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

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Basic information

Entry
Database: PDB / ID: 8cfv
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H04
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
benzyl (cyanomethyl)carbamate / ADENINE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 H04
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)212,44738
Polymers206,9404
Non-polymers5,50734
Water25,9601441
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33360 Å2
ΔGint-218 kcal/mol
Surface area56410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.019, 132.869, 98.904
Angle α, β, γ (deg.)90.00, 101.20, 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, 1475 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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.: 16 / 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: Chemical ChemComp-3S9 / benzyl (cyanomethyl)carbamate


Mass: 190.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1441 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
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: 1.88→48.5 Å / Num. obs: 151098 / % possible obs: 98.8 % / Redundancy: 4.58 % / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.14 / Net I/σ(I): 9.19
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.88-1.991.416235800.541.5951
1.99-2.130.851229380.7210.961
2.13-2.30.491214220.8590.5591
2.3-2.520.306197700.9410.3481
2.52-2.810.202179260.9770.2271
2.81-3.240.12158380.9910.1361
3.24-3.970.064134080.9960.0731
3.97-5.60.04104040.9980.0451
5.6-48.50.03358120.9990.0371

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→48.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2016 1056 0.7 %
Rwork0.1595 --
obs0.1598 151042 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14228 0 342 1441 16011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614996
X-RAY DIFFRACTIONf_angle_d0.76820347
X-RAY DIFFRACTIONf_dihedral_angle_d13.7645575
X-RAY DIFFRACTIONf_chiral_restr0.0522267
X-RAY DIFFRACTIONf_plane_restr0.0062692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.960.29051260.270517841X-RAY DIFFRACTION95
1.96-2.060.28641320.237218790X-RAY DIFFRACTION99
2.07-2.190.251320.218759X-RAY DIFFRACTION99
2.19-2.360.21271330.180318854X-RAY DIFFRACTION99
2.36-2.60.21521330.163918842X-RAY DIFFRACTION99
2.6-2.980.20951340.151318920X-RAY DIFFRACTION100
2.98-3.750.16851330.136918946X-RAY DIFFRACTION100
3.75-48.50.17671330.137119034X-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)
11.7887-0.1-0.59140.95661.04231.28180.0442-0.0030.2306-0.14090.0115-0.059-0.2243-0.0531-0.09480.40890.0111-0.04950.19690.00970.3366-4.177962.9275-16.5934
21.6444-0.0783-0.26990.76420.45111.61880.0145-0.00450.1975-0.1669-0.02660.0544-0.1248-0.06960.0120.3170.0242-0.04660.1895-0.0270.284-12.785461.0617-17.4949
32.5072-1.54770.83014.2075-2.49916.7842-0.0815-0.2140.22080.07490.1410.6727-0.3188-0.7875-0.09250.30320.0533-0.03460.3619-0.07980.422-25.399863.032-13.6645
45.1123-0.3578-1.17183.22960.29724.16990.05140.01240.1359-0.0256-0.12780.52140.069-0.74190.07010.33220.0273-0.0880.3575-0.07550.3158-26.55958.259-24.2762
51.1647-0.76240.82981.0115-0.56771.5866-0.02290.0552-0.0454-0.2061-0.01630.262-0.1044-0.21570.04870.2854-0.0043-0.04640.2245-0.02880.2724-15.607444.7548-25.3405
60.92480.25140.52071.01070.57132.13080.0294-0.1486-0.02060.0491-0.05050.1899-0.0167-0.27780.02370.17390.0109-0.00290.21730.00040.2374-15.566828.8402-14.0097
72.09630.9325-0.34074.0728-1.80353.67530.0332-0.3654-0.03910.3874-0.09410.1251-0.143-0.40550.00680.18890.0079-0.00550.2677-0.02790.1935-14.63235.58-2.6884
81.49070.3361-1.2682.68820.75961.72430.12430.64040.1317-0.6418-0.18470.4412-0.1596-0.52440.01850.46280.0614-0.09440.3728-0.00120.2762-18.565658.5976-34.7644
91.57130.0929-0.21131.51190.34831.0660.12750.27230.1742-0.3838-0.1229-0.0498-0.30880.00340.00360.43860.0261-0.0050.24480.05540.242-1.346547.1567-44.5175
104.387-3.65931.17945.06111.07762.4326-1.10410.53780.5636-0.10210.54941.5521-0.33340.53080.54460.41380.0229-00.16630.02590.3359-9.631549.5244-19.0801
111.0793-0.37580.53460.8589-0.07891.2263-0.1396-0.20830.12340.19840.1179-0.0887-0.07090.00790.02190.21880.0249-0.02540.2263-0.02590.178312.860234.30969.703
121.0406-0.6091-0.09541.27060.42580.6616-0.00830.03050.2414-0.11510.0725-0.2693-0.19690.1489-0.06710.245-0.06910.02110.2309-0.00060.267219.19143.9008-16.7712
132.35440.3361-0.83633.6965-1.70092.81420.09240.04090.47650.20830.0289-0.2973-0.63370.0438-0.08230.2868-0.02460.01060.2025-0.02520.279112.734553.3977-10.2241
