[English] 日本語
Yorodumi
- PDB-9k3w: Crystal structure of putative transcription regulator (dr_2454) f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9k3w
TitleCrystal structure of putative transcription regulator (dr_2454) from Deinococcus radiodurans
ComponentsTranscriptional regulator, PbsX family
KeywordsUNKNOWN FUNCTION / Helix-turn-helix motif
Function / homologyHelix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Transcriptional regulator, PbsX family
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKhakerwala, Z. / Kumar, A. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India) India
CitationJournal: To Be Published
Title: Crystal structure of putative transcription regulator (dr_2454) from Deinococcus radiodurans
Authors: Khakerwala, Z. / Kumar, A. / Makde, R.D.
History
DepositionOct 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator, PbsX family
B: Transcriptional regulator, PbsX family
C: Transcriptional regulator, PbsX family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1614
Polymers21,9673
Non-polymers1941
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.779, 29.618, 115.750
Angle α, β, γ (deg.)90.000, 93.360, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 38 or (resid 39...
d_2ens_1(chain "B" and (resid 2 through 38 or (resid 39...
d_3ens_1(chain "C" and resid 2 through 63)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 2 - 63 / Label seq-ID: 2 - 63

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC

NCS oper:
IDCodeMatrixVector
1given(0.454100943113, -0.890841269232, 0.0139343638767), (-0.890273566744, -0.454309993193, -0.0318654427449), (0.0347175722175, 0.00206473177431, -0.999395030537)16.3519509163, 30.8767693806, 77.4373087159
2given(0.644204133244, 0.750204459922, 0.148977525234), (0.742222681186, -0.660200624807, 0.115067921411), (0.184679523078, 0.0364472676385, -0.982122736952)-19.86442066, 35.0522625327, 38.8983552521

-
Components

#1: Protein Transcriptional regulator, PbsX family


Mass: 7322.319 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_2454 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RRN4
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.76 % / Description: it was a cuboidal crystal
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES pH7 30% Jeffamine ED-2001 pH7
Temp details: temperature fluctuation was there from 293-294

