[English] 日本語
Yorodumi
- PDB-5m5k: S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m5k
TitleS-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine and cordycepin
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / SAHase / SAH / SAM-dependent methylation / nitrogen fixation / symbiotic bacteria / NAD / conformational transition / molecular gate / adenosine / cordycepin
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 / 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 ...Adenosylhomocysteinase-like / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3'-DEOXYADENOSINE / ACETATE ION / ADENOSINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Adenosylhomocysteinase
Similarity search - Component
Biological speciesBradyrhizobium elkanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsManszewski, T. / Mueller-Dieckamann, J. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre2013/10/M/NZ1/00251 Poland
Citation
Journal: IUCrJ / Year: 2017
Title: Crystallographic and SAXS studies of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium elkanii.
Authors: Manszewski, T. / Szpotkowski, K. / Jaskolski, M.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: An enzyme captured in two conformational states: crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii.
Authors: Manszewski, T. / Singh, K. / Imiolczyk, B. / Jaskolski, M.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).
Authors: Brzezinski, K. / Dauter, Z. / Jaskolski, M.
#3: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2008
Title: Purification, crystallization and preliminary crystallographic studies of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus).
Authors: Brzezinski, K. / Bujacz, G. / Jaskolski, M.
#4: Journal: Nat. Struct. Biol. / Year: 1998
Title: Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength.
Authors: Turner, M.A. / Yuan, C.S. / Borchardt, R.T. / Hershfield, M.S. / Smith, G.D. / Howell, P.L.
History
DepositionOct 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
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)215,14619
Polymers210,9494
Non-polymers4,19715
Water26,8421490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28830 Å2
ΔGint-121 kcal/mol
Surface area60420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.162, 176.283, 102.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 52737.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium elkanii (bacteria) / Gene: ahcY, BeSAHase / Production host: Escherichia coli (E. coli) / References: UniProt: A0A087WNH6, adenosylhomocysteinase

-
Non-polymers , 8 types, 1505 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-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-3AD / 3'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1490 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium acetate, 16% PEG 4000, 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.223 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: May 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.223 Å / Relative weight: 1
ReflectionResolution: 1.84→47.82 Å / Num. obs: 168719 / % possible obs: 98.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 21.26 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 16.62
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 5.08 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.01 / % possible all: 91.7

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LVC

4lvc


Resolution: 1.84→47.82 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / Phase error: 17.96
Details: Riding H atoms were added. TLS parameters were included.
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 1243 0.74 %RANDOM
Rwork0.1461 ---
obs0.1464 168719 98.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.84→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14489 0 282 1490 16261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01515309
X-RAY DIFFRACTIONf_angle_d1.38120761
X-RAY DIFFRACTIONf_dihedral_angle_d15.2719229
X-RAY DIFFRACTIONf_chiral_restr0.0812320
X-RAY DIFFRACTIONf_plane_restr0.0082648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8346-1.90810.27931220.239116520X-RAY DIFFRACTION89
1.9081-1.99490.24631380.198918509X-RAY DIFFRACTION99
1.9949-2.10010.25131390.167118728X-RAY DIFFRACTION100
2.1001-2.23170.20661390.153118730X-RAY DIFFRACTION100
2.2317-2.4040.19391390.145418768X-RAY DIFFRACTION100
2.404-2.64590.18091400.143118805X-RAY DIFFRACTION100
2.6459-3.02870.18991400.148518882X-RAY DIFFRACTION100
3.0287-3.81560.19951410.138318988X-RAY DIFFRACTION100
3.8156-47.83240.14851450.122119515X-RAY DIFFRACTION100
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)
10.94510.111-0.09421.8124-0.86131.15490.0242-0.0817-0.2051-0.1404-0.0189-0.05280.18620.034-0.00790.19720.0223-0.04240.13450.03840.352831.64881.790834.6784
21.94012.2035-0.27653.59620.06020.1690.0937-0.13030.20070.2227-0.14980.6763-0.0489-0.02540.06530.20850.0093-0.02490.23030.03870.361717.78711.648.7755
30.86410.0280.23711.16320.50731.3510.0436-0.0474-0.2108-0.0024-0.02180.03110.1061-0.1352-0.02310.1149-0.0176-0.02080.11430.03530.17359.859320.77228.3336
40.336-0.06190.01551.6838-0.06670.51960.0199-0.2097-0.17630.3044-0.0546-0.26470.02690.04360.02060.1926-0.0001-0.08940.2350.06330.276137.353822.906248.4672
50.79370.3849-0.12630.6202-0.03360.73510.0887-0.30040.1150.0967-0.0844-0.0178-0.06080.09760.01620.1649-0.02220.00170.2547-0.06940.12820.101758.471659.8692
60.51570.86510.11383.14930.89563.46040.1666-0.39640.06340.2317-0.2141-0.1838-0.21630.15530.03270.1873-0.0253-0.02790.4365-0.05040.165131.370257.01269.9759
70.06170.0303-0.15220.7763-0.06681.71770.0153-0.2522-0.00130.0825-0.0787-0.08140.22870.20380.0920.12520.0113-0.02680.28690.00070.136726.475344.261252.3032
81.38230.3952-0.09523.0857-0.16420.75630.0359-0.1211-0.00960.023-0.0145-0.2143-0.02840.077-0.0270.0915-0.0014-0.01650.1614-0.0170.127439.032647.679438.0159
90.37430.10640.00320.64590.01120.47790.0118-0.209-0.03020.0897-0.0206-0.01140.0198-0.02190.01790.130.0016-0.01020.19850.00630.098718.667441.427950.1819
100.69920.023-0.22140.94190.03820.9001-0.09490.2461-0.2042-0.25760.1073-0.2424-0.00810.0965-0.01460.259-0.07390.04930.2601-0.11270.248521.616520.6105-8.87
110.58940.20220.11020.54430.03390.4211-0.02870.1299-0.1271-0.130.04-0.14250.02910.0413-0.01380.1511-0.01580.02650.1444-0.04330.143127.325432.06398.595
122.7029-1.31931.21262.3426-1.21261.5167-0.00890.02270.11780.11620.0480.1883-0.2078-0.114-0.04870.2119-0.00680.02650.13870.00020.175525.197678.128512.0479
130.57940.1276-0.1450.37650.0310.332-0.00750.09290.0413-0.09040.01050.0132-0.0983-0.0524-0.01110.18060.0096-0.02250.1519-0.00820.1418.330656.076615.3221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 137 )
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 230 )
3X-RAY DIFFRACTION3chain 'A' and (resid 231 through 393 )
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 473 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 162 )
6X-RAY DIFFRACTION6chain 'B' and (resid 163 through 198 )
7X-RAY DIFFRACTION7chain 'B' and (resid 199 through 248 )
8X-RAY DIFFRACTION8chain 'B' and (resid 249 through 361 )
9X-RAY DIFFRACTION9chain 'B' and (resid 362 through 473 )
10X-RAY DIFFRACTION10chain 'C' and (resid 3 through 230 )
11X-RAY DIFFRACTION11chain 'C' and (resid 231 through 473 )
12X-RAY DIFFRACTION12chain 'D' and (resid 6 through 190 )
13X-RAY DIFFRACTION13chain 'D' and (resid 191 through 473 )

+
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