[English] 日本語
Yorodumi
- PDB-4fk1: Crystal Structure of Putative Thioredoxin Reductase TrxB from Bac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fk1
TitleCrystal Structure of Putative Thioredoxin Reductase TrxB from Bacillus anthracis
Components(Putative thioredoxin ...) x 2
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha beta beta sandwich / reductase / cytosol
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / nucleotide binding
Similarity search - Function
FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FAD-dependent oxidoreductase / Putative thioredoxin reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsMaltseva, N. / Kim, Y. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Putative Thioredoxin Reductase TrxB from Bacillus anthracis
Authors: Maltseva, N. / Kim, Y. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJun 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_seq_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_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative thioredoxin reductase
B: Putative thioredoxin reductase
C: Putative thioredoxin reductase
D: Putative thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,46713
Polymers137,1354
Non-polymers3,3329
Water2,558142
1
A: Putative thioredoxin reductase
B: Putative thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1555
Polymers68,5602
Non-polymers1,5953
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-45 kcal/mol
Surface area24210 Å2
MethodPISA
2
C: Putative thioredoxin reductase
D: Putative thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3128
Polymers68,5762
Non-polymers1,7366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-60 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.558, 54.096, 140.037
Angle α, β, γ (deg.)90.00, 93.04, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Putative thioredoxin ... , 2 types, 4 molecules ABDC

#1: Protein Putative thioredoxin reductase /


Mass: 34279.754 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BA_2768, GBAA_2768 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q81PN4, UniProt: A0A6L8PLA6*PLUS
#2: Protein Putative thioredoxin reductase /


Mass: 34295.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BA_2768, GBAA_2768 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q81PN4, UniProt: A0A6L8PLA6*PLUS

-
Non-polymers , 4 types, 151 molecules

#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M magnesium chloride, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 48483 / Num. obs: 48483 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 36.61 Å2 / Rsym value: 0.092 / Net I/σ(I): 7.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.476 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3FBS

