[English] 日本語
Yorodumi
- PDB-1jnz: Structure of adenylylsulfate reductase from the hyperthermophilic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jnz
TitleStructure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6 resolution
Components(adenylylsulfate ...) x 2
KeywordsOXIDOREDUCTASE / sulfur metabolism / adenylylsulfate reductase / iron-sulfur flavoprotein / catalysis
Function / homology
Function and homology information


succinate dehydrogenase activity / fermentation / anaerobic respiration / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 / Adenylylsulphate reductase, beta subunit, C-terminal domain / Adenylylsulphate reductase, beta subunit / Adenylylsulphate reductase, alpha subunit / Adenylylsulphate reductase, beta subunit, C-terminal / APS reductase, beta subunit, C-terminal domain superfamily / Adenosine-5'-phosphosulfate reductase beta subunit / 4Fe-4S binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / FAD-dependent oxidoreductase SdhA/FrdA/AprA ...Signal recognition particle alu RNA binding heterodimer, srp9/1 / Adenylylsulphate reductase, beta subunit, C-terminal domain / Adenylylsulphate reductase, beta subunit / Adenylylsulphate reductase, alpha subunit / Adenylylsulphate reductase, beta subunit, C-terminal / APS reductase, beta subunit, C-terminal domain superfamily / Adenosine-5'-phosphosulfate reductase beta subunit / 4Fe-4S binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / Other non-globular / 4Fe-4S dicluster domain / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / Special / FAD/NAD(P)-binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Plaits / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / SULFITE ION / : / : / Adenylylsulfate reductase, subunit A (AprA) / Adenylylsulfate reductase, subunit B (AprB)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFritz, G. / Roth, A. / Schiffer, A. / Buechert, T. / Bourenkov, G. / Bartunik, H.D. / Huber, H. / Stetter, K.O. / Kroneck, P.M. / Ermler, U.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6-A resolution
Authors: Fritz, G. / Roth, A. / Schiffer, A. / Buchert, T. / Bourenkov, G. / Bartunik, H.D. / Huber, H. / Stetter, K.O. / Kroneck, P.M. / Ermler, U.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray analysis of adenylylsulfate reductase from Archaeoglobus fulgidus
Authors: Roth, A. / Fritz, G. / Buechert, T. / Huber, H. / Stetter, K.O. / Ermler, U. / Kroneck, P.M.H.
History
DepositionJul 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: adenylylsulfate reductase
B: adenylylsulfate reductase
C: adenylylsulfate reductase
D: adenylylsulfate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,74212
Polymers180,6054
Non-polymers3,1388
Water28,3741575
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28470 Å2
ΔGint-206 kcal/mol
Surface area46820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.600, 113.500, 193.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe second part of the biological assembly is generated by rotation matrix -0.999932 -0.011239 0.003138 0.010826 -0.793178 0.608894 -0.004354 0.608886 0.793246 translation vector 174.4428 -1.5140 0.7045

-
Components

-
Adenylylsulfate ... , 2 types, 4 molecules ACBD

#1: Protein adenylylsulfate reductase


Mass: 73344.617 Da / Num. of mol.: 2 / Fragment: A SUBUNIT / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus DSM 4304 (archaea) / Species: Archaeoglobus fulgidus / Strain: DSM4304
References: GenBank: 2648886, UniProt: O28603*PLUS, adenylyl-sulfate reductase
#2: Protein adenylylsulfate reductase


Mass: 16957.650 Da / Num. of mol.: 2 / Fragment: B SUBUNIT / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus DSM 4304 (archaea) / Species: Archaeoglobus fulgidus / Strain: DSM4304
References: GenBank: 2648887, UniProt: O28604*PLUS, adenylyl-sulfate reductase

-
Non-polymers , 4 types, 1583 molecules

#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1575 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG 4000, sodium acetate, sodium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.06 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 29, 1999 / Details: Double focussing X-ray optics
RadiationMonochromator: double crystal monochromator, Si(111), 1st crystal water cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 54495 / Num. obs: 53527 / % possible obs: 79.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.08
Reflection shellResolution: 2.5→2.53 Å / Rsym value: 0.26 / % possible all: 71.7

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JNR

1jnr


Resolution: 2.5→26.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2640335.29 / Data cutoff high rms absF: 2640335.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2705 5.1 %RANDOM
Rwork0.161 ---
obs0.161 53527 95.2 %-
all-54495 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.0423 Å2 / ksol: 0.341563 e/Å3
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--3.33 Å20 Å2
3----3.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2.5→26.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12670 0 146 1575 14391
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.224 433 5 %
Rwork0.144 8188 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2COF.PAR
X-RAY DIFFRACTION3WATER.PARAM
X-RAY DIFFRACTION4SULFIT_ADDUKT.PAR

+
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://pdbjlvh1.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