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

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Basic information

Entry
Database: PDB / ID: 8cfu
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H02
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 / 3-cyclopentyl-1-(piperazin-1-yl)propan-1-one / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 H02
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)212,47137
Polymers206,9404
Non-polymers5,53033
Water29,8871659
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33190 Å2
ΔGint-189 kcal/mol
Surface area56740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.550, 133.900, 97.950
Angle α, β, γ (deg.)90.00, 101.21, 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 , 8 types, 1692 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-RDV / 3-cyclopentyl-1-(piperazin-1-yl)propan-1-one


Mass: 210.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H22N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 94.971 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: PO4
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1659 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
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: 1.5→46.68 Å / Num. obs: 295826 / % possible obs: 96.9 % / Redundancy: 4.63 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.115 / Net I/σ(I): 9.27
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.5-1.591.581464280.3621.7881
1.59-1.71.016443360.5571.1541
1.7-1.830.631417730.790.711
1.83-2.010.339385920.9290.3811
2.01-2.250.181351050.9740.2061
2.25-2.590.107311320.990.1211
2.59-3.170.065264330.9960.0741
3.17-4.480.036206000.9980.0411
4.48-46.680.029114270.9990.0331

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→37.08 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 3106 1.05 %
Rwork0.1538 --
obs0.1541 295783 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14257 0 347 1659 16263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915036
X-RAY DIFFRACTIONf_angle_d0.99620399
X-RAY DIFFRACTIONf_dihedral_angle_d13.9895617
X-RAY DIFFRACTIONf_chiral_restr0.0872274
X-RAY DIFFRACTIONf_plane_restr0.0082698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.38251320.332512382X-RAY DIFFRACTION90
1.52-1.550.30071380.319413064X-RAY DIFFRACTION96
1.55-1.570.33491400.299513166X-RAY DIFFRACTION96
1.57-1.60.31471390.289413116X-RAY DIFFRACTION96
1.6-1.630.32571380.277312990X-RAY DIFFRACTION95
1.63-1.670.30861400.257413201X-RAY DIFFRACTION96
1.67-1.70.27831400.239513159X-RAY DIFFRACTION96
1.7-1.740.25461410.223713278X-RAY DIFFRACTION97
1.74-1.790.2371410.212313263X-RAY DIFFRACTION97
1.79-1.830.21861410.190113281X-RAY DIFFRACTION97
1.83-1.890.23991410.176613344X-RAY DIFFRACTION97
1.89-1.950.1831410.159213316X-RAY DIFFRACTION97
1.95-2.020.22681420.148913363X-RAY DIFFRACTION97
2.02-2.10.15991430.138713449X-RAY DIFFRACTION98
2.1-2.190.19051420.132213341X-RAY DIFFRACTION98
2.19-2.310.15121420.131213448X-RAY DIFFRACTION98
2.31-2.450.18121430.132513488X-RAY DIFFRACTION98
2.45-2.640.18541440.133613524X-RAY DIFFRACTION98
2.64-2.910.15761440.129613558X-RAY DIFFRACTION99
2.91-3.330.16391440.124613577X-RAY DIFFRACTION99
3.33-4.20.14291450.114913636X-RAY DIFFRACTION99
4.2-37.080.16181450.146313733X-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)
