[English] 日本語
Yorodumi
- PDB-1xma: Structure of a transcriptional regulator from Clostridium thermoc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xma
TitleStructure of a transcriptional regulator from Clostridium thermocellum Cth-833
ComponentsPredicted transcriptional regulator
KeywordsTRANSCRIPTION / Clostridium thermocellum / transcriptional regulator / Southeast Collaboratory for Structural Genomics / SECSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / Transcriptional regulator, PadR-like family
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SAD / sad / Resolution: 2.301 Å
AuthorsYang, H. / Chen, L. / Lee, D. / Habel, J. / Nguyen, J. / Chang, S.-H. / Kataeva, I. / Xu, H. / Chang, J. / Zhao, M. ...Yang, H. / Chen, L. / Lee, D. / Habel, J. / Nguyen, J. / Chang, S.-H. / Kataeva, I. / Xu, H. / Chang, J. / Zhao, M. / Horanyi, P. / Florence, Q. / Zhou, W. / Tempel, W. / Lin, D. / Praissman, J. / Zhang, H. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Ljungdahl, L. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Structure of a transcriptional regulator from Clostridium thermocellum Cth-833
Authors: Yang, H. / Chen, L. / Lee, D. / Habel, J. / Nguyen, J. / Chang, S.-H. / Kataeva, I. / Xu, H. / Chang, J. / Zhao, M. / Horanyi, P. / Florence, Q. / Zhou, W. / Tempel, W. / Lin, D. / ...Authors: Yang, H. / Chen, L. / Lee, D. / Habel, J. / Nguyen, J. / Chang, S.-H. / Kataeva, I. / Xu, H. / Chang, J. / Zhao, M. / Horanyi, P. / Florence, Q. / Zhou, W. / Tempel, W. / Lin, D. / Praissman, J. / Zhang, H. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Ljungdahl, L. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics
History
DepositionOct 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 18, 2020Group: Data collection / Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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_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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Predicted transcriptional regulator
B: Predicted transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,36019
Polymers33,5582
Non-polymers80217
Water72140
1
A: Predicted transcriptional regulator
hetero molecules

B: Predicted transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,36019
Polymers33,5582
Non-polymers80217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_456x-1,y,z+11
Buried area3530 Å2
ΔGint-113 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.483, 52.160, 51.076
Angle α, β, γ (deg.)90.00, 92.46, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Predicted transcriptional regulator


Mass: 16779.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 48858444, UniProt: A3DGR1*PLUS
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.8 Å3/Da / Density % sol: 31.81 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 8.5% v/v isopropanol, 10% w/v PEG 4000, 15% v/v glycerol, 0.085M TRIS, modified microbatch, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 92 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 10985 / Rmerge(I) obs: 0.049
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.280.151143.8
2.28-2.370.17162.5
2.37-2.480.119179.5
2.48-2.610.105198.2
2.61-2.770.091100
2.77-2.990.0631100
2.99-3.290.0481100
3.29-3.760.047199.6
3.76-4.730.0371100
4.73-300.0441100

-
Phasing

PhasingMethod: sad
Phasing MADD res high: 3 Å / D res low: 20 Å / FOM : 0.43 / Reflection: 4792
Phasing MAD shell
Resolution (Å)FOM Reflection
9.91-200.42267
6.56-9.910.51405
5.22-6.560.45522
4.46-5.220.46598
3.96-4.460.45661
3.6-3.960.39715
3.32-3.60.42777
3.09-3.320.38847
Phasing dmFOM : 0.58 / FOM acentric: 0.58 / FOM centric: 0.62 / Reflection: 10972 / Reflection acentric: 10282 / Reflection centric: 690
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.3-19.5560.920.920.8653044882
3.9-6.30.90.910.8416541512142
3.1-3.90.830.840.7120501915135
2.8-3.10.610.610.6320761963113
2.4-2.80.340.340.3633893233156
2.2-2.40.190.180.271273121162

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
ISASphasing
RefinementMethod to determine structure: SAD / Resolution: 2.301→18.239 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26676 518 5.1 %RANDOM
Rwork0.20534 ---
obs0.20853 9669 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.084 Å2
Baniso -1Baniso -2Baniso -3
1--0.072 Å20 Å20.024 Å2
2--0.033 Å20 Å2
3---0.041 Å2
Refinement stepCycle: LAST / Resolution: 2.301→18.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 17 40 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221748
X-RAY DIFFRACTIONr_bond_other_d00.021608
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9782348
X-RAY DIFFRACTIONr_angle_other_deg3.79333745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4423.33381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42115345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2211512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021858
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02372
X-RAY DIFFRACTIONr_nbd_refined0.1930.2330
X-RAY DIFFRACTIONr_nbd_other0.2370.21274
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2836
X-RAY DIFFRACTIONr_nbtor_other0.1090.2810
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2570.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.0571.51007
X-RAY DIFFRACTIONr_mcbond_other01.5422
X-RAY DIFFRACTIONr_mcangle_it3.21621640
X-RAY DIFFRACTIONr_scbond_it2.3233741
X-RAY DIFFRACTIONr_scangle_it3.3244.5708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 37 -
Rwork0.226 472 -
obs--100 %

+
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