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- PDB-8cfw: Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. ... -

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Basic information

Entry
Database: PDB / ID: 8cfw
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H05
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / Fragment screening / protein-ligand complex / drug discovery / SAM-DEPENDENT METHYLATION REACTIONS / SAHase / AHCY
Function / homology
Function and homology information


L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol
Similarity search - Function
Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENINE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Chem-RE4 / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsMalecki, P.H. / Gawel, M. / Stepniewska, M. / Brzezinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA BIS 2018/30/E/NZ1/00729 Poland
CitationJournal: To be published
Title: Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with fragment F2X-Entry H05
Authors: Malecki, P.H. / Gawel, M. / Stepniewska, M. / Brzezinski, K.
History
DepositionFeb 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,70439
Polymers206,9404
Non-polymers5,76435
Water28,8421601
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33690 Å2
ΔGint-234 kcal/mol
Surface area56300 Å2
Unit cell
Length a, b, c (Å)73.830, 132.770, 98.480
Angle α, β, γ (deg.)90.00, 100.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase


Mass: 51735.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: ahcY, sahH, PA0432 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase

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Non-polymers , 7 types, 1636 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5
#4: Chemical ChemComp-RE4 / 6-methyl-N~4~-[(pyridin-3-yl)methyl]pyrimidine-2,4-diamine


Mass: 215.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1601 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM KH2PO4, 20% (w/v) PEG8000, 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 27, 2021
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.61→46.12 Å / Num. obs: 234190 / % possible obs: 97.3 % / Redundancy: 4.66 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.098 / Net I/σ(I): 10.87
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.61-1.711.322369000.4721.51
1.71-1.820.829353080.7070.9311
1.82-1.970.47330330.8880.5271
1.97-2.160.251304890.9590.2831
2.16-2.410.143277360.9840.1631
2.41-2.780.089245780.9940.1011
2.78-3.410.053208760.9970.0591
3.41-4.80.032162320.9990.0361
4.8-46.120.02890380.9990.0311

