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- PDB-6b6m: Cyanase from Serratia proteamaculans -

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Basic information

Entry
Database: PDB / ID: 6b6m
TitleCyanase from Serratia proteamaculans
ComponentsCyanate hydrataseCyanase
KeywordsLYASE / Cyanase
Function / homology
Function and homology information


cyanate metabolic process / cyanase / cyanate hydratase activity / DNA binding
Similarity search - Function
Cyanate lyase, C-terminal / Cyanate hydratase / Cyanate lyase, C-terminal domain superfamily / Cyanate lyase C-terminal domain / Cyanate lyase C-terminal domain, Cyanate hydratase / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsXu, Y.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: SIMBAD: a sequence-independent molecular-replacement pipeline.
Authors: Simpkin, A.J. / Simkovic, F. / Thomas, J.M.H. / Savko, M. / Lebedev, A. / Uski, V. / Ballard, C. / Wojdyr, M. / Wu, R. / Sanishvili, R. / Xu, Y. / Lisa, M.N. / Buschiazzo, A. / Shepard, W. / ...Authors: Simpkin, A.J. / Simkovic, F. / Thomas, J.M.H. / Savko, M. / Lebedev, A. / Uski, V. / Ballard, C. / Wojdyr, M. / Wu, R. / Sanishvili, R. / Xu, Y. / Lisa, M.N. / Buschiazzo, A. / Shepard, W. / Rigden, D.J. / Keegan, R.M.
History
DepositionOct 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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: Cyanate hydratase
B: Cyanate hydratase
C: Cyanate hydratase
D: Cyanate hydratase
E: Cyanate hydratase


Theoretical massNumber of molelcules
Total (without water)85,8645
Polymers85,8645
Non-polymers00
Water8,953497
1
A: Cyanate hydratase
B: Cyanate hydratase
C: Cyanate hydratase
D: Cyanate hydratase
E: Cyanate hydratase

A: Cyanate hydratase
B: Cyanate hydratase
C: Cyanate hydratase
D: Cyanate hydratase
E: Cyanate hydratase


Theoretical massNumber of molelcules
Total (without water)171,72810
Polymers171,72810
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area60510 Å2
ΔGint-387 kcal/mol
Surface area50600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.560, 94.130, 89.110
Angle α, β, γ (deg.)90.00, 125.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-292-

HOH

21E-292-

HOH

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Components

#1: Protein
Cyanate hydratase / Cyanase / Cyanase / Cyanate hydrolase / Cyanate lyase