141.05630.66080.51130.45850.60442.1071-0.0209-0.0921-0.23320.24060.1225-0.15680.24660.217-0.11310.28010.0605-0.03630.2136-0.01860.199920.139620.869711.326
152.35850.0070.23241.7771-0.09241.73320.076-0.2227-0.25380.08180.0041-0.02180.24680.0421-0.07810.2237-0.0092-0.01850.20620.03760.219810.95858.2974-5.4272
166.9217-3.98623.43012.5292-3.01946.3653-0.3834-0.4667-0.4435-0.1579-0.06740.0559-0.38430.44860.44720.3837-0.075-0.05330.27150.04030.26899.399134.47350.6661
172.05430.00850.22681.1235-0.32662.52520.09890.1438-0.3766-0.13570.0483-0.20870.48980.1769-0.14010.3240.0551-0.00440.3311-0.11340.374231.37262.8522-35.9584
181.9745-0.27680.79860.84150.19752.01310.1731-0.2384-0.43220.16790.0351-0.10740.31950.135-0.1570.30250.0001-0.01240.28590.00490.348525.30475.3714-21.736
190.71420.13720.41720.66360.59682.39640.0910.0131-0.22490.0354-0.02670.03360.3419-0.0518-0.05310.22730.0104-0.0310.16140.00080.2722.17735.637-22.147
203.1070.8732-0.58752.602-0.43222.1929-0.03610.2356-0.5823-0.24630.07950.00910.5298-0.0676-0.05370.3210.0251-0.05530.2008-0.04440.28692.2231-0.1854-33.9941
211.0329-0.7123-0.35641.81531.2741.9517-0.0128-0.0696-0.03020.22740.2054-0.45720.21310.4318-0.14930.19110.0064-0.03190.3462-0.0470.330734.902819.1583-17.8718
2222-3.14439.3038-3.093120.0314-1.03470.3638-0.80030.23910.02051.16441.5096-0.26350.3192-0.03950.11730.5001-0.31380.643321.91569.5042-31.4182
231.3863-0.4641-1.47761.3804-0.8634.05720.06750.2771-0.2865-0.3155-0.11360.00060.3647-0.04510.06120.35190.05-0.10730.2806-0.09630.3351-3.61723.5364-53.146
241.85010.16070.45981.0674-0.63612.51630.0353-0-0.1539-0.1440.00590.20680.1823-0.1897-0.04580.28520.048-0.07260.2721-0.07810.3114-17.218913.2868-50.8874
250.5515-0.4265-0.06910.88350.04170.75010.11780.1817-0.1897-0.1689-0.0604-0.01770.17090.0646-0.05270.32140.0781-0.07060.3001-0.08440.2455-5.370511.7287-56.4157
262.8922-0.98970.3971.54990.27942.33230.1950.471-0.058-0.3893-0.1845-0.1614-0.04180.2666-0.00320.40210.0865-0.03430.3927-0.05210.2215-7.401920.158-66.9874
271.4635-0.67590.72190.7299-0.17390.7998-0.00110.16880.1095-0.1876-0.06270.0561-0.1165-0.0210.06080.30030.0232-0.03840.2784-0.02010.2254-8.014327.7937-52.4159
281.6056-0.65390.47441.21720.52440.86470.01220.13740.1363-0.17340.0082-0.1105-0.20730.167-0.00810.2632-0.01960.03390.20340.01360.15968.337537.0312-38.0623
292.0292-0.22881.53591.53070.36011.3754-0.02720.28050.186-0.1987-0.0323-0.1616-0.23810.27820.05590.3472-0.02560.0740.35380.02680.252914.814138.3597-46.2391
301.7878-0.3898-0.34111.62460.31321.10940.11190.48370.091-0.548-0.0715-0.182-0.19730.1425-0.03450.3864-0.00280.09270.41380.02030.229417.525528.822-52.7427
312.51830.4060.1212.0681-0.16112.01050.1070.5092-0.0175-0.5403-0.0518-0.4455-0.14570.4194-0.03070.32530.04710.09560.3541-0.02050.248918.351523.9543-50.768
320.70830.09270.68960.4254-0.22382.673-0.11740.05790.0168-0.06710.05430.1876-0.3497-0.23870.06720.28670.0762-0.05920.2968-0.07290.2557-21.131925.5179-54.2617
331.66820.33180.05611.4405-0.09331.38360.01770.01580.0563-0.0796-0.06390.2538-0.1131-0.26750.05570.23660.0289-0.0590.2761-0.04420.2486-22.534827.8696-31.806
343.38122.39671.24185.2761-2.51323.6754-0.3631-0.21920.1222-0.78060.40790.8284-0.08490.5674-0.05990.34620.1119-0.06560.3816-0.08080.3003-2.968119.1838-47.9286
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 215 )
12X-RAY DIFFRACTION12chain 'B' and (resid 216 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 10 through 150 )
18X-RAY DIFFRACTION18chain 'C' and (resid 151 through 215 )
19X-RAY DIFFRACTION19chain 'C' and (resid 216 through 350 )
20X-RAY DIFFRACTION20chain 'C' and (resid 351 through 383 )
21X-RAY DIFFRACTION21chain 'C' and (resid 384 through 469 )
22X-RAY DIFFRACTION22chain 'C' and (resid 502 through 502 )
23X-RAY DIFFRACTION23chain 'D' and (resid 8 through 34 )
24X-RAY DIFFRACTION24chain 'D' and (resid 35 through 63 )
25X-RAY DIFFRACTION25chain 'D' and (resid 64 through 112 )
26X-RAY DIFFRACTION26chain 'D' and (resid 113 through 150 )
27X-RAY DIFFRACTION27chain 'D' and (resid 151 through 215 )
28X-RAY DIFFRACTION28chain 'D' and (resid 216 through 279 )
29X-RAY DIFFRACTION29chain 'D' and (resid 280 through 305 )
30X-RAY DIFFRACTION30chain 'D' and (resid 306 through 350 )
31X-RAY DIFFRACTION31chain 'D' and (resid 351 through 383 )
32X-RAY DIFFRACTION32chain 'D' and (resid 384 through 424 )
33X-RAY DIFFRACTION33chain 'D' and (resid 425 through 469 )
34X-RAY DIFFRACTION34chain 'D' and (resid 502 through 502 )

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