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- PDB-2q1z: Crystal Structure of Rhodobacter sphaeroides SigE in complex with... -

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Basic information

Entry
Database: PDB / ID: 2q1z
TitleCrystal Structure of Rhodobacter sphaeroides SigE in complex with the anti-sigma ChrR
Components
  • Anti-Sigma factor ChrR, transcriptional activator ChrR
  • RpoE, ECF SigE
KeywordsTRANSCRIPTION / ECF sigma factor / anti-sigma factor / cupin fold / Zinc binding transcription factor
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA binding / metal ion binding
Similarity search - Function
Anti-sigma factor ChrR, putative / Anti-sigma factor, zinc-finger domain / ChrR-like cupin domain / Anti-sigma factor, zinc-finger domain superfamily / ChrR Cupin-like domain / Putative zinc-finger / Putative zinc-finger / RNA polymerase sigma-70 like / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 ...Anti-sigma factor ChrR, putative / Anti-sigma factor, zinc-finger domain / ChrR-like cupin domain / Anti-sigma factor, zinc-finger domain superfamily / ChrR Cupin-like domain / Putative zinc-finger / Putative zinc-finger / RNA polymerase sigma-70 like / 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 / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Arc Repressor Mutant, subunit A / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Anti-sigma-E factor ChrR / ECF RNA polymerase sigma factor RpoE
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsCampbell, E.A. / Darst, S.A.
CitationJournal: Mol.Cell / Year: 2007
Title: A conserved structural module regulates transcriptional responses to diverse stress signals in bacteria.
Authors: Campbell, E.A. / Greenwell, R. / Anthony, J.R. / Wang, S. / Lim, L. / Das, K. / Sofia, H.J. / Donohue, T.J. / Darst, S.A.
History
DepositionMay 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_alt_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_id / _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: RpoE, ECF SigE
B: Anti-Sigma factor ChrR, transcriptional activator ChrR
C: RpoE, ECF SigE
D: Anti-Sigma factor ChrR, transcriptional activator ChrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6928
Polymers83,4304
Non-polymers2624
Water0
1
A: RpoE, ECF SigE
B: Anti-Sigma factor ChrR, transcriptional activator ChrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8464
Polymers41,7152
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-72 kcal/mol
Surface area15410 Å2
MethodPISA, PQS
2
C: RpoE, ECF SigE
D: Anti-Sigma factor ChrR, transcriptional activator ChrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8464
Polymers41,7152
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-75 kcal/mol
Surface area15450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.601, 119.640, 280.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Number of models2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label alt-ID: A / End auth comp-ID: ASP / End label alt-ID: A / End label comp-ID: ASP / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ALAALABB86 - 19486 - 194
2ASPASPDD87 - 19487 - 194
DetailsThe biological assembly (a heterodimer of RpoE and ChrR) is generated by chains A and B or chains C and D

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Components

#1: Protein RpoE, ECF SigE


Mass: 21027.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: rpoE / Plasmid: pET28a derivitive / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: Q3IYV6
#2: Protein Anti-Sigma factor ChrR, transcriptional activator ChrR


Mass: 20687.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: chrR / Plasmid: pET28a derivitive / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P40685
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: sodium acetate, 1.6-1.9M sodium formate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.2806 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2004
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2806 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. all: 29380 / Num. obs: 29316 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.75 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 32.64
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2870 / Rsym value: 0.49 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementResolution: 2.4→35 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.877 / SU B: 44.021 / SU ML: 0.458 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3293 1491 5.2 %RANDOM
Rwork0.28411 ---
all0.28646 29380 --
obs0.28646 27356 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.344 Å2
Baniso -1Baniso -2Baniso -3
1-5.13 Å20 Å20 Å2
2---1.01 Å20 Å2
3----4.12 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 4 0 5189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0217056
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9469590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6675933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93623.213305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.732151037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6381562
X-RAY DIFFRACTIONr_chiral_restr0.0970.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025462
X-RAY DIFFRACTIONr_nbd_refined0.2420.21827
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23259
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2132
X-RAY DIFFRACTIONr_metal_ion_refined0.1610.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3690.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.22
X-RAY DIFFRACTIONr_mcbond_it0.4061.54780
X-RAY DIFFRACTIONr_mcangle_it0.6927333
X-RAY DIFFRACTIONr_scbond_it1.18832554
X-RAY DIFFRACTIONr_scangle_it1.8594.52257
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 707 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.480.5
medium thermal0.472
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 95 -
Rwork0.35 1727 -
obs-2870 85.7 %
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)
11.8256-1.89330.71776.84241.02792.9279-0.2221-0.46090.1001-0.0390.23830.1288-0.1896-0.192-0.0162-0.42860.0053-0.0257-0.20020.0138-0.35432.685618.7605160.2999
24.37660.07121.78628.53731.61949.3266-0.27480.00271.2601-0.98710.20380.0781-1.1553-0.30280.0710.36140.0894-0.2467-0.3107-0.02950.083527.083346.2562150.9795
32.61984.83440.456610.29041.85514.26180.989-0.45210.58412.4484-1.18790.37660.9481-0.64750.19890.9163-0.48560.1786-0.031-0.1948-0.449625.233221.5601194.099
46.36433.5231-0.947612.46852.963410.2770.28170.03320.490.7234-0.1908-0.285-1.10910.6148-0.09080.0144-0.2716-0.1347-0.1606-0.0004-0.171440.637445.5962184.9246
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 180
2X-RAY DIFFRACTION1B2 - 77
3X-RAY DIFFRACTION1B196
4X-RAY DIFFRACTION2B86 - 194
5X-RAY DIFFRACTION2B197
6X-RAY DIFFRACTION3C5 - 175
7X-RAY DIFFRACTION3D2 - 74
8X-RAY DIFFRACTION3D196
9X-RAY DIFFRACTION4D87 - 194
10X-RAY DIFFRACTION4D197

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