Mass: 17172.783 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia proteamaculans (strain 568) (bacteria)
Strain: 568 / Gene: cynS, Spro_1533 / Production host: Escherichia coli (E. coli) / References: UniProt: A8GBZ7, cyanase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5 / Details: 0.1M magnesium acetate 10%PEG10000 0.1M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.91→43.533 Å / Num. obs: 69947 / % possible obs: 97.9 % / Redundancy: 4 % / Rrim(I) all: 0.123 / Net I/σ(I): 10.26
Reflection shellResolution: 1.91→2 Å / Redundancy: 3.1 % / Num. unique obs: 8089 / Rrim(I) all: 0.833 / % possible all: 88.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→43.533 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.63
RfactorNum. reflection% reflection
Rfree0.2019 3547 5.07 %
Rwork0.16 --
obs0.1621 69940 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.91→43.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5982 0 0 497 6479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076158
X-RAY DIFFRACTIONf_angle_d0.8148389
X-RAY DIFFRACTIONf_dihedral_angle_d2.8265224
X-RAY DIFFRACTIONf_chiral_restr0.05996
X-RAY DIFFRACTIONf_plane_restr0.0061081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.93620.32621100.2861916X-RAY DIFFRACTION71
1.9362-1.96390.29321200.24832546X-RAY DIFFRACTION94
1.9639-1.99320.2541400.21222620X-RAY DIFFRACTION98
1.9932-2.02430.24661200.20272724X-RAY DIFFRACTION100
2.0243-2.05750.2381510.19682661X-RAY DIFFRACTION100
2.0575-2.0930.26341290.19152695X-RAY DIFFRACTION100
2.093-2.1310.25121590.18712666X-RAY DIFFRACTION100
2.131-2.1720.24051380.1772696X-RAY DIFFRACTION100
2.172-2.21640.22121480.17682649X-RAY DIFFRACTION100
2.2164-2.26460.22681580.17772700X-RAY DIFFRACTION100
2.2646-2.31720.21971590.16292690X-RAY DIFFRACTION100
2.3172-2.37520.23621420.16312699X-RAY DIFFRACTION100
2.3752-2.43940.20891540.16432666X-RAY DIFFRACTION100
2.4394-2.51120.21661580.16342664X-RAY DIFFRACTION100
2.5112-2.59220.20791540.16692690X-RAY DIFFRACTION100
2.5922-2.68480.20031440.16042673X-RAY DIFFRACTION100
2.6848-2.79230.20551370.16522707X-RAY DIFFRACTION100
2.7923-2.91940.18981180.1542708X-RAY DIFFRACTION100
2.9194-3.07330.17171400.15932720X-RAY DIFFRACTION100
3.0733-3.26570.20951520.152684X-RAY DIFFRACTION100
3.2657-3.51780.19621380.15212697X-RAY DIFFRACTION100
3.5178-3.87160.18781420.1472696X-RAY DIFFRACTION100
3.8716-4.43140.16651470.12732724X-RAY DIFFRACTION100
4.4314-5.58120.16841560.12782721X-RAY DIFFRACTION100
5.5812-43.54450.15611330.14832781X-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)
13.4719-1.48230.26392.0329-0.43891.4437-0.0771-0.1986-0.02760.22180.04210.13080.0381-0.09380.06520.1876-0.0073-0.00450.2239-0.07490.1531-4.1414-4.602823.0289
20.7163-0.00530.39592.66350.4362.885-0.0164-0.14310.48090.2188-0.0417-0.0745-0.13060.1526-0.00590.1677-0.0103-0.01020.1519-0.09420.24810.65023.816219.0666
34.82233.12462.94783.7402-0.06644.26730.2564-0.63820.60970.4429-0.34750.3173-0.34190.4224-0.0530.32980.0251-0.05680.3462-0.21610.2929-0.67144.760729.5206
