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- PDB-6ptg: Structure of RNA polymerase binding protein and transcriptional r... -

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Basic information

Entry
Database: PDB / ID: 6ptg
TitleStructure of RNA polymerase binding protein and transcriptional regulator Dks from Chlamydia trachomatis L2 (LGV434)
ComponentsDnaK Suppressor
KeywordsTRANSCRIPTION / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyDksA, N-terminal domain superfamily / Zinc finger, DksA/TraR C4-type / Prokaryotic dksA/traR C4-type zinc finger / Prokaryotic dksA C4-type zinc finger profiles. / zinc ion binding / DnaK Suppressor
Function and homology information
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of RNA polymerase binding protein and transcriptional regulator Dks from Chlamydia trachomatis L2 (LGV434)
Authors: Abendroth, J. / Buchko, G.W. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.title / _entity.pdbx_fragment ..._citation.title / _entity.pdbx_fragment / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DnaK Suppressor
B: DnaK Suppressor


Theoretical massNumber of molelcules
Total (without water)29,9742
Polymers29,9742
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-7 kcal/mol
Surface area10500 Å2
2
A: DnaK Suppressor


Theoretical massNumber of molelcules
Total (without water)14,9871
Polymers14,9871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: DnaK Suppressor


Theoretical massNumber of molelcules
Total (without water)14,9871
Polymers14,9871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.420, 83.420, 99.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 25 or (resid 63...
21(chain B and (resid 2 through 25 or resid 63...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHR(chain A and (resid 2 through 25 or (resid 63...AA2 - 2510 - 33
12THRTHRTYRTYR(chain A and (resid 2 through 25 or (resid 63...AA63 - 6771 - 75
13METMETSERSER(chain A and (resid 2 through 25 or (resid 63...AA1 - 1229 - 130
14METMETSERSER(chain A and (resid 2 through 25 or (resid 63...AA1 - 1229 - 130
15METMETSERSER(chain A and (resid 2 through 25 or (resid 63...AA1 - 1229 - 130
16METMETSERSER(chain A and (resid 2 through 25 or (resid 63...AA1 - 1229 - 130
21PROPROTHRTHR(chain B and (resid 2 through 25 or resid 63...BB2 - 2510 - 33
22THRTHRVALVAL(chain B and (resid 2 through 25 or resid 63...BB63 - 11071 - 118
23LYSLYSLYSLYS(chain B and (resid 2 through 25 or resid 63...BB111119
24PROPROGLYGLY(chain B and (resid 2 through 25 or resid 63...BB2 - 12310 - 131
25PROPROGLYGLY(chain B and (resid 2 through 25 or resid 63...BB2 - 12310 - 131
26PROPROGLYGLY(chain B and (resid 2 through 25 or resid 63...BB2 - 12310 - 131

