[English] 日本語
Yorodumi
- PDB-1vm9: The X-ray Structure of the cys84ala cys85ala double mutant of the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vm9
TitleThe X-ray Structure of the cys84ala cys85ala double mutant of the [2Fe-2S] Ferredoxin subunit of Toluene-4-Monooxygenase from Pseudomonas Mendocina KR1
ComponentsToluene-4-monooxygenase system protein C
KeywordsELECTRON TRANSPORT / STRUCTURAL GENOMICS / CESG / PROTEIN STRUCTURE INITIATIVE / PSI / FERREDOXIN / FES / [2FE-2S] CLUSTER / RIESKE PROTEIN / TOLUENE-4-MONOOXYGENASE SUBUNIT / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


toluene catabolic process / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Mainly Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Toluene-4-monooxygenase system, ferredoxin component
Similarity search - Component
Biological speciesPseudomonas mendocina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.48 Å
AuthorsWesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Bingman, C.A. / Allard, S.T.M. / Moe, L.A. / Fox, B.G. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of T4moC, the Rieske-type ferredoxin component of toluene 4-monooxygenase.
Authors: Moe, L.A. / Bingman, C.A. / Wesenberg, G.E. / Phillips, G.N. / Fox, B.G.
History
DepositionSep 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_label_atom_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Toluene-4-monooxygenase system protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5527
Polymers12,1411
Non-polymers4116
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.510, 52.400, 83.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe asymmetric unit contains a monomer with no higher oligomeric state apparent from symmetry.

-
Components

#1: Protein Toluene-4-monooxygenase system protein C


Mass: 12141.370 Da / Num. of mol.: 1 / Mutation: C84A,C85A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Strain: KR1 / Gene: tmoC / Plasmid details: pET15b derivative / Plasmid: pT4CD15bTET(C84AC85A) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q00458
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10 MG/ML PROTEIN, 0.100M MES-ACETATE, 0.16M MAGNESIUM CHLORIDE, 24 PERCENT W/V MEPEG 5000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 32-ID10.97924
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDFeb 27, 2004RH MIRROR
RIGAKU RAXIS IV2IMAGE PLATEMar 3, 2004MULTILAYER
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DIAMOND 111 MIRRORSINGLE WAVELENGTHMx-ray1
2Osmic CMF12-38Cu6SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
21.54181
ReflectionResolution: 1.48→50 Å / Num. obs: 16626 / % possible obs: 99.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.055 / Χ2: 0.899 / Net I/σ(I): 32.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allΧ2% possible all
1.48-1.5311.80.2777.7516210.59999.8
1.53-1.5911.80.217.7516350.62799.6
1.59-1.6711.80.1657.7516400.69499.8
1.67-1.7511.80.1217.7516230.76899.9
1.75-1.8611.80.0917.7516580.832100
1.86-2.0111.80.077.7516610.991100
2.01-2.2111.80.0587.7516521.056100
2.21-2.5311.80.0517.7516621.241100
2.53-3.1911.80.0457.7516970.989100
3.19-5011.80.0457.7517771.05499.8

-
Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.9 Å / D res low: 20 Å / FOM : 0.32 / Reflection: 7764
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
17.5267.89219.297FE22.10.8
28.8519.29621.233FE34.31.06
Phasing MAD shell
Resolution (Å)FOM Reflection
6.67-200.43421
4.27-6.670.37666
3.36-4.270.37835
2.85-3.360.39987
2.52-2.850.361091
2.29-2.520.331185
2.1-2.290.261275
1.96-2.10.181304
Phasing dmFOM : 0.68 / FOM acentric: 0.69 / FOM centric: 0.66 / Reflection: 7766 / Reflection acentric: 6735 / Reflection centric: 1031
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.4-19.5870.940.940.86371252119
3.4-5.40.940.950.891086875211
2.7-3.40.870.880.813301139191
2.4-2.70.740.760.6113201162158
2-2.40.580.590.4622972067230
1.9-20.350.360.2913621240122

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.1.24refinement
PDB_EXTRACT1data extraction
HKL-2000data reduction
HKL-2000data scaling
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.48→33.925 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.18 / WRfactor Rwork: 0.156 / SU B: 1.07 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1759 838 5.048 %RANDOM
Rwork0.1548 ---
all0.156 ---
obs0.15586 15761 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 14.035 Å2
Baniso -1Baniso -2Baniso -3
1-0.288 Å20 Å20 Å2
2--0.692 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.48→33.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms845 0 18 133 996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021878
X-RAY DIFFRACTIONr_bond_other_d0.0020.02747
X-RAY DIFFRACTIONr_angle_refined_deg2.4271.9541188
X-RAY DIFFRACTIONr_angle_other_deg0.99531759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1215109
X-RAY DIFFRACTIONr_chiral_restr0.1180.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02974
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02157
X-RAY DIFFRACTIONr_nbd_refined0.1940.2164
X-RAY DIFFRACTIONr_nbd_other0.2550.2860
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2420
X-RAY DIFFRACTIONr_nbtor_other0.0880.2496
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.289
X-RAY DIFFRACTIONMetal-ion: refined atoms0.0740.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.216
X-RAY DIFFRACTIONr_mcbond_it1.6832542
X-RAY DIFFRACTIONr_mcbond_other0.3572224
X-RAY DIFFRACTIONr_mcangle_it2.8844877
X-RAY DIFFRACTIONr_mcangle_other1.3994742
X-RAY DIFFRACTIONr_scbond_it4.246336
X-RAY DIFFRACTIONr_scbond_other0.9756523
X-RAY DIFFRACTIONr_scangle_it6.6088308
X-RAY DIFFRACTIONr_scangle_other2.97381017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.48-1.51870.213660.19610891199
1.519-1.56020.271600.2111351200
1.56-1.60530.197420.19810841128
1.605-1.65460.17640.18410511118
1.655-1.70880.193430.17510601103
1.709-1.76860.188560.1579791036
1.769-1.83510.191410.1659731014
1.835-1.90980.151620.159927989
1.91-1.99450.225430.164883926
1.994-2.09150.176480.17847895
2.091-2.20410.164570.156814871
2.204-2.33720.202380.144773811
2.337-2.49770.163360.134737773
2.498-2.69660.2400.15663703
2.697-2.95220.146280.159647675
2.952-3.29750.15330.139568601
3.297-3.80160.144290.134528557
3.802-4.64150.169160.124432448
4.641-6.50350.178250.139353378
6.503-33.9250.188110.204218231

+
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