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

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Open data


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Basic information

Entry
Database: PDB / ID: 8cfp
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment F09
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 / : / 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 F09
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)213,20543
Polymers206,9404
Non-polymers6,26539
Water30,3731686
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33650 Å2
ΔGint-215 kcal/mol
Surface area56060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.830, 132.890, 98.710
Angle α, β, γ (deg.)90.00, 101.06, 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, 1725 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-UI4 / 4-pyridin-2-ylphenol


Mass: 171.195 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H9NO / Feature type: SUBJECT OF INVESTIGATION
#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.: 16 / Source method: obtained synthetically / Formula: PO4
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1686 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
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→48.44 Å / Num. obs: 235432 / % possible obs: 97.6 % / Redundancy: 4.64 % / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.112 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.61-1.711.469371510.4111.6681
1.71-1.820.976354870.6491.0971
1.82-1.970.548332620.8580.6151
1.97-2.160.293306310.9490.331
2.16-2.410.166278950.980.1881
2.41-2.780.105246880.9920.1181
2.78-3.410.06209790.9970.0671
3.41-4.810.032162900.9990.0361
4.81-48.440.02890490.9990.0311

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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→48.44 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1889 2471 1.05 %
Rwork0.1575 --
obs0.1579 235354 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14228 0 399 1686 16313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115071
X-RAY DIFFRACTIONf_angle_d0.99420447
X-RAY DIFFRACTIONf_dihedral_angle_d13.8985599
X-RAY DIFFRACTIONf_chiral_restr0.0662269
X-RAY DIFFRACTIONf_plane_restr0.0082703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.640.35281320.326212367X-RAY DIFFRACTION93
1.64-1.670.35951350.30412777X-RAY DIFFRACTION97
1.67-1.710.33281360.284612731X-RAY DIFFRACTION97
1.71-1.750.28711360.268112845X-RAY DIFFRACTION97
1.75-1.790.28081360.247912832X-RAY DIFFRACTION97
1.79-1.840.2741370.224912851X-RAY DIFFRACTION97
1.84-1.90.21581370.205712913X-RAY DIFFRACTION97
1.9-1.960.25271360.188812849X-RAY DIFFRACTION98
1.96-2.030.22571380.171412958X-RAY DIFFRACTION98
2.03-2.110.19821360.156312994X-RAY DIFFRACTION98
2.11-2.20.17691380.143812968X-RAY DIFFRACTION98
2.2-2.320.17191380.14312991X-RAY DIFFRACTION98
2.32-2.470.19131390.142413074X-RAY DIFFRACTION99
2.47-2.660.17651380.144413071X-RAY DIFFRACTION99
2.66-2.920.19351400.142113115X-RAY DIFFRACTION99
2.92-3.350.16331390.137513128X-RAY DIFFRACTION99
3.35-4.220.13441400.119913189X-RAY DIFFRACTION99
4.22-48.440.16341400.143913230X-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)
11.2392-0.2904-0.30510.93570.69890.75320.0302-0.0270.1646-0.0969-0.0192-0.0462-0.1821-0.0199-0.03050.27090.0108-0.03420.15420.00230.2345-4.126362.9336-16.6477