11.9927-1.2829-1.37351.75091.91362.59860.08670.02630.2211-0.1221-0.0408-0.1347-0.2691-0.0404-0.04690.1706-0.0168-0.04370.1330.01710.2167-4.030664.0789-16.768
21.2652-0.25680.43091.1098-0.10362.0325-0.0262-0.04590.1246-0.01160.00550.1271-0.1385-0.140.00730.14690.0291-0.02990.1469-0.02390.198-17.760661.2864-17.1592
35.3168-0.6965-0.28023.1014-0.45984.0877-0.05780.0497-0.0196-0.25940.02890.305-0.0169-0.37890.01640.11360.0031-0.06910.2181-0.00910.1532-27.658254.5924-27.3501
40.4134-0.01880.21450.46670.02720.54210.0034-0.0548-0.0260.00790.01130.1120.0231-0.1185-0.02330.1179-0.0028-0.00360.18880.00510.1769-14.836332.8766-15.7324
52.34241.2881-0.59563.8306-1.92552.60230.0446-0.2579-0.03290.41370.01330.1897-0.0761-0.2694-0.10150.14340.01680.01850.1926-0.01920.126-14.534936.3488-2.226
62.433-0.1928-0.61862.14230.40640.5969-0.01210.46330.1931-0.4059-0.06820.3144-0.2049-0.15090.04280.22490.0151-0.06250.21790.00860.1921-18.79458.8346-34.635
71.63340.10740.29431.42410.57422.92720.0480.17610.1296-0.274-0.07350.022-0.20060.07610.01750.19770.0222-0.00620.17060.05540.1637-1.839547.1661-44.5147
86.631-2.43713.697.16851.29973.1779-0.88230.28030.42290.42360.60961.3236-0.130.53940.31420.14870.0002-0.01050.17930.00440.213-9.708249.9621-18.9059
91.1883-0.08680.30951.3317-0.2580.8849-0.1053-0.18060.07150.24620.09780.0029-0.0642-0.08290.0110.190.0422-0.01940.219-0.01630.12665.624635.100412.2034
101.3185-1.09931.3583.2184-0.55363.6663-0.2719-0.17250.34280.36470.1253-0.3395-0.37210.12010.11770.22120.0238-0.10370.2408-0.05540.242620.831540.034515.7927
113.33460.81651.27112.6821-0.32255.9218-0.1455-0.06350.11330.17010.0821-0.4357-0.05390.31310.05820.17030.0486-0.07510.1541-0.01890.235127.127130.896810.1359
120.5347-0.21230.07820.5656-0.05230.4518-0.01350.04790.14920.0046-0.0258-0.1703-0.03850.12460.04320.1199-0.0189-0.01760.20560.02050.198417.987341.0894-14.2682
132.65911.3996-1.14843.9645-2.162.85320.08040.0550.41740.2478-0.0436-0.1857-0.42210.09590.00670.1588-0.0095-0.01830.1641-0.00540.231312.929153.5789-10.6313
142.80750.01061.98360.71120.16193.80760.0233-0.0539-0.19510.2290.0786-0.13160.21570.3083-0.10530.18280.0297-0.03540.1697-0.00980.152120.108121.203211.3266
152.3337-0.64820.19842.2229-0.02561.81280.0605-0.094-0.20610.10110.00880.0170.24690.0779-0.06820.16690.0049-0.02720.16750.03290.12610.34298.6227-5.0316
162.63251.0964-1.73484.7051-5.67796.9233-0.3013-0.6807-0.5174-0.4240.22060.5163-1.46460.28380.05860.25020.0161-0.02630.20.00670.17179.558934.91810.6542
171.50870.2153-0.13271.9752-0.54290.9640.0630.221-0.0825-0.2455-0.0626-0.25560.18370.2755-0.01930.24530.09860.01580.3545-0.02910.216229.8876.0047-38.5022
183.8139-0.10861.73833.57141.01932.4040.20590.2871-0.461-0.1043-0.0151-0.17760.41570.2722-0.12080.34830.1239-0.03850.2924-0.02630.283629.989-7.9721-29.5175
194.7953-0.8261-0.32636.1503-0.41093.37710.1504-0.2459-0.25480.2359-0.0511-0.20410.38420.2207-0.05190.26530.0518-0.07950.2511-0.0010.180430.6747-2.7909-18.0402
201.776-0.46910.87730.5296-0.10981.27170.0557-0.0074-0.0920.0139-0.0206-0.10180.1320.1911-0.03070.17470.03620.00230.19310.01770.155618.959811.4143-24.3413
210.5250.02660.34190.71520.21191.69650.08610.0117-0.1412-0.0651-0.01970.07340.2477-0.073-0.06390.18820.0032-0.03830.17020.00870.1941.18115.911-21.5609
223.80171.6896-0.90213.2176-0.45281.9356-0.00930.2825-0.405-0.10130.04790.06260.3884-0.1764-0.0570.27350.004-0.05070.1795-0.02380.17630.7372-0.0367-33.3355
