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- PDB-5h6x: The crystal structure of RpoS fragment including a partial region... -

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Basic information

Entry
Database: PDB / ID: 5h6x
TitleThe crystal structure of RpoS fragment including a partial region 1.2 and region 2 from intracellular pathogen Legionella pneumophila
ComponentsRNA polymerase sigma factor RpoS
KeywordsTRANSCRIPTION / intracellular pathogen / RNA polymerase / regulatory factor
Function / homology
Function and homology information


DNA-templated transcription initiation => GO:0006352 / sigma factor activity / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
RNA polymerase sigma factor RpoS / Sigma-70 factors family signature 1. / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 ...RNA polymerase sigma factor RpoS / Sigma-70 factors family signature 1. / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA polymerase sigma factor RpoS / RNA polymerase sigma factor RpoS
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, N. / Chen, X. / Gong, X. / Ge, H.
Funding support China, 1items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31270770 China
CitationJournal: Crystals / Year: 2018
Title: High-Resolution Crystal Structure of RpoS Fragment including a Partial Region 1.2 and Region 2 from the Intracellular Pathogen Legionella pneumophila
Authors: Zhang, N. / Chen, X. / Gong, X. / Li, T. / Xie, Z. / Hameed, M.F. / Wang, M. / Ge, H.
History
DepositionNov 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_type.id / _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: RNA polymerase sigma factor RpoS
B: RNA polymerase sigma factor RpoS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5715
Polymers23,4332
Non-polymers1383
Water3,333185
1
A: RNA polymerase sigma factor RpoS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8554
Polymers11,7171
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-8 kcal/mol
Surface area6450 Å2
MethodPISA
2
B: RNA polymerase sigma factor RpoS


Theoretical massNumber of molelcules
Total (without water)11,7171
Polymers11,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area6560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.910, 68.905, 70.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 101 - 191 / Label seq-ID: 7 - 97

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles :
ID
1
2

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Components

#1: Protein RNA polymerase sigma factor RpoS / Sigma S / Sigma-38


Mass: 11716.687 Da / Num. of mol.: 2 / Fragment: UNP residues 77-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: rpoS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S4T1, UniProt: Q5ZW04*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1.96 Å3/Da / Density % sol: 37.27 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: 12% PEG8000 0.2M NaCl 0.1M Hepes pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2013
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 25054 / % possible obs: 99.9 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 31.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 6.1 / Num. measured obs: 1217 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4yg2

4yg2


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.717 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19218 1274 5.1 %RANDOM
Rwork0.16435 ---
obs0.16578 23727 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20 Å2
2--0.7 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 8 185 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191637
X-RAY DIFFRACTIONr_bond_other_d0.0060.021643
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9762208
X-RAY DIFFRACTIONr_angle_other_deg1.04933774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9635202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56822.56478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30515326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0591519
X-RAY DIFFRACTIONr_chiral_restr0.0780.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021809
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02388
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5460 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 99 -
Rwork0.206 1686 -
obs--98.18 %

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