21.4016-0.0749-0.29340.84960.44381.316-0.0004-0.00760.1925-0.06790.00050.0447-0.1671-0.05450.00280.22190.0191-0.02620.1368-0.01910.2114-12.753361.0556-17.537
32.1022-2.25621.39353.7274-1.66734.9067-0.1045-0.25340.12040.18890.11060.4135-0.4043-0.6045-0.06060.20360.0569-0.02420.2662-0.06910.3071-25.416263.0495-13.6671
44.40490.0576-1.15622.44690.18933.99840.00790.0150.1672-0.0309-0.05490.3584-0.142-0.53280.05280.2470.0271-0.06130.2559-0.04140.256-26.576458.2431-24.2003
50.749-0.5890.66840.9212-0.27761.40780.03560.0305-0.0304-0.1532-0.05980.1664-0.0336-0.13810.02540.2112-0.0084-0.01910.1798-0.01570.2129-15.554644.7393-25.3345
60.7070.11020.38310.7010.2381.39450.02-0.1072-0.03730.0544-0.02160.12480.0089-0.19380.00220.1417-0.00060.0030.16870.00480.1805-15.542828.9213-13.9471
71.62570.9749-0.13583.1268-1.31922.49730.0616-0.2999-0.01770.3014-0.08520.125-0.0383-0.2665-0.00030.15160.0070.0190.2119-0.01420.1523-14.557535.6622-2.6322
81.34790.1877-1.0792.1710.56331.27630.04830.45760.1421-0.4052-0.12740.4186-0.2369-0.37770.05480.29680.0532-0.06910.2462-0.00630.2195-18.599958.4475-34.8863
91.43960.091-0.22321.18790.21020.92450.07440.20740.1654-0.2486-0.0686-0.0157-0.20220.0099-0.0080.2880.0108-0.00790.18350.04020.1866-1.301947.1147-44.5674
104.8945-4.41080.76565.9171.38332.3363-0.65840.0150.52-0.53050.28031.0254-0.30310.03530.37230.20740.00560.01960.17030.03750.2442-9.565749.5274-19.0601
111.94990.55550.85332.09461.03781.6975-0.0312-0.2380.20520.1642-0.05640.0901-0.0971-0.19750.08250.23070.04690.0130.24630.00150.1838-1.128739.295911.8067
121.4449-0.17211.42991.4314-0.3222.81790.0562-0.262-0.16250.16030.07360.08040.259-0.1691-0.12570.23990.03290.01460.25160.00940.16887.841324.836913.2514
130.74090.01120.05241.3257-0.03290.6609-0.0519-0.15480.05220.14680.03820.0061-0.0698-0.04270.00930.20050.031-0.01980.2123-0.01830.16647.703937.967211.5309
141.3525-0.97080.51232.1296-0.35691.5407-0.1525-0.13570.26560.16830.109-0.1024-0.24140.06070.0320.25310.0098-0.07230.2361-0.0530.217920.466439.784215.9915
150.998-0.6690.63460.7785-0.19870.96450.0088-0.07980.04470.03620.0194-0.08850.0980.0684-0.01570.1647-0.0152-0.00930.1796-0.00250.168219.704330.83222.0974
160.8309-0.431-0.03410.94270.3540.5527-0.00160.0240.1622-0.05560.0477-0.1832-0.11730.1027-0.05020.1698-0.04580.00720.15990.00550.18419.259843.8899-16.8495
171.85520.2935-0.77333.4783-1.78092.46650.06010.030.36350.12540.0646-0.1777-0.39580.0367-0.08820.2074-0.02070.00810.1462-0.01940.231912.81353.4162-10.3084
180.9930.51180.47250.32310.47941.9120.029-0.0616-0.20470.16090.0696-0.11420.23330.219-0.1050.21170.0287-0.03610.1568-0.00240.158720.204720.928211.3017
191.6551-0.09090.01571.5373-0.06761.33350.0369-0.1674-0.1540.09090.00120.0090.19370.0596-0.03080.1832-0.01-0.01760.16140.03370.167310.95998.3282-5.3766
205.45183.2278-5.35224.2637-6.41429.7317-0.1454-0.1352-0.1298-0.2727-0.02240.2269-0.31410.20630.16950.2705-0.0329-0.05760.18890.00460.21739.564534.52680.6423
211.26380.5294-0.01932.0722-0.05942.1097-0.09190.2894-0.2148-0.37920.2482-0.25540.21430.14-0.16230.22130.02710.02460.3035-0.07070.234528.07877.4155-45.8698
222.16740.18830.35241.8489-0.59120.8336-0.010.0931-0.01110.06910.0254-0.33170.05430.282-0.0170.18690.01820.01620.2951-0.06140.280237.429911.9937-32.3662