47.4027-0.0091-3.23763.1784-0.06842.8734-0.0591-0.6325-0.35480.2596-0.1166-0.1283-0.035-0.25120.1520.28320.0348-0.05110.3759-0.09270.22351.4141-3.577331.2801
51.57170.28651.18710.22510.06081.15990.0062-0.0670.13540.0063-0.03860.0340.1037-0.04870.04160.17580.0115-0.00360.1295-0.0170.1523-0.4295-9.989910.748
61.46120.4854-0.2470.6062-0.16221.4949-0.07560.06210.11610.0097-0.0313-0.0739-0.14590.06380.11640.14830.0075-0.02820.13180.02320.19013.7536-1.1567-4.2598
77.7595-3.44410.93151.5657-0.36080.1982-0.0052-0.28510.57480.0459-0.0076-0.1358-0.158-0.05240.07680.3022-0.0186-0.08640.1753-0.04480.3722-3.12239.41895.7066
82.4512-2.60151.03663.0359-0.43882.17210.1340.13380.5181-0.3498-0.16530.2229-0.4356-0.19690.02160.28090.0388-0.0760.1734-0.04080.3138-8.170410.085-0.4837
97.3681-4.8961-1.03965.07730.13771.3017-0.1628-0.06340.18920.18730.3737-0.80360.26680.2754-0.1620.2323-0.0489-0.03060.2318-0.02570.323321.59930.9904-2.3801
102.5614-0.0665-0.96944.2263-2.29164.5032-0.1404-0.21070.0471-0.2749-0.20510.0194-0.3799-0.07880.28410.22180.0216-0.02510.22960.09380.198412.567-5.6313-15.8274
116.4985-1.88761.86544.1832-1.75721.5340.10350.447-0.267-0.264-0.02370.12890.2297-0.1378-0.06190.2207-0.02980.04870.20050.01480.151723.0854-19.0702-19.1417
121.1074-0.5662-1.72327.34382.39713.5276-0-0.0085-0.13130.5733-0.1145-0.67170.1490.22960.05930.08910.03710.07650.20450.00450.281535.3635-18.5596-14.6747
132.21780.84760.23581.4506-0.40861.9142-0.21810.0540.1944-0.27370.0762-0.32730.00910.05240.11210.1386-0.02580.04080.14310.01980.223828.4774-9.8412-10.3747
142.78480.23271.10625.9021-0.36744.0488-0.25450.250.2181-0.62830.1947-0.4316-0.18680.61430.07550.2678-0.02990.08730.29760.13080.295132.2254-7.9448-20.4807
150.93920.06440.23091.6558-0.5090.7673-0.02880.24640.1134-0.259-0.0267-0.03280.02470.04810.0460.16250.00340.0050.2010.04720.160219.3158-13.0652-14.3955
160.58840.0534-0.05481.17210.40941.2133-0.0457-0.04570.07270.1002-0.0263-0.0672-0.01090.02870.08380.13840.0097-0.01540.14970.00310.14718.8187-14.875510.8349
176.0094-6.30950.38988.0491-0.37020.4686-0.0381-0.05150.4686-0.3305-0.0034-0.851-0.16110.24510.05670.2041-0.04510.00050.23880.01190.307932.962-15.24632.9585
189.0998-7.11250.37086.6273-0.39662.24620.1569-0.1551-0.0042-0.1573-0.0617-0.83270.25290.3758-0.18890.149-0.0021-0.03910.2521-0.0040.208834.1829-21.30818.0552
197.3062-1.8192-0.55362.46130.26992.4030.2234-0.21880.84590.1994-0.1417-0.026-0.4036-0.5023-0.02390.21340.0391-0.00540.2198-0.05290.284714.71622.611112.9871
200.76560.21570.32832.3741-0.46572.5855-0.1073-0.1369-0.0129-0.1592-0.248-0.29380.10150.27940.43650.20630.02050.04190.22390.05610.243411.648-34.909123.0183
212.58541.9120.95237.20031.28811.5705-0.0138-0.11040.18660.426-0.11750.6858-0.0178-0.14580.14540.2050.03130.01230.2373-0.01470.12859.157-18.281128.9441
225.2398-3.5263-0.4896.52222.094.93620.15330.08590.06680.2856-0.0076-0.3516-0.18640.2061-0.13070.207-0.0104-0.03310.2029-0.03030.14920.6862-11.566829.8172
232.8813-0.8075-0.00372.4757-0.91482.65930.0447-0.341-0.00130.19240.0112-0.28330.08810.1299-0.00170.17290.0258-0.02730.1926-0.01510.142222.3529-21.577224.9497