3fbs


Resolution: 2.404→46.613 Å / SU ML: 0.28 / Isotropic thermal model: mixed / σ(F): 1.34 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 2438 5.04 %
Rwork0.1714 --
obs0.1744 48370 99.44 %
all-48370 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.7 Å2
Refinement stepCycle: LAST / Resolution: 2.404→46.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9401 0 222 142 9765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099901
X-RAY DIFFRACTIONf_angle_d1.14513454
X-RAY DIFFRACTIONf_dihedral_angle_d18.3473664
X-RAY DIFFRACTIONf_chiral_restr0.0751497
X-RAY DIFFRACTIONf_plane_restr0.0051722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4044-2.45350.31481470.24962586X-RAY DIFFRACTION96
2.4535-2.50680.32461670.24052622X-RAY DIFFRACTION99
2.5068-2.56510.26771390.22782707X-RAY DIFFRACTION100
2.5651-2.62930.29091240.22722661X-RAY DIFFRACTION100
2.6293-2.70030.2841370.21032719X-RAY DIFFRACTION100
2.7003-2.77980.26481290.19922686X-RAY DIFFRACTION100
2.7798-2.86950.2971520.20382698X-RAY DIFFRACTION100
2.8695-2.97210.25591430.20092679X-RAY DIFFRACTION100
2.9721-3.0910.31951400.20422704X-RAY DIFFRACTION100
3.091-3.23170.27431470.18042685X-RAY DIFFRACTION100
3.2317-3.4020.24421440.1792740X-RAY DIFFRACTION100
3.402-3.61510.25571590.17642682X-RAY DIFFRACTION100
3.6151-3.89410.21711220.16522735X-RAY DIFFRACTION100
3.8941-4.28570.18731370.1382735X-RAY DIFFRACTION100
4.2857-4.90530.15471490.1272729X-RAY DIFFRACTION100
4.9053-6.17790.19991370.15062767X-RAY DIFFRACTION100
6.1779-46.6220.17971650.1472797X-RAY DIFFRACTION99
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)
13.77090.97771.08634.78121.38665.02740.0411-0.05450.2103-0.203-0.067-0.8274-0.59960.86460.00680.3411-0.09870.020.4114-0.010.447126.39278.724156.3879
22.91660.85820.53655.4920.21877.22580.3019-0.30.04040.283-0.2043-0.01650.3336-0.2982-0.10660.5119-0.1729-0.13280.7051-0.05190.411628.325112.515690.237
33.85311.11645.10160.94670.65128.8951-0.4271-0.2850.43440.02790.04670.1093-1.3341-0.26590.40660.52680.03410.00350.4248-0.11550.489516.241717.911865.9579
49.86520.21077.46442.835-1.53078.8104-0.275-0.7530.48650.212-0.10360.0712-0.8769-0.58390.33710.34380.0185-0.00950.2865-0.0450.307313.59548.524557.4062
50.15130.3645-0.34331.2471-1.14771.3460.6667-0.5701-0.6210.9294-0.3679-0.42161.2399-0.5373-0.18221.3747-0.5518-0.29760.8830.2230.545712.8865-14.796774.5615
68.09292.34641.93884.88822.8156.13470.1855-0.46330.07910.1716-0.38720.18740.0724-0.45880.1990.4669-0.0586-0.05070.28520.01520.23152.3422-12.63142.3492
70.97391.087-1.21522.9218-2.90392.90370.351-0.8396-0.02620.7944-0.4990.2420.2934-1.21620.13270.8654-0.4644-0.13671.1588-0.00080.6632-0.588-13.701463.6662
82.7732-0.4631-1.83372.62480.70223.82630.3571-0.4010.11110.4061-0.53480.53680.5505-1.5510.10370.7277-0.4369-0.01961.0353-0.04040.56475.5592-1.866875.9074
93.2726-1.11510.90862.0974-0.04394.2643-0.1492-0.21340.10730.19950.0470.3368-0.4261-0.57740.13850.25940.04490.04310.20310.03780.29459.58180.68329.559
101.5235-0.4851.42850.5423-0.7132.4838-0.3066-0.29210.24780.34480.14920.0538-0.8483-0.44850.21450.51380.10860.00980.2916-0.00170.38396.006511.02656.4293
118.2226-2.53371.26667.0862-1.11976.1520.09290.45950.5592-0.5588-0.2382-0.3437-0.34170.52790.12340.2872-0.0148-0.01640.25440.01240.225710.023612.0468-23.9751
125.6796-0.87250.84445.6998-2.51946.35080.06530.1317-0.1422-0.12840.06630.6620.0007-1.014-0.14830.31030.0015-0.07930.2749-0.00320.3766-4.68738.5503-23.6342
132.28690.22783.01990.3216-0.10394.3694-0.61440.07950.46490.24630.1049-0.1406-1.81130.53430.4721.0389-0.1726-0.14620.41790.10590.581415.850518.34813.7988
143.6547-0.70923.09243.79750.56845.0007-0.38060.20020.4251-0.0519-0.12630.1075-1.36710.53520.48370.4441-0.0790.00220.25950.05180.334221.12919.63111.9629
155.0551-0.03074.06377.4927-3.40655.1282-0.11040.5601-0.2232-0.1522-0.1061-0.14420.03230.43180.23880.15760.02520.00760.2166-0.03150.197424.6732-7.5229-10.6822
160.4181-0.4262-0.27521.435-0.11545.5578-0.031-0.0487-0.14820.08130.008-0.12180.42920.63860.01560.20320.0345-0.01120.2640.00010.311330.1232-12.86060.1863
176.0817-1.14520.92935.0137-2.16086.8884-0.306-0.54650.16880.61180.0521-0.5-0.39810.7970.22220.37160.0475-0.04550.473-0.01340.240239.0656-6.302229.1195
181.6219-0.56430.05370.9719-0.78324.0955-0.05160.1380.0171-0.001-0.1668-0.3402-0.03040.94990.26020.2297-0.0368-0.02450.4153-0.01120.385740.912-4.16344.2715
191.71580.6479-1.56992.5097-1.2462.29450.0342-0.08760.12990.0991-0.0563-0.1929-0.45850.61520.03980.1923-0.04820.00160.2909-0.00930.294330.00251.7405-7.4229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3:115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 :223 )
3X-RAY DIFFRACTION3chain 'A' and (resid 224:260 )
4X-RAY DIFFRACTION4chain 'A' and (resid 261:301 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4:115 )
6X-RAY DIFFRACTION6chain 'B' and (resid 116:223 )
7X-RAY DIFFRACTION7chain 'B' and (resid 224:240 )
8X-RAY DIFFRACTION8chain 'B' and (resid 241:301 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3:69 )
10X-RAY DIFFRACTION10chain 'C' and (resid 70:141 )
11X-RAY DIFFRACTION11chain 'C' and (resid 142:203 )
12X-RAY DIFFRACTION12chain 'C' and (resid 204:223 )
13X-RAY DIFFRACTION13chain 'C' and (resid 224:260 )
14X-RAY DIFFRACTION14chain 'C' and (resid 261:301 )
15X-RAY DIFFRACTION15chain 'D' and (resid 3:25 )
16X-RAY DIFFRACTION16chain 'D' and (resid 26:141 )
17X-RAY DIFFRACTION17chain 'D' and (resid 142:221 )
18X-RAY DIFFRACTION18chain 'D' and (resid 222:250 )
19X-RAY DIFFRACTION19chain 'D' and (resid 251:301 )

+
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