231.9249-0.3017-0.91553.60340.02760.771-0.1203-0.228-0.10180.44250.0245-0.59350.09720.5050.12960.23410.0817-0.03090.386-0.00040.27437.42427.3413-19.9572
241.27870.00360.63361.50770.02312.4897-0.04390.12540.07480.01350.0262-0.3192-0.0070.35910.0080.12280.0146-0.00960.29210.03090.247931.287629.0634-16.413
251.99022.00011.99892.01392.01052.0116-0.6789-0.4917-0.3382-0.9662-0.1348-0.21881.8891.98180.86630.28590.05570.02660.3043-0.00960.231220.67329.1723-31.1614
261.2403-0.06930.16130.9429-0.33051.12370.1480.1457-0.1883-0.2018-0.07430.1050.23570.0236-0.05730.29830.053-0.10110.2282-0.05090.203-9.861910.0404-53.2545
272.5243-0.50390.61291.81370.69822.50240.17340.29250.0004-0.3796-0.1365-0.0063-0.03790.1595-0.02630.30650.0682-0.05660.2850.00450.1554-11.06824.2414-64.319
280.5091-0.0720.23510.5901-0.10530.57220.04440.08240.038-0.0984-0.0592-0.01770.00520.06420.01190.15830.01160.00210.20670.0150.1312.889132.7459-40.5542
290.9519-0.4486-0.09151.97570.06840.73250.12150.18020.055-0.2635-0.1082-0.2388-0.00880.1593-0.0160.22360.0320.0420.32340.0510.169415.678531.4284-50.6982
302.77211.1277-0.61532.428-0.29071.94370.03320.3-0.135-0.2957-0.016-0.40960.03780.3075-0.02860.23060.07960.03740.29460.00060.182217.227823.3042-50.7186
310.2332-0.03450.28130.45380.18961.49560.03880.0663-0.042-0.1583-0.07930.1725-0.0371-0.21280.02760.16420.0021-0.0670.2155-0.01040.202-22.763727.1662-41.817
321.99792.00191.9952.00581.99891.9921-0.1071-0.01980.526-2.4431-0.38371.8490.4940.60580.48180.25360.0072-0.05850.26050.01570.2035-4.122319.1538-47.451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 178 )
4X-RAY DIFFRACTION4chain 'A' and (resid 179 through 350 )
5X-RAY DIFFRACTION5chain 'A' and (resid 351 through 383 )
6X-RAY DIFFRACTION6chain 'A' and (resid 384 through 424 )
7X-RAY DIFFRACTION7chain 'A' and (resid 425 through 469 )
8X-RAY DIFFRACTION8chain 'A' and (resid 502 through 502 )
9X-RAY DIFFRACTION9chain 'B' and (resid 9 through 112 )
10X-RAY DIFFRACTION10chain 'B' and (resid 113 through 150 )
11X-RAY DIFFRACTION11chain 'B' and (resid 151 through 178 )
12X-RAY DIFFRACTION12chain 'B' and (resid 179 through 350 )
13X-RAY DIFFRACTION13chain 'B' and (resid 351 through 383 )
14X-RAY DIFFRACTION14chain 'B' and (resid 384 through 424 )
15X-RAY DIFFRACTION15chain 'B' and (resid 425 through 469 )
16X-RAY DIFFRACTION16chain 'B' and (resid 503 through 503 )
17X-RAY DIFFRACTION17chain 'C' and (resid 8 through 112 )
18X-RAY DIFFRACTION18chain 'C' and (resid 113 through 150 )
19X-RAY DIFFRACTION19chain 'C' and (resid 151 through 178 )
20X-RAY DIFFRACTION20chain 'C' and (resid 179 through 215 )
21X-RAY DIFFRACTION21chain 'C' and (resid 216 through 350 )
22X-RAY DIFFRACTION22chain 'C' and (resid 351 through 383 )
23X-RAY DIFFRACTION23chain 'C' and (resid 384 through 424 )
24X-RAY DIFFRACTION24chain 'C' and (resid 425 through 469 )
25X-RAY DIFFRACTION25chain 'C' and (resid 502 through 502 )
26X-RAY DIFFRACTION26chain 'D' and (resid 8 through 112 )
27X-RAY DIFFRACTION27chain 'D' and (resid 113 through 178 )
28X-RAY DIFFRACTION28chain 'D' and (resid 179 through 279 )
29X-RAY DIFFRACTION29chain 'D' and (resid 280 through 350 )
30X-RAY DIFFRACTION30chain 'D' and (resid 351 through 383 )
31X-RAY DIFFRACTION31chain 'D' and (resid 384 through 469 )
32X-RAY DIFFRACTION32chain 'D' and (resid 502 through 502 )

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