231.36140.12080.25491.27540.21851.60520.07430.1686-0.4734-0.0770.0671-0.23010.41030.1616-0.12260.27640.0429-0.020.2177-0.0820.3230.1249-1.1496-36.4388
244.0858-0.3698-0.10114.61010.30862.84760.0866-0.1006-0.52130.1846-0.0342-0.21940.52750.0298-0.05980.36330.0217-0.07180.26370.00210.347833.6796-4.0567-23.0863
251.6823-0.24950.55740.2120.27470.89930.0831-0.1554-0.20490.10650.0279-0.04290.16180.0392-0.11750.2323-0.0145-0.00170.20660.02240.250521.55748.176-21.4272
260.53630.02550.250.59190.31771.86370.06430.0053-0.15180.0199-0.01410.04220.2407-0.0767-0.04760.1814-0.0075-0.02070.13510.00930.21012.16455.6546-22.0714
272.87111.0125-0.41841.8159-0.23371.7216-0.01740.2022-0.4272-0.13080.03840.05060.3824-0.1786-0.01240.2526-0.0071-0.04180.1632-0.0340.23582.1788-0.1952-33.9125
282.30840.5449-1.60942.55230.53741.6322-0.0082-0.3685-0.32370.57380.0139-0.47460.28650.53970.05720.2710.0359-0.08670.2734-0.02610.272338.43117.8563-19.8331
291.2169-0.41930.15071.2620.26771.6925-0.0512-0.02440.0620.01190.1284-0.3544-0.11830.3211-0.08110.1502-0.037-0.00030.2337-0.0220.253831.662529.3342-16.1176
306.3484-0.82690.50975.5467-0.73146.3523-0.2263-1.0998-0.0436-0.40020.10210.52440.44170.90310.13820.16510.0034-0.01480.3067-0.07370.296521.83539.4865-31.3458
310.8845-0.28810.31440.8886-0.13720.88430.11230.1935-0.0984-0.2075-0.08090.04990.0880.0337-0.0320.23870.0354-0.0510.2265-0.05420.1735-8.928114.1408-58.3229
321.7239-0.59860.93220.328-0.1871.1517-0.06370.06940.1003-0.0888-0.03140.0149-0.1639-0.01890.10790.1989-0.0049-0.0210.164-0.01140.1662-5.511628.6702-48.4615
331.051-0.4901-0.16731.35020.30160.64990.05370.18180.1109-0.1933-0.0409-0.1569-0.13590.1166-0.01040.2025-0.02650.02190.20770.02310.150912.804634.2355-44.8315
343.10040.5515-0.3292.0943-0.32691.48710.0650.4024-0.0619-0.315-0.0764-0.375-0.08640.24480.00240.23630.01670.04790.25410.00470.198818.352523.8409-50.8105
350.41760.11210.38540.38350.20911.51130.01790.0611-0.0084-0.0844-0.06440.1328-0.0987-0.24160.04790.14240.0219-0.03330.1951-0.01990.171-21.863826.7968-42.4389
363.4682.82120.87325.9217-2.85843.7335-0.2814-0.2116-0.0151-0.22780.14460.61960.06460.53250.1210.16320.0515-0.01440.3036-0.05580.1812-2.971119.1466-47.8876
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 34 )
22X-RAY DIFFRACTION22chain 'C' and (resid 35 through 63 )
23X-RAY DIFFRACTION23chain 'C' and (resid 64 through 134 )
24X-RAY DIFFRACTION24chain 'C' and (resid 135 through 165 )
25X-RAY DIFFRACTION25chain 'C' and (resid 166 through 215 )
26X-RAY DIFFRACTION26chain 'C' and (resid 216 through 350 )
27X-RAY DIFFRACTION27chain 'C' and (resid 351 through 383 )
28X-RAY DIFFRACTION28chain 'C' and (resid 384 through 424 )
29X-RAY DIFFRACTION29chain 'C' and (resid 425 through 469 )
30X-RAY DIFFRACTION30chain 'C' and (resid 502 through 502 )
31X-RAY DIFFRACTION31chain 'D' and (resid 8 through 165 )
32X-RAY DIFFRACTION32chain 'D' and (resid 166 through 215 )
33X-RAY DIFFRACTION33chain 'D' and (resid 216 through 350 )
34X-RAY DIFFRACTION34chain 'D' and (resid 351 through 383 )
35X-RAY DIFFRACTION35chain 'D' and (resid 384 through 469 )
36X-RAY DIFFRACTION36chain 'D' and (resid 502 through 502 )

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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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