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→36.28 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1821 2458 1.05 %
Rwork0.158 --
obs0.1582 234137 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14228 0 361 1601 16190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715010
X-RAY DIFFRACTIONf_angle_d0.85720368
X-RAY DIFFRACTIONf_dihedral_angle_d13.7085570
X-RAY DIFFRACTIONf_chiral_restr0.0572267
X-RAY DIFFRACTIONf_plane_restr0.0072691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.640.31291300.314612281X-RAY DIFFRACTION93
1.64-1.670.31281340.288412655X-RAY DIFFRACTION96
1.67-1.710.33981350.274112708X-RAY DIFFRACTION97
1.71-1.750.26261350.252212732X-RAY DIFFRACTION97
1.75-1.790.2521360.227412787X-RAY DIFFRACTION97
1.79-1.840.20791360.201712806X-RAY DIFFRACTION97
1.84-1.90.22681360.185112814X-RAY DIFFRACTION97
1.9-1.960.20221360.177112783X-RAY DIFFRACTION97
1.96-2.030.20341370.164612913X-RAY DIFFRACTION97
2.03-2.110.2011360.156212898X-RAY DIFFRACTION98
2.11-2.20.18881370.148612896X-RAY DIFFRACTION98
2.2-2.320.20491380.150812939X-RAY DIFFRACTION98
2.32-2.470.19711380.147913001X-RAY DIFFRACTION98
2.47-2.660.16741380.152813014X-RAY DIFFRACTION98
2.66-2.920.18671380.147313015X-RAY DIFFRACTION98
2.92-3.350.17911390.14313098X-RAY DIFFRACTION99
3.35-4.210.13181390.124913119X-RAY DIFFRACTION99
4.21-36.280.14711400.14813220X-RAY DIFFRACTION98
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)
11.4543-0.2335-0.30790.9410.85021.14560.0239-0.00380.1476-0.14120.0003-0.0394-0.1970.0014-0.04720.28410.0031-0.01640.14370.0070.2346-4.135862.9618-16.6784
21.6192-0.0145-0.53150.96930.39471.90640.03280.00950.1848-0.09950.00430.0806-0.1637-0.1051-0.02460.23230.0201-0.01580.1288-0.01730.2104-12.737661.0909-17.5653
32.0087-1.81860.87933.7038-2.68636.1072-0.0721-0.11340.06270.17030.2040.4089-0.4174-0.7649-0.16510.23960.0666-0.01830.2972-0.04130.3223-25.379363.1663-13.7233
45.7274-0.7214-1.76253.65310.76674.5612-0.01330.0830.00260.0359-0.15430.46280.1448-0.84130.16430.3004-0.0173-0.05710.3896-0.05880.2573-26.576358.303-24.3109
50.9538-0.8360.93841.1487-0.67531.8074-0.00620.0141-0.108-0.20250.00960.2411-0.0651-0.28260.00590.2649-0.0161-0.02050.2331-0.0250.2596-15.686744.8819-25.5107
60.61720.230.34620.65730.30561.36860.0213-0.1061-0.02490.059-0.01990.112-0.0178-0.2066-0.00040.14350.01340.01470.17960.01240.1956-15.615328.9187-13.9128
71.90551.0668-0.29843.3357-1.30252.75210.044-0.33090.00110.2959-0.0690.1396-0.0591-0.2686-0.0240.16120.02030.02430.2092-0.01050.1656-14.67335.7347-2.6045
81.40710.3295-1.23062.91830.5131.55550.02150.64830.0613-0.5225-0.11170.5378-0.2387-0.5780.04130.34930.0626-0.07270.3743-0.01210.2357-18.531858.5244-34.8581
91.41530.1047-0.20551.29980.43680.80340.06180.21020.1631-0.2823-0.05770.0337-0.28280.0006-0.00190.3154-0.0017-0.00160.19630.04510.1831-1.363847.0626-44.5779
106.1865-5.7633.45996.569-1.92543.3378-0.70680.12210.3035-0.46960.39871.0096-0.17710.13210.3070.22930.02450.03150.1430.03810.2461-9.577549.5019-19.0587
112.19460.59950.84412.4920.95071.5139-0.0981-0.21060.24550.18010.03640.1283-0.0826-0.14850.0620.24420.06510.01420.2522-0.00030.1918-1.187839.294211.9107
121.7294-0.02351.51691.5389-0.29383.1470.0489-0.3145-0.18020.18330.06540.05460.2409-0.1988-0.11270.2350.04560.02220.24780.01220.16227.743924.801913.3246
130.74820.02690.14311.3599-0.1670.6657-0.0541-0.14980.05680.14060.03850.0119-0.1305-0.03980.01490.20930.0348-0.01130.2197-0.02380.1737.638137.920111.6017
141.6502-1.05160.5822.3045-0.50791.8359-0.1494-0.15120.24070.18520.1153-0.1254-0.24790.07810.03470.24340.0128-0.05420.217-0.05410.191520.408939.721616.0611
151.0639-0.62650.77610.6139-0.31311.079-0.0168-0.06340.04290.05350.034-0.06810.0560.0914-0.00540.1788-0.0131-0.00170.2062-0.00550.176219.700530.87682.2655
160.7658-0.4447-0.17291.14020.3890.5787-0.00920.05080.1707-0.06230.0456-0.2096-0.14070.1421-0.04040.187-0.05260.01260.18860.00840.210719.234843.8339-16.7941
172.07810.3504-0.73893.6654-1.79872.47460.03950.03030.39750.12290.0347-0.1716-0.42750.065-0.05380.1989-0.02880.00640.1449-0.020.215312.805253.3906-10.2222
181.68570.4231.18310.33360.28592.120.0439-0.0892-0.23650.18650.0858-0.07160.18830.1247-0.1460.22580.0361-0.01570.1735-0.00830.173920.147920.898811.3283
191.925-0.21210.06311.6058-0.19661.42790.037-0.196-0.17380.0751-0.00840.01660.18660.0547-0.02260.1742-0.00530.00020.1690.04020.165910.91358.3268-5.3232
203.8018-1.996-0.72215.7366-4.80715.8737-0.0942-0.1753-0.1918-0.30980.00680.1401-0.43180.330.07760.288-0.0108-0.04360.201-0.00750.22429.484934.49540.6522
211.9440.29850.5621.65420.19592.3040.10560.0972-0.38320.01420.0134-0.19160.48790.0817-0.09040.23450.04150.0190.2437-0.06360.283931.89422.0997-34.5205