244.6437-1.8508-0.07563.9748-1.74552.6861-0.2774-0.99930.18181.07050.3878-0.29360.3461-0.0085-0.01560.40350.0519-0.11910.4016-0.03470.167320.9412-22.651135.7888
255.8163-1.1316-1.65393.133.93884.9797-0.0386-0.7628-0.47841.029-0.12930.1751-0.0664-0.32790.04830.42760.03570.0240.32630.06870.134113.8379-27.478334.8929
260.1514-0.3262-0.09861.6307-0.69760.9115-0.0872-0.26990.09290.04280.22090.10550.0112-0.2476-0.1470.1293-0.016-0.02430.1492-0.00620.156710.761-22.358314.0467
271.2277-0.5187-0.33540.71920.35121.10980.02280.1046-0.0151-0.0862-0.0727-0.0921-0.05780.00220.0570.1333-0.02140.01080.12670.0150.174623.1402-19.43431.4012
280.12440.34380.21242.46461.57811.00010.018-0.1788-0.13120.37450.1635-0.72320.04020.1024-0.14030.18230.0107-0.03660.21880.00950.225828.389-12.554314.9196
291.906-0.85150.0952.04441.65781.7861-0.21260.05340.24790.3420.3136-0.4182-0.10930.1835-0.01290.1442-0.0188-0.01690.18270.00680.226328.2672-6.019410.2355
303.74492.19260.43867.49023.13753.4210.18420.3929-0.43530.24890.3448-0.31680.5361-0.1337-0.53620.20370.0234-0.04480.20740.00040.261331.3734-35.5140.4356
314.24362.1566-0.72925.0257-1.47455.2869-0.08530.0123-0.42440.2435-0.1390.13430.0419-0.32830.27560.1541-0.00230.03530.28060.02730.2529-9.9266-43.970616.5329
327.6242-0.78122.69712.7255-0.7851.9692-0.1564-0.55750.28010.04740.08410.0228-0.0742-0.33910.05330.2095-0.00210.01410.24060.03680.12593.3011-38.727327.2735
333.90153.08441.52877.45323.34456.23830.0985-0.5166-0.5625-0.02710.2073-0.38950.18240.1299-0.19960.2084-0.0017-0.05410.2360.10950.211813.3701-47.142427.8394
341.2481.0623-1.17194.0769-0.48552.1599-0.1299-0.3337-0.31380.23320.13080.05190.2766-0.053-0.03470.22180.01990.01190.14880.08180.21575.7165-50.451720.113
354.572-0.69881.22753.3210.28323.3548-0.0045-0.547-0.29840.509-0.10130.24740.0925-0.09260.12010.2657-0.02330.03340.3370.14080.2219-1.0493-49.677730.0887
360.6265-0.04810.29050.20660.21110.6107-0.0651-0.1359-0.08130.15020.0339-0.0964-0.079-0.1487-0.00950.16540.0292-0.00310.16230.03750.15971.938-38.880612.8748
370.7206-0.02490.32441.10150.65471.7369-0.00980.1004-0.1394-0.0940.0168-0.0766-0.02120.0283-0.01560.1240.00620.01630.1355-0.00460.17212.6055-44.3705-1.5948
385.48233.5534.62792.30613.0013.85440.2391-0.2402-0.00820.2261-0.1499-0.0670.438-0.0005-0.0980.24910.00650.01160.15410.07140.239117.9778-50.45912.0523
394.34853.15014.99454.16552.93575.99760.2889-0.0472-0.50280.2134-0.0392-0.56460.2120.1932-0.1660.14720.040.01120.12250.00740.29225.0972-47.14219.4237
408.6457-1.57355.05630.546-0.77663.48580.43010.2343-0.5082-0.38980.00870.07420.3171-0.3128-0.35210.2754-0.0111-0.03110.1797-0.07350.26361.025-56.4968-8.1654
411.4320.95890.30874.90140.42131.2765-0.01390.2868-0.0078-0.2209-0.03930.09460.00860.0230.03780.1781-0.0060.0390.2642-0.01830.1519.419-38.8816-18.5712
423.3654-0.0852-0.25571.9952-0.85451.57910.03750.1204-0.29960.0425-0.0155-0.11160.07690.00790.00070.11780.01220.02840.1633-0.0570.17525.6458-43.4069-11.296
431.50960.82550.9173.65660.72932.8245-0.18070.4709-0.2174-0.35260.1419-0.2942-0.00240.24280.09130.23830.00620.11320.2996-0.04620.234829.3459-38.934-21.7056
