid 203:212)
35X-RAY DIFFRACTION35(chain B and resid 213:237)
36X-RAY DIFFRACTION36(chain B and resid 238:253)
37X-RAY DIFFRACTION37(chain B and resid 254:260)
38X-RAY DIFFRACTION38(chain B and resid 261:276)
39X-RAY DIFFRACTION39(chain B and resid 277:288)
40X-RAY DIFFRACTION40(chain B and resid 289:299)

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