222.6042-0.44421.08170.31240.26831.15650.1371-0.2549-0.25390.13320.0027-0.03020.24110.0392-0.1480.2279-0.01940.01760.2190.03690.243921.61338.1693-21.3848
230.60190.01690.16990.65070.32151.74880.06470.0237-0.1811-0.0081-0.00010.04440.2817-0.0552-0.05940.1785-0.0033-0.01460.13250.01080.22012.11394.4937-24.3142
240.9461-0.6542-0.0941.75321.28241.948-0.0403-0.0505-0.05120.22370.1738-0.29620.24650.3122-0.10190.1555-0.0077-0.00710.2755-0.01210.266734.911319.0909-17.8378
251.99271.99521.99572.00432.00412.00390.011-1.5337-0.5989-0.2706-0.0350.57760.22671.36250.03940.13190.00050.01130.3798-0.0710.326621.79759.4913-31.3346
261.7423-0.8885-1.39431.6018-0.88314.29650.10790.1772-0.2378-0.2833-0.1275-0.01450.3980.02440.02780.24830.0289-0.06110.2117-0.06670.2572-3.81823.419-53.0579
273.03740.12350.58630.9754-0.60512.58170.0622-0.0331-0.1781-0.0997-0.00980.15370.0866-0.172-0.05550.21570.0259-0.03830.1823-0.05330.2357-17.41913.2487-50.6927
280.96-0.2812-0.07070.78-0.12280.91350.07730.1777-0.1429-0.1603-0.03650.01870.16850.0872-0.03520.26250.0445-0.0340.2516-0.05250.2116-5.568911.6151-56.3255
293.2045-1.05540.45891.59430.12262.26420.16270.4015-0.0877-0.2851-0.1746-0.12170.05050.27690.01140.29720.0609-0.01610.3098-0.02760.1694-7.625320.0515-66.899
301.3198-0.630.99930.4524-0.30271.00860.0120.10620.0474-0.1248-0.05480.0189-0.0698-0.00770.05860.2308-0.0021-0.01070.2284-0.00370.1908-8.150927.7261-52.3376
311.3617-0.65830.16551.37410.48870.75350.00920.0870.1269-0.0657-0.0082-0.09-0.14810.10920.01270.2223-0.03260.01710.18550.01550.15728.336336.8696-38.0298
322.26790.15411.11062.03060.18061.02410.03090.15670.1641-0.1731-0.0459-0.2049-0.18920.23930.02730.2466-0.03290.06520.2890.03510.210414.766938.1796-46.3024
331.753-0.6169-0.54951.59520.15120.91750.10230.34640.1033-0.3713-0.0757-0.1583-0.15770.1196-0.02990.2777-0.0230.05720.32350.02170.176917.424328.6423-52.7914
343.08510.626-0.41481.9736-0.21291.19890.0610.31830.0073-0.2847-0.0418-0.336-0.10350.276-0.01210.23690.00620.06140.28380.00640.197818.250723.7929-50.8338
350.45220.04170.69960.429-0.31282.4831-0.03950.05620.0123-0.05410.01050.16-0.2307-0.21480.02580.19570.0425-0.02670.2298-0.0330.2078-21.275425.4731-54.081
361.66730.34750.2131.4826-0.28111.49990.0408-0.04150.0218-0.033-0.00840.2194-0.072-0.2356-0.02910.15050.0102-0.01520.1946-0.00540.1889-22.60527.8939-31.7348
372.3530.28091.26146.4487-5.19615.1324-0.3045-0.0594-0.0816-0.42830.28050.87280.050.5195-0.00660.22110.0358-0.02910.3104-0.05720.2281-3.083819.0915-47.8215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 112 )
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 134 )
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 165 )
5X-RAY DIFFRACTION5chain 'A' and (resid 166 through 215 )
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 350 )
7X-RAY DIFFRACTION7chain 'A' and (resid 351 through 383 )
8X-RAY DIFFRACTION8chain 'A' and (resid 384 through 424 )
9X-RAY DIFFRACTION9chain 'A' and (resid 425 through 469 )
10X-RAY DIFFRACTION10chain 'A' and (resid 502 through 502 )
11X-RAY DIFFRACTION11chain 'B' and (resid 9 through 34 )
12X-RAY DIFFRACTION12chain 'B' and (resid 35 through 63 )
13X-RAY DIFFRACTION13chain 'B' and (resid 64 through 112 )
14X-RAY DIFFRACTION14chain 'B' and (resid 113 through 150 )
15X-RAY DIFFRACTION15chain 'B' and (resid 151 through 215 )
16X-RAY DIFFRACTION16chain 'B' and (resid 216 through 350 )
17X-RAY DIFFRACTION17chain 'B' and (resid 351 through 383 )
18X-RAY DIFFRACTION18chain 'B' and (resid 384 through 424 )
19X-RAY DIFFRACTION19chain 'B' and (resid 425 through 469 )
20X-RAY DIFFRACTION20chain 'B' and (resid 503 through 503 )
21X-RAY DIFFRACTION21chain 'C' and (resid 10 through 165 )
22X-RAY DIFFRACTION22chain 'C' and (resid 166 through 215 )
23X-RAY DIFFRACTION23chain 'C' and (resid 216 through 383 )
24X-RAY DIFFRACTION24chain 'C' and (resid 384 through 469 )
25X-RAY DIFFRACTION25chain 'C' and (resid 502 through 502 )
26X-RAY DIFFRACTION26chain 'D' and (resid 8 through 34 )
27X-RAY DIFFRACTION27chain 'D' and (resid 35 through 63 )
28X-RAY DIFFRACTION28chain 'D' and (resid 64 through 112 )
29X-RAY DIFFRACTION29chain 'D' and (resid 113 through 150 )
30X-RAY DIFFRACTION30chain 'D' and (resid 151 through 215 )
31X-RAY DIFFRACTION31chain 'D' and (resid 216 through 279 )
32X-RAY DIFFRACTION32chain 'D' and (resid 280 through 305 )
33X-RAY DIFFRACTION33chain 'D' and (resid 306 through 350 )
34X-RAY DIFFRACTION34chain 'D' and (resid 351 through 383 )
35X-RAY DIFFRACTION35chain 'D' and (resid 384 through 424 )
36X-RAY DIFFRACTION36chain 'D' and (resid 425 through 469 )
37X-RAY DIFFRACTION37chain 'D' and (resid 502 through 502 )

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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