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Components

#1: Protein DnaK Suppressor


Mass: 14986.935 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (strain L2 (LGV434)) (bacteria)
Strain: L2 (LGV434) / Plasmid: ChtrB.19237.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: O84412*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Optimization screen HRCS_B5_PEG4000-3350, based on Hampton Research Crystal Screen B5, condition H3: 200mM Lithium sulfate, 25% (w/V) PEG 4000, 100mM Tris Base / HCl pH 8.5: ChtrB.19237.a.B1. ...Details: Optimization screen HRCS_B5_PEG4000-3350, based on Hampton Research Crystal Screen B5, condition H3: 200mM Lithium sulfate, 25% (w/V) PEG 4000, 100mM Tris Base / HCl pH 8.5: ChtrB.19237.a.B1.PW38581 at 24mg/ml, grown at 14C: cryo: 15% EG: tray 310000 h3: puck lkp6-3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 27, 2019
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.95→30.024 Å / Num. obs: 8668 / % possible obs: 98.8 % / Redundancy: 6.108 % / Biso Wilson estimate: 63.378 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.074 / Χ2: 0.998 / Net I/σ(I): 20.54 / Num. measured all: 52942
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.95-3.036.2250.6253.1239096356280.890.68298.9
3.03-3.116.3530.4814.1938186106010.8970.52498.5
3.11-3.26.2150.3425.7936795985920.9670.37399
3.2-3.36.1960.2357.7436435935880.9870.25799.2
3.3-3.416.2680.1819.835735745700.9920.19799.3
3.41-3.536.2430.13312.3933465425360.9980.14598.9
3.53-3.666.2250.11714.6132935365290.9960.12798.7
3.66-3.816.140.08319.632055275220.9970.0999.1
3.81-3.986.1550.07721.3129424834780.9980.08599
3.98-4.176.2130.06225.1129704814780.9980.06899.4
4.17-4.46.1350.04929.5727364504460.9980.05399.1
4.4-4.666.1450.04533.325444184140.9990.04999
4.66-4.996.0520.0531.0924454094040.9980.05598.8
4.99-5.396.0130.04631.6422793813790.9980.0599.5
5.39-5.95.9370.05228.7220843543510.9990.05799.2
5.9-6.65.8220.04234.7818343163150.9980.04699.7
6.6-7.625.8930.03144.3117152932910.9990.03499.3
7.62-9.335.6860.02549.1139324824510.02898.8
9.33-13.195.4790.02356.0610521951920.9990.02598.5
13.19-30.0244.4220.02545.494821281090.9990.02885.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3500)refinement
PDB_EXTRACT3.25data extraction
MR-Rosettaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MR-Rosetta, using input from PDB codes 4ijj, 1tjl, 2kq9, 2kgo, and 5w1s

4ijj

1tjl

2kq9

2kgo

5w1s


Resolution: 2.95→30.024 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.85
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 835 9.65 %0
Rwork0.1823 ---
obs0.1866 8651 98.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 181.16 Å2 / Biso mean: 73.7569 Å2 / Biso min: 29.84 Å2
Refinement stepCycle: final / Resolution: 2.95→30.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 0 23 1293
Biso mean---53.43 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041280
X-RAY DIFFRACTIONf_angle_d0.5421721
X-RAY DIFFRACTIONf_dihedral_angle_d13.278808
X-RAY DIFFRACTIONf_chiral_restr0.039211
X-RAY DIFFRACTIONf_plane_restr0.004216
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A788X-RAY DIFFRACTION4.587TORSIONAL
12B788X-RAY DIFFRACTION4.587TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9502-3.13490.32791330.2636127199
3.1349-3.37660.2671320.2246127199
3.3766-3.71590.24931230.1949130498
3.7159-4.25230.24141490.1679128799
4.2523-5.35250.20981290.1566132299
5.3525-30.0240.19561690.1746136199
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)
18.87372.40310.19232.40640.18494.2583-0.09470.30350.03670.2396-0.1994-1.2785-0.22831.2890.19950.5145-0.0597-0.0560.8427-0.1250.569456.904231.049157.9523
26.0476-1.06350.08835.721-4.72313.9824-0.3134-0.12410.31320.9276-0.10310.2913-1.4389-0.03040.36380.66260.0018-0.02320.7396-0.19370.580747.328236.639360.7916
39.45041.4106-5.66666.9949-1.03843.4138-0.4779-0.1208-0.36410.6748-0.0451-0.32570.3773-0.11980.52060.54760.0378-0.0990.5607-0.09490.383746.80924.227460.2933
44.6453-2.16270.2984.5834-0.02820.0238-0.03641.359-0.0611-1.50790.13660.7433-0.8416-1.92390.0080.78590.0917-0.04711.02770.14290.465432.919929.063159.2556
53.35072.7747-1.60747.73590.59499.8565-0.5892-0.479-0.8587-0.31390.0209-0.56640.82740.38770.59530.67050.02080.02920.45960.06650.5945.74036.775841.0841
67.0672.92071.14166.58292.66467.8260.0714-0.73750.1362-0.207-0.089-0.0913-0.07460.04480.08240.45870.01390.04150.42260.01980.302444.916519.991843.3261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 81 )A25 - 81
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 109 )A82 - 109
4X-RAY DIFFRACTION4chain 'A' and (resid 110 through 122 )A110 - 122
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 81 )B2 - 81
6X-RAY DIFFRACTION6chain 'B' and (resid 82 through 123 )B82 - 123

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