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.977 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 20, 2022 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.6→25.3 Å / Num. obs: 21529 / % possible obs: 97.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 24.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.023 / Χ2: 1.01 / Net I/σ(I): 22.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.947 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1051 / CC1/2: 0.819 / Χ2: 1.02 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→25.3 Å / SU ML: 0.193 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2457 1067 4.96 %
Rwork0.2065 20452 -
obs0.2083 21519 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 13 97 1627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481546
X-RAY DIFFRACTIONf_angle_d0.82282072
X-RAY DIFFRACTIONf_chiral_restr0.042239
X-RAY DIFFRACTIONf_plane_restr0.0057269
X-RAY DIFFRACTIONf_dihedral_angle_d12.5729604
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.05836168805
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.0665851156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.670.34691170.29452513X-RAY DIFFRACTION95.26
1.67-1.760.30341230.25372518X-RAY DIFFRACTION96.18
1.76-1.870.241210.24172515X-RAY DIFFRACTION96.35
1.87-2.020.25771590.22472502X-RAY DIFFRACTION96.66
2.02-2.220.2771160.21572567X-RAY DIFFRACTION96.93
2.22-2.540.25721550.20892550X-RAY DIFFRACTION97.83
2.54-3.20.24691480.22352600X-RAY DIFFRACTION97.9
3.2-25.30.21991280.17912687X-RAY DIFFRACTION97.84
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)
17.616871517040.5512602386861.905997880167.449755633181.645878648653.26003876337-0.1348007047770.500595407386-0.372730301889-0.335708145620.0285986310266-0.5243532879020.08025055012481.056349414720.1041114902840.222839332365-0.008057239955630.04819788814670.1825209311170.01239415369050.2842975646530.83810.7332.311
23.43820776991-1.91187377309-2.26349872844.652198410210.7149690331374.64207616497-0.1667231068060.18486760827-0.134075422454-0.1399203739280.05620305362270.3016637749660.171175678928-0.07448766219290.1421185259080.176538945698-0.0334373087342-0.002869812374870.1664022510380.0002286763025750.244035097297-9.86211.1130.93
34.366643132381.506470153185.377399924374.5571402751.555005516856.63469888533-0.03125871853880.440980652023-0.0375015090648-0.00600619395380.0243829534975-0.223140121341-0.281759963660.2687623896930.05202055531120.251800832547-0.02587279173450.02437576510.223016374950.03558320916350.218371202886-5.19221.4327.899
43.149466290923.260458139353.45826886033.676385458034.004182226374.345666644610.04547587761560.787915007279-0.635361898705-1.20044585053-0.0609574109344-0.74826753804-0.1826644789610.578278288933-0.0820096490760.370686629565-0.03560801017150.03379461584650.3972384707170.01129445935910.3096462430461.98817.57722.639
57.77223316362-1.94575117944-4.048392046096.756667798462.705831502412.63133267027-0.350482232962-1.031579373840.1398690205761.371952706570.133427967527-0.6092951872391.265444292160.804183034090.2074357996120.396598835920.0754917231031-0.05902142555980.2818833616610.02500021240630.2909373604878.37924.0347.574
66.28489017031-1.04588473141-1.661993116645.55373151384-0.8930630916824.183675078020.0780829836223-0.3925870765570.3508879922040.959364612057-0.03722685313790.0106802549692-0.4933117689590.113827219875-0.01522262205560.323724982628-0.01410948687930.02909467561230.1287043052350.01037701494320.2091591609572.7232.23744.968
76.582223540970.7947829199130.9392009449255.58348107040.9692751713525.062710779470.207847040374-0.793272230827-0.3897158353440.7145829484650.172025669524-0.1578778853430.671392309345-0.142920610652-0.4114301458820.3741334350640.00772742408651-0.01540866674480.2667521417040.02025637770510.177744634591-0.77822.78353.159
85.40698907838-2.53165080946-3.800783869392.450226606961.293602599662.94338788530.168188003002-0.2728227959980.2353098750970.115459333699-0.01432936631640.230796388735-1.013767370440.0824376907581-0.1470139342290.3442100776280.0625891299262-0.02347910187770.446860190091-0.01856947432840.21378536026-6.27432.6439.301
96.25997856813-1.137758814994.605656865842.4044301392-2.443041670747.488563249450.6470387894430.828604827515-0.551542205377-0.867605672881-0.5573380319050.4110524811790.1054738507070.1290432188150.1018329088150.3576410275040.160910607224-0.09569505968350.560802836141-0.1686023380150.334718292568-8.04525.7180.488
101.82248740303-3.385272496990.9361642172159.353687826471.117156182198.21318461350.2815970558760.503694434056-1.29255565959-0.05003195654750.01079898834180.9760785375970.36430223834-1.22201610798-0.1770286679190.3101585693390.0514139006193-0.04514585868420.759382645635-0.07454578773870.588327875215-14.74624.0316.292
118.37787661532-0.537297216626-4.13998777845.433183255263.830190975224.379138563451.115523747740.2134937357720.149879038132-1.428029077010.661075917272.37813118643-0.672566528964-2.15379096785-0.874377115510.43828209473-0.0554314128918-0.2800876863810.9350047861430.2344582107810.579317734732-15.45325.05615.481
127.069624135513.30335866089-3.897679764964.70354428721-5.056612331255.405300419830.1883583390480.566235333318-0.399444295141-0.828921333816-0.3710311953290.04069076498250.3553238704550.2002643073560.1916960002190.3034387044070.00335973098637-0.03409936178440.377261073597-0.04603486466250.227820908605-3.12420.26111.635
137.31367845593-2.70207667604-5.572911994958.840094866423.759138404899.02416555242-0.0363242262862-0.1322029420120.1063123458930.961398255334-0.1893191844240.285081400998-0.3102278214190.2256889052020.1100413427690.357271848837-0.0930594151243-0.01995895717320.2901624083090.05037161636570.192650112592-3.14527.76518.878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:16 )A1 - 16
2X-RAY DIFFRACTION2( CHAIN A AND RESID 17:42 )A17 - 42
3X-RAY DIFFRACTION3( CHAIN A AND RESID 43:53 )A43 - 53
4X-RAY DIFFRACTION4( CHAIN A AND RESID 54:63 )A54 - 63
5X-RAY DIFFRACTION5( CHAIN B AND RESID 2:12 )B2 - 12
6X-RAY DIFFRACTION6( CHAIN B AND RESID 13:42 )B13 - 42
7X-RAY DIFFRACTION7( CHAIN B AND RESID 43:65 )B43 - 65
8X-RAY DIFFRACTION8( CHAIN C AND RESID 2:13 )C2 - 13
9X-RAY DIFFRACTION9( CHAIN C AND RESID 14:24 )C14 - 24
10X-RAY DIFFRACTION10( CHAIN C AND RESID 25:35 )C25 - 35
11X-RAY DIFFRACTION11( CHAIN C AND RESID 36:42 )C36 - 42
12X-RAY DIFFRACTION12( CHAIN C AND RESID 43:53 )C43 - 53
13X-RAY DIFFRACTION13( CHAIN C AND RESID 54:65 )C54 - 65

+
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