[English] 日本語
Yorodumi
- PDB-7o5l: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Syn... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o5l
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803 cocrystallized with adenosine in the presence of Rb+ cations
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS
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
ADENOSINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RUBIDIUM ION / Adenosylhomocysteinase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsMalecki, P.H. / Imiolczyk, B. / Barciszewski, J. / Czyrko-Horczak, J. / Brzezinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2013/09/B/NZ1/01880 Poland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Biochemical and structural insights into an unusual, alkali-metal-independent S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803.
Authors: Malecki, P.H. / Imiolczyk, B. / Barciszewski, J. / Czyrko-Horczak, J. / Sliwiak, J. / Gawel, M. / Wozniak, K. / Jaskolski, M. / Brzezinski, K.
History
DepositionApr 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosylhomocysteinase
C: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,89313
Polymers92,5342
Non-polymers2,36011
Water11,530640
1
A: Adenosylhomocysteinase
C: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
C: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,78626
Polymers185,0674
Non-polymers4,71922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area29800 Å2
ΔGint-257 kcal/mol
Surface area51460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.770, 196.070, 82.052
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-846-

HOH

21C-788-

HOH

-
Components

-
Protein , 1 types, 2 molecules AC

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


Mass: 46266.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: ahcY, sll1234 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): E. coli / Variant (production host): CodonPlus(DE3)-RIPL / References: UniProt: P74008, adenosylhomocysteinase

-
Non-polymers , 5 types, 651 molecules

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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Rb / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.5
Details: 0.2MSodium fluoride, 0.1MBis-Tris propane pH 7.5, 20% w/vPEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2018
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.74→48.634 Å / Num. obs: 98599 / % possible obs: 99.2 % / Redundancy: 12.418 % / Biso Wilson estimate: 25.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.129 / Χ2: 0.844 / Net I/σ(I): 13.7 / Num. measured all: 1224382
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.74-1.8511.0271.4331.3616706115905151500.6871.50295.3
1.85-1.9813.3440.8462.8519945414952149470.8930.879100
1.98-2.1313.6760.4795.5819132713996139900.9640.498100
2.13-2.3412.6310.2939.0916229712853128490.9830.306100
2.34-2.6113.4350.19614.0215726211707117050.9930.204100
2.61-3.0112.4380.12619.9412837610322103210.9970.132100
3.01-3.6910.9280.07329.8195792877587660.9980.07699.9
3.69-5.211.2580.05541.7577779690969090.9990.057100
5.2-48.63411.3660.04743.845034397639620.9990.04999.6

-
Processing

Software
NameVersionClassification
PHENIX1.19refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONF

3onf


Resolution: 1.74→48.63 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2144 2097 2.13 %
Rwork0.1875 96395 -
obs0.1881 98492 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.45 Å2 / Biso mean: 34.9205 Å2 / Biso min: 14.73 Å2
Refinement stepCycle: final / Resolution: 1.74→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6340 0 136 667 7143
Biso mean--25.08 39.03 -
Num. residues----830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.780.35061230.34365619574288
1.78-1.830.27631400.265464186558100
1.83-1.880.24241390.225564016540100
1.88-1.930.23171400.215364256565100
1.93-1.990.2721400.220364456585100
1.99-2.070.25961400.205964126552100
2.07-2.150.23981410.187664616602100
2.15-2.250.21711400.186164446584100
2.25-2.360.22251390.190764656604100
2.36-2.510.24841410.188664736614100
2.51-2.710.24341410.195464766617100
2.71-2.980.22241420.192264986640100
2.98-3.410.19721420.18565146656100
3.41-4.30.18771430.157265896732100
4.3-48.630.17581460.173567556901100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.73540.7173-0.05751.6188-0.28562.4747-0.0818-0.1218-0.21610.0236-0.0842-0.2305-0.0030.38470.13090.12780.03360.03520.23850.04680.243626.193229.32531.7232
21.84050.29770.04181.8038-0.45272.6297-0.1395-0.0763-0.2932-0.10540.0794-0.05770.12770.2710.05130.17090.01710.06560.1790.03330.218920.731324.0422-4.1429
33.60371.16010.91764.5891-0.99636.8055-0.28770.2309-0.1372-0.18090.08390.15620.1478-0.08640.18180.22210.01170.08510.13840.03150.282511.330915.509-8.9845
40.6935-0.0265-0.36012.33040.00710.9138-0.1099-0.0663-0.2587-0.0739-0.0690.02250.26030.06670.17170.18430.01530.04430.1590.02830.21986.707620.28074.397
51.49960.7605-0.46572.403-0.44781.17430.0212-0.07360.0127-0.0235-0.09210.1292-0.0179-0.10740.07230.15180.0238-0.01390.1903-0.02420.1521-7.231837.71288.2092
63.9089-0.84141.08833.6638-1.31524.16210.04780.505-0.0488-0.3719-0.19270.04340.0957-0.0730.12450.18570.0227-0.02030.2642-0.04230.1446-6.836437.7936-8.4773
74.1502-3.38335.36123.1035-3.39926.57170.17620.1164-0.0993-0.2819-0.090.1970.1037-0.10240.04360.20210.02430.00130.2101-0.00070.16210.310740.328-7.105
80.49190.71030.2744.90451.60182.1903-0.0251-0.1706-0.27540.1776-0.0212-0.08850.38040.150.03430.19120.05410.06250.22580.09140.267416.156517.376713.5578
98.5457.551-5.11089.4597-8.07317.72760.2776-0.5721-0.52820.2013-0.5465-0.31510.09830.43560.27340.23970.03480.01310.1603-0.01610.257910.791722.158739.7888
101.65450.3067-0.35942.57670.66663.0727-0.01510.27730.2628-0.39650.116-0.3195-0.55560.407-0.10930.4002-0.02790.03690.42750.09350.467611.288470.4953-4.4179
111.0641-0.2444-0.24581.21570.37921.22130.0051-0.0310.101-0.00660.024-0.114-0.07940.1789-0.0340.1725-0.0345-0.01450.21110.01880.173320.253353.100115.7362
122.1463-0.1475-1.06930.07840.07181.34680.2740.19110.6171-0.0405-0.0976-0.0559-0.5575-0.1171-0.17360.41810.05030.00420.28160.04790.3864-4.411170.05336.8211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 45 )A9 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 110 )A46 - 110
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 143 )A111 - 143
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 208 )A144 - 208
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 284 )A209 - 284
6X-RAY DIFFRACTION6chain 'A' and (resid 285 through 323 )A285 - 323
7X-RAY DIFFRACTION7chain 'A' and (resid 324 through 355 )A324 - 355
8X-RAY DIFFRACTION8chain 'A' and (resid 356 through 402 )A356 - 402
9X-RAY DIFFRACTION9chain 'A' and (resid 403 through 425 )A403 - 425
10X-RAY DIFFRACTION10chain 'C' and (resid 9 through 193 )C9 - 193
11X-RAY DIFFRACTION11chain 'C' and (resid 194 through 343 )C194 - 343
12X-RAY DIFFRACTION12chain 'C' and (resid 344 through 421 )C344 - 421

+
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://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