[English] 日本語
Yorodumi
- PDB-3kcm: The crystal structure of thioredoxin protein from Geobacter metal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kcm
TitleThe crystal structure of thioredoxin protein from Geobacter metallireducens
ComponentsThioredoxin family protein
KeywordsOXIDOREDUCTASE / SGX / thioredoxin protein / PSI / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / Redox-active center
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
: / Redoxin / Redoxin / AhpC/TSA family / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...: / Redoxin / Redoxin / AhpC/TSA family / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacter metallireducens GS-15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of thioredoxin protein from Geobacter metallireducens
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin family protein
B: Thioredoxin family protein
C: Thioredoxin family protein
D: Thioredoxin family protein
E: Thioredoxin family protein
F: Thioredoxin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,97512
Polymers105,3986
Non-polymers5766
Water3,567198
1
A: Thioredoxin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6622
Polymers17,5661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6622
Polymers17,5661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thioredoxin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6622
Polymers17,5661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thioredoxin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6622
Polymers17,5661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Thioredoxin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6622
Polymers17,5661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Thioredoxin family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6622
Polymers17,5661
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.986, 74.555, 82.410
Angle α, β, γ (deg.)100.66, 109.05, 99.07
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Thioredoxin family protein


Mass: 17566.367 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens GS-15 (bacteria)
Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: 11211k2, Gmet_2452 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)-codon +RIL -stratagene / References: UniProt: Q39SU7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium sulfate, 30% Polyethylene glycol 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→75.36 Å / Num. all: 39095 / Num. obs: 36844 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.3
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 7.2 / % possible all: 53.3

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HDC

3hdc


Resolution: 2.45→75.36 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.884 / SU B: 20.769 / SU ML: 0.222 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26974 1953 5 %RANDOM
Rwork0.21417 ---
obs0.21699 36844 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.659 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å21.22 Å2-0.14 Å2
2--0.83 Å2-0.06 Å2
3----2.58 Å2
Refinement stepCycle: LAST / Resolution: 2.45→75.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6492 0 30 198 6720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226660
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.9699057
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6395834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.77124.403268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.969151108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7321533
X-RAY DIFFRACTIONr_chiral_restr0.1150.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214957
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_it0.7371.54186
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46626789
X-RAY DIFFRACTIONr_scbond_it3.02432474
X-RAY DIFFRACTIONr_scangle_it4.684.52268
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 158 -
Rwork0.317 2371 -
obs--83.25 %
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)
11.12490.2507-0.27451.5050.18711.7404-0.00510.0934-0.0534-0.07850.0020.0235-0.1332-0.16140.0030.07380.0190.03120.06590.01360.0289-3.9192-22.6675-6.4562
21.8802-0.65960.22382.2895-0.32231.09130.0395-0.0059-0.0268-0.0602-0.0010.08230.0398-0.1001-0.03850.0601-0.0111-0.0350.04560.00460.0217-15.45634.75195.0281
31.508-0.1433-0.2311.81450.72411.7028-0.02260.00890.01570.05080.0191-0.0357-0.1256-0.0320.00350.0890.04190.00150.04420.01960.0152-1.9562-33.70921.4255
40.9874-0.1926-0.25731.6235-0.10052.37390.09060.03460.03850.01340.00610.0334-0.0422-0.0138-0.09660.01580.01430.01570.05270.01540.02317.3998-27.7382-33.3686
50.7770.3837-0.20191.3435-0.31561.75260.03460.0606-0.051-0.03620.05070.03410.09610.0224-0.08520.06360.0146-0.03550.0590.01330.0337-5.46357.361531.4648
61.12330.15460.58211.760.3712.37440.0537-0.0427-0.0349-0.08-0.0305-0.07420.08710.0276-0.02330.08250.0217-0.00430.0110.00590.0198-13.014216.0298-22.4967
70.01090.0109-0.02060.140.05990.2161-0.0162-0.0151-0.004-0.03910.03480.04150.00880.0035-0.01860.10510.0031-0.03780.1213-0.00330.109-4.6274-8.9237-1.1838
80.1544-0.2044-0.2940.74280.23660.62590.04920.02930.0380.0150.0218-0.0712-0.1011-0.0423-0.07110.02370.0093-0.00240.13440.03880.067-2.0254-8.8761-0.5034
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 165
2X-RAY DIFFRACTION2B27 - 161
3X-RAY DIFFRACTION3C28 - 166
4X-RAY DIFFRACTION4D29 - 170
5X-RAY DIFFRACTION5E29 - 145
6X-RAY DIFFRACTION6F29 - 166
7X-RAY DIFFRACTION7A7 - 227
8X-RAY DIFFRACTION7C1 - 238
9X-RAY DIFFRACTION7B9 - 244
10X-RAY DIFFRACTION7E2 - 237
11X-RAY DIFFRACTION7D11 - 246
12X-RAY DIFFRACTION7F16 - 243
13X-RAY DIFFRACTION8A1
14X-RAY DIFFRACTION8C6
15X-RAY DIFFRACTION8B2
16X-RAY DIFFRACTION8E4
17X-RAY DIFFRACTION8D3
18X-RAY DIFFRACTION8F5

+
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