440.98090.02960.01150.30220.29730.73130.0189-0.0066-0.11610.0171-0.02380.00390.0542-0.12140.02830.12320.01350.00470.08780.00770.15510.925-39.86473.1904
450.7559-0.06410.11691.74090.56340.8390.01920.1234-0.1777-0.0789-0.0612-0.0709-0.04780.07310.09760.15120.04630.02530.2270.02350.250221.4617-45.60654.9071
467.35154.88663.48163.67843.40134.54690.1267-0.0866-0.82830.16940.0854-0.35420.5415-0.0014-0.13910.25490.05760.00270.19950.02150.362413.6893-56.77862.2763
470.8289-0.6743-0.49713.79353.87954.007-0.1533-0.33160.1134-0.20830.41-0.6067-0.47970.1886-0.2240.23490.0346-0.0110.2225-0.01560.265227.3327-32.786216.683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 91 )
6X-RAY DIFFRACTION6chain 'A' and (resid 92 through 125 )
7X-RAY DIFFRACTION7chain 'A' and (resid 126 through 134 )
8X-RAY DIFFRACTION8chain 'A' and (resid 135 through 148 )
9X-RAY DIFFRACTION9chain 'A' and (resid 149 through 156 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 8 )
11X-RAY DIFFRACTION11chain 'B' and (resid 9 through 24 )
12X-RAY DIFFRACTION12chain 'B' and (resid 25 through 33 )
13X-RAY DIFFRACTION13chain 'B' and (resid 34 through 54 )
14X-RAY DIFFRACTION14chain 'B' and (resid 55 through 65 )
15X-RAY DIFFRACTION15chain 'B' and (resid 66 through 91 )
16X-RAY DIFFRACTION16chain 'B' and (resid 92 through 125 )
17X-RAY DIFFRACTION17chain 'B' and (resid 126 through 134 )
18X-RAY DIFFRACTION18chain 'B' and (resid 135 through 148 )
19X-RAY DIFFRACTION19chain 'B' and (resid 149 through 156 )
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 8 )
21X-RAY DIFFRACTION21chain 'C' and (resid 9 through 25 )
22X-RAY DIFFRACTION22chain 'C' and (resid 26 through 33 )
23X-RAY DIFFRACTION23chain 'C' and (resid 34 through 54 )
24X-RAY DIFFRACTION24chain 'C' and (resid 55 through 65 )
25X-RAY DIFFRACTION25chain 'C' and (resid 66 through 76 )
26X-RAY DIFFRACTION26chain 'C' and (resid 77 through 91 )
27X-RAY DIFFRACTION27chain 'C' and (resid 92 through 125 )
28X-RAY DIFFRACTION28chain 'C' and (resid 126 through 134 )
29X-RAY DIFFRACTION29chain 'C' and (resid 135 through 148 )
30X-RAY DIFFRACTION30chain 'C' and (resid 149 through 156 )
31X-RAY DIFFRACTION31chain 'D' and (resid 2 through 8 )
32X-RAY DIFFRACTION32chain 'D' and (resid 9 through 25 )
33X-RAY DIFFRACTION33chain 'D' and (resid 26 through 33 )
34X-RAY DIFFRACTION34chain 'D' and (resid 34 through 54 )
35X-RAY DIFFRACTION35chain 'D' and (resid 55 through 75 )
36X-RAY DIFFRACTION36chain 'D' and (resid 76 through 91 )
37X-RAY DIFFRACTION37chain 'D' and (resid 92 through 125 )
38X-RAY DIFFRACTION38chain 'D' and (resid 126 through 134 )
39X-RAY DIFFRACTION39chain 'D' and (resid 135 through 148 )
40X-RAY DIFFRACTION40chain 'D' and (resid 149 through 156 )
41X-RAY DIFFRACTION41chain 'E' and (resid 2 through 32 )
42X-RAY DIFFRACTION42chain 'E' and (resid 33 through 54 )
43X-RAY DIFFRACTION43chain 'E' and (resid 55 through 76 )
44X-RAY DIFFRACTION44chain 'E' and (resid 77 through 115 )
45X-RAY DIFFRACTION45chain 'E' and (resid 116 through 134 )
46X-RAY DIFFRACTION46chain 'E' and (resid 135 through 148 )
47X-RAY DIFFRACTION47chain 'E' and (resid 149 through 156 )

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