[English] 日本語
Yorodumi
- PDB-8cfw: Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. ... -

+
Open data


ID or keywords:

Loading...

-
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


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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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

Read more