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- PDB-3q7r: 1.6A resolution structure of the ChxR receiver domain from Chlamy... -

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Basic information

Entry
Database: PDB / ID: 3q7r
Title1.6A resolution structure of the ChxR receiver domain from Chlamydia trachomatis
ComponentsTranscriptional regulatory protein
KeywordsTRANSCRIPTION / ChxR / receiver domain / transcription factor / OmpR / Chlamydia
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / identical protein binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Atypical response regulator protein ChxR / Transcriptional regulatory protein
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsHickey, J. / Lovell, S. / Battaile, K.P. / Hu, L. / Middaugh, C.R. / Hefty, P.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The atypical response regulator protein ChxR has structural characteristics and dimer interface interactions that are unique within the OmpR/PhoB subfamily.
Authors: Hickey, J.M. / Lovell, S. / Battaile, K.P. / Hu, L. / Middaugh, C.R. / Hefty, P.S.
History
DepositionJan 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulatory protein
B: Transcriptional regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6454
Polymers28,5212
Non-polymers1242
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-8 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.867, 41.268, 45.171
Angle α, β, γ (deg.)90.000, 105.520, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Transcriptional regulatory protein


Mass: 14260.336 Da / Num. of mol.: 2 / Fragment: unp residues 2-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: 434/Bu / Gene: CTLon_0888 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0BA84, UniProt: A0A0H3MDW1*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 20% PEG 3350, 0.2M sodium thiocyanate, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→23.66 Å / Num. obs: 35320 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 13.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3523 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 75.32 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å35.12 Å
Translation1.6 Å35.12 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→23.66 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8659 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 20.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 1768 5.01 %RANDOM
Rwork0.1883 ---
obs0.1894 35309 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.887 Å2 / ksol: 0.459 e/Å3
Displacement parametersBiso max: 98.98 Å2 / Biso mean: 28.8457 Å2 / Biso min: 9.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.135 Å20 Å2-0.0167 Å2
2--0.1602 Å2-0 Å2
3----0.0252 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 8 108 1817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151788
X-RAY DIFFRACTIONf_angle_d1.5132432
X-RAY DIFFRACTIONf_chiral_restr0.11275
X-RAY DIFFRACTIONf_plane_restr0.009307
X-RAY DIFFRACTIONf_dihedral_angle_d11.967665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.65720.2881600.231233613521100
1.6572-1.72350.25941750.215833233498100
1.7235-1.80190.22561740.188433823556100
1.8019-1.89690.21621740.180332913465100
1.8969-2.01570.20661760.179733303506100
2.0157-2.17120.22141670.16733713538100
2.1712-2.38950.19231830.17133203503100
2.3895-2.73490.21561940.174533593553100
2.7349-3.4440.20091800.191233943574100
3.444-23.66440.19271850.1853410359598
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)
10.57470.0544-0.28490.2888-0.08120.1532-0.04210.17650.0293-0.03160.0034-0.25750.02340.01630.00370.1715-0.00140.04220.1295-0.00140.114235.02230.39327.3675
20.0328-0.02910.02220.05340.00540.0212-0.14290.0517-0.0967-0.3480.16130.1228-0.0250.1584-0.00170.363-0.05260.01390.25640.00180.10231.48380.3731-1.3529
30.31250.1467-0.18060.2331-0.03520.1120.1640.251-0.0738-0.14930.1095-0.0417-0.09390.26640.01670.22390.02170.04310.16920.04490.136335.02175.0155.2133
40.09530.150.0450.17840.07810.02330.01650.0301-0.06080.04670.0385-0.0085-0.076-0.043700.1631-0.00250.01550.09920.00390.129633.20876.268815.2762
50.0793-0.0174-0.13620.00490.01280.3586-0.1282-0.1956-0.18130.1790.0516-0.38920.090.16820.00470.15580.008-0.01040.10050.00260.103431.66822.912426.0649
60.97890.0974-0.35930.6633-0.31650.1974-0.03760.03050.0282-0.07160.03960.0450.0014-0.0584-00.1362-0.0106-0.00180.0942-0.00160.10523.26951.952620.4598
70.1258-0.0573-0.00490.03220.01220.0021-0.04110.49350.12420.0702-0.15310.10890.0602-0.3761-0.00040.2062-0.0005-0.03370.2621-0.0070.14322.72192.1695.6244
80.1377-0.0758-0.02350.05560.08080.2618-0.1552-0.3811-0.04480.05340.1360.37370.0383-0.54340.00050.1068-0.0224-0.0120.38530.05460.38030.6753-0.572321.0281
90.0650.00590.02140.019-0.00040.0048-0.0681-0.14320.0605-0.0373-0.00620.1163-0.1315-0.451600.16160.0484-0.00330.3556-0.03070.37993.78723.01928.7323
100.1288-0.0446-0.05230.0706-0.00930.16960.00230.33080.29360.00550.01820.0157-0.2522-0.84710.00420.19730.0392-0.04810.3502-0.02830.46310.196.107420.4436
110.0967-0.03010.00020.0151-0.00540.00450.03980.5094-0.17460.0039-0.03350.17550.1363-0.036400.1595-0.0296-0.06490.35020.01880.28074.4397-0.872711.0384
120.1322-0.4260.06361.4039-0.14270.21280.20650.5961-0.28560.04120.01840.7401-0.03550.32660.01470.1193-0.0337-0.10350.57140.01050.26788.4999-2.3357.0083
130.4076-0.1794-0.10970.2372-0.03210.06230.00940.29-0.3169-0.13210.06870.1639-0.0099-0.3982-00.1845-0.0534-0.04470.3892-0.0440.224214.8985-5.51798.5473
140.19510.01290.16440.1118-0.01340.1269-0.1362-0.1810.191-0.10610.00650.276-0.0936-0.0090.00040.1523-0.0074-0.01820.20170.04090.262712.40374.002722.4235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:19)A2 - 19
2X-RAY DIFFRACTION2(chain A and resid 20:26)A20 - 26
3X-RAY DIFFRACTION3(chain A and resid 27:36)A27 - 36
4X-RAY DIFFRACTION4(chain A and resid 37:51)A37 - 51
5X-RAY DIFFRACTION5(chain A and resid 52:57)A52 - 57
6X-RAY DIFFRACTION6(chain A and resid 58:95)A58 - 95
7X-RAY DIFFRACTION7(chain A and resid 96:111)A96 - 111
8X-RAY DIFFRACTION8(chain B and resid 4:19)B4 - 19
9X-RAY DIFFRACTION9(chain B and resid 20:24)B20 - 24
10X-RAY DIFFRACTION10(chain B and resid 25:37)B25 - 37
11X-RAY DIFFRACTION11(chain B and resid 43:54)B43 - 54
12X-RAY DIFFRACTION12(chain B and resid 55:74)B55 - 74
13X-RAY DIFFRACTION13(chain B and resid 75:95)B75 - 95
14X-RAY DIFFRACTION14(chain B and resid 96:110)B96 - 110

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