[English] 日本語
Yorodumi
- PDB-3mm6: Dissimilatory sulfite reductase cyanide complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mm6
TitleDissimilatory sulfite reductase cyanide complex
Components(Sulfite reductase, dissimilatory-type subunit ...) x 2
KeywordsOXIDOREDUCTASE / alpha-beta-protein
Function / homology
Function and homology information


dissimilatory sulfite reductase system / dissimilatory sulfite reductase activity / sulfite reductase (ferredoxin) activity / sulfite reductase complex (NADPH) / sulfite reductase activity / sulfate assimilation / 4 iron, 4 sulfur cluster binding / electron transfer activity / heme binding / membrane / metal ion binding
Similarity search - Function
Sulphite reductase, dissimilatory-type beta subunit / Alpha-Beta Plaits - #2500 / Alpha-Beta Plaits - #3340 / Helix Hairpins - #1420 / Sulphite reductase, dissimilatory-type alpha subunit / Nitrite and sulphite reductase 4Fe-4S domain containing protein / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain ...Sulphite reductase, dissimilatory-type beta subunit / Alpha-Beta Plaits - #2500 / Alpha-Beta Plaits - #3340 / Helix Hairpins - #1420 / Sulphite reductase, dissimilatory-type alpha subunit / Nitrite and sulphite reductase 4Fe-4S domain containing protein / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like half domain / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / Helix Hairpins / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Helix non-globular / Special / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CYANIDE ION / IRON/SULFUR CLUSTER / SIROHEME / Sulfite reductase, dissimilatory-type subunit alpha / Sulfite reductase, dissimilatory-type subunit beta
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsParey, K. / Warkentin, E. / Kroneck, P.M.H. / Ermler, U.
CitationJournal: Biochemistry / Year: 2010
Title: Reaction cycle of the dissimilatory sulfite reductase from Archaeoglobus fulgidus.
Authors: Parey, K. / Warkentin, E. / Kroneck, P.M. / Ermler, U.
History
DepositionApr 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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_ncs_dom_lim / 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_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_auth_comp_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.ptnr2_label_comp_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_atom_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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Dec 27, 2023Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfite reductase, dissimilatory-type subunit alpha
B: Sulfite reductase, dissimilatory-type subunit beta
D: Sulfite reductase, dissimilatory-type subunit alpha
E: Sulfite reductase, dissimilatory-type subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,98119
Polymers178,4234
Non-polymers6,55815
Water13,133729
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34980 Å2
ΔGint-206 kcal/mol
Surface area50010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.540, 68.680, 145.630
Angle α, β, γ (deg.)90.00, 107.57, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12D
22A
13B
23E

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERALAALA3AA1 - 1742 - 175
211SERSERALAALA3DC1 - 1742 - 175
121METMETMETMET3AA176177
221METMETMETMET3DC176177
131CYSCYSGLYGLY3AA185 - 218186 - 219
231CYSCYSGLYGLY3DC185 - 218186 - 219
141PROPROASPASP3AA220 - 222221 - 223
241PROPROASPASP3DC220 - 222221 - 223
151VALVALVALVAL2AA224 - 386225 - 387
251VALVALVALVAL2DC224 - 386225 - 387
161SF4SF4SRMSRM4AF - E575 - 580
261SF4SF4SRMSRM4DN - M575 - 580
112LYSLYSMETMET3DC387 - 416388 - 417
212LYSLYSMETMET3AA387 - 416388 - 417
113GLUGLUASNASN3BB4 - 1804 - 180
213GLUGLUASNASN3ED4 - 1804 - 180
123ALAALATRPTRP3BB184 - 366184 - 366
223ALAALATRPTRP3ED184 - 366184 - 366
133SRMSRMSRMSRM4BL570
233SRMSRMSRMSRM4ES570
143SF4SF4SF4SF44BJ - K585 - 586
243SF4SF4SF4SF44EQ - R585 - 586

NCS ensembles :
ID
1
2
3

-
Components

-
Sulfite reductase, dissimilatory-type subunit ... , 2 types, 4 molecules ADBE

#1: Protein Sulfite reductase, dissimilatory-type subunit alpha / Hydrogensulfite reductase subunit alpha


Mass: 47589.730 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus (archaea) / References: UniProt: Q59109, EC: 1.8.99.3
#2: Protein Sulfite reductase, dissimilatory-type subunit beta / Hydrogensulfite reductase subunit beta


Mass: 41621.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus (archaea) / References: UniProt: Q59110, EC: 1.8.99.3

-
Non-polymers , 4 types, 744 molecules

#3: Chemical
ChemComp-SRM / SIROHEME


Mass: 916.661 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H44FeN4O16
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CN
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 291 K / pH: 6.5
Details: 20% PEG 4000, 100 mM Na-citrate, 0.2 M NaCl, 5% (v/v) 2-propanol, 10 mM KCN, 10 mM Cr(II) EDTA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99997
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2007
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 3.38 % / Rmerge(I) obs: 0.125 / Rsym value: 0.078 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.19 / Rsym value: 0.535 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
MAR345data collection
REFMAC5.6.0046refinement
XDSdata reduction
XDSdata scaling
REFMAC5.6.0046phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C7B

3c7b
PDB Unreleased entry


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.796 / SU ML: 0.121 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21698 6694 5 %RANDOM
Rwork0.1796 ---
obs0.18147 127259 95.44 %-
all-127364 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.639 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å22.06 Å2
2---1.81 Å20 Å2
3---4.77 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12462 0 322 729 13513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02213231
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3442.01318372
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70851556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71723.811572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.609152214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2081576
X-RAY DIFFRACTIONr_chiral_restr0.1750.21876
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02110052
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1500TIGHT POSITIONAL0.110.05
1A741MEDIUM POSITIONAL0.980.5
1A829LOOSE POSITIONAL0.245
1A1500TIGHT THERMAL2.670.5
1A741MEDIUM THERMAL6.082
1A829LOOSE THERMAL3.310
2D120TIGHT POSITIONAL0.040.05
2D132LOOSE POSITIONAL0.055
2D120TIGHT THERMAL8.790.5
2D132LOOSE THERMAL8.3610
3B1440TIGHT POSITIONAL0.160.05
3B79MEDIUM POSITIONAL0.150.5
3B1443LOOSE POSITIONAL0.255
3B1440TIGHT THERMAL4.890.5
3B79MEDIUM THERMAL132
3B1443LOOSE THERMAL4.7910
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 490 -
Rwork0.288 9304 -
obs--95.54 %
Refinement TLS params.Method: refined / Origin x: 56.781 Å / Origin y: 17.005 Å / Origin z: 39.598 Å
111213212223313233
T0.2486 Å2-0.0337 Å20.0332 Å2-0.2237 Å2-0.0172 Å2--0.0169 Å2
L0.9334 °20.1507 °2-0.1278 °2-0.9452 °2-0.1007 °2--0.6437 °2
S-0.0657 Å °0.3675 Å °-0.0423 Å °-0.3819 Å °0.0565 Å °-0.1152 Å °-0.0094 Å °0.0888 Å °0.0093 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 417
2X-RAY DIFFRACTION1D1 - 417
3X-RAY DIFFRACTION1A2570 - 2576
4X-RAY DIFFRACTION1D2570 - 2576
5X-RAY DIFFRACTION1B4 - 366
6X-RAY DIFFRACTION1E4 - 366
7X-RAY DIFFRACTION1D2580 - 2586
8X-RAY DIFFRACTION1E2580 - 2586

+
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