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- PDB-7cg5: Structure of the sensor domain (long construct) of the anti-sigma... -

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Basic information

Entry
Database: PDB / ID: 7cg5
TitleStructure of the sensor domain (long construct) of the anti-sigma factor RsgI4 in Pseudobacteroides cellulosolvens
ComponentsAnti-sigma factor RsgI, N-terminal
KeywordsTRANSCRIPTION / Sugar binding protein
Function / homologyAnti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / membrane / Anti-sigma factor RsgI, N-terminal
Function and homology information
Biological speciesPseudobacteroides cellulosolvens ATCC 35603 = DSM 2933 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsDong, S. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31661143023 China
CitationJournal: To Be Published
Title: Structure of the sensor domain of the anti-sigma factor RsgI4 in Pseudobacteroides cellulosolvens
Authors: Dong, S. / Chen, C. / Feng, Y.
History
DepositionJun 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-sigma factor RsgI, N-terminal


Theoretical massNumber of molelcules
Total (without water)14,5261
Polymers14,5261
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6500 Å2
Unit cell
Length a, b, c (Å)71.230, 71.230, 127.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Anti-sigma factor RsgI, N-terminal


Mass: 14526.462 Da / Num. of mol.: 1 / Fragment: sensor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudobacteroides cellulosolvens ATCC 35603 = DSM 2933 (bacteria)
Gene: Bccel_2225 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0L6JMH4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M phosphate-citrate (pH4.2), 0.2 M lithium sulfate and 19% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 2.85→44.31 Å / Num. obs: 5638 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 57.43 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.174 / Net I/σ(I): 9.12
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 2.58 / Num. unique obs: 401 / CC1/2: 0.971 / Rrim(I) all: 0.672 / % possible all: 100

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Processing

Software
NameVersionClassification
XDS20191211data reduction
PHASER2.8.3phasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CG1

7cg1


Resolution: 2.85→35.61 Å / SU ML: 0.3926 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.5754
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2859 557 9.92 %
Rwork0.2406 5058 -
obs0.2449 5615 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.64 Å2
Refinement stepCycle: LAST / Resolution: 2.85→35.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms766 0 0 2 768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067781
X-RAY DIFFRACTIONf_angle_d0.92041059
X-RAY DIFFRACTIONf_chiral_restr0.0552131
X-RAY DIFFRACTIONf_plane_restr0.0045127
X-RAY DIFFRACTIONf_dihedral_angle_d5.7201101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.140.34841380.33631261X-RAY DIFFRACTION99.36
3.14-3.590.36011400.27221241X-RAY DIFFRACTION99.57
3.59-4.520.26711410.23261284X-RAY DIFFRACTION99.79
4.53-35.610.25281380.21031272X-RAY DIFFRACTION99.72
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)
17.27455339209-4.531985954760.582178457087.838371714820.1097806078056.11019963794-0.3377844230910.897250350527-0.395214744065-0.0272253125731-0.148492244217-0.2452201338240.707590670810.3547424382450.5830621007040.6963940975110.07821381375550.09295744593190.4936829874850.06457800151380.47653157961.74489403967-21.78624631515.43761089107
23.13946916262-3.08267984484.085379695487.4346189853-2.826331624528.262348376181.259906815750.553484861486-0.535119925556-2.7920660958-0.756218548983-0.6660471134911.288267323850.589894465387-0.2670284931011.04038148854-0.1482600602770.1151731072210.361040368360.0811245517520.7045682768684.03921891579-28.07158902977.2078090731
37.023648171994.44872611598-2.53202533519.3844390606-2.010217805238.89974441153-0.6404874909360.4761608069050.04300197154051.045299098090.5046753786250.2719692463650.319064674222-0.8163098567130.04274441809550.499892548180.08117232466540.04986818882940.3929686393660.05680079467230.3558408852434.83073966721-19.22199542115.9606192964
47.865832509165.15535427745-0.5915860221324.5145166788-2.899757232935.57256506427-0.1435428104510.156890209014-1.475288354630.5978072917520.00743366975035-0.5147376061051.63852215464-0.319098575982-0.2701010976941.453141969910.04144539892190.107994683550.4828537791750.113154238760.6346270567642.67213181471-31.527522431810.9345020645
52.434397130110.8862337664750.5779677419788.17929618341-3.333940825714.9547703090.560939515190.28180478643-0.00640594603247-0.0162425283421-0.3397720738960.4459795770710.2071548209130.756869167359-0.2731867001460.3998032232910.162995923480.08261967405010.5310927049470.0677978406820.3632619987290.0722414725457-13.644347156911.0971782041
61.77500549687-3.002159390642.573420215849.07385872996-7.677316739498.66711064571-0.5528531402330.008780828899660.3861087084150.98941153646-0.275996531392-1.08340205779-0.226315428449-0.2242156801750.8163989523280.617212791846-0.116915744392-0.03608921872960.46136035062-0.01857344725390.5063363458699.60539284425-19.45969512419.99003885052
7-0.00981594836248-0.01223804042570.1567901631350.9709137729360.3395347963330.3138136119360.623735185584-1.382530439260.408347167142-0.714663940667-0.1759000114020.3164902028830.724596985732-0.317258454941-0.1646244081580.485468817687-0.1263197464430.05680390155950.809552239978-0.1487190535230.653511162354-20.5411839219-4.14436963971.68198978598
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 16 )1 - 161 - 16
22chain 'A' and (resid 17 through 36 )17 - 3617 - 26
33chain 'A' and (resid 37 through 60 )37 - 6027 - 50
44chain 'A' and (resid 61 through 71 )61 - 7151 - 61
55chain 'A' and (resid 72 through 86 )72 - 8662 - 76
66chain 'A' and (resid 87 through 98 )87 - 9877 - 88
77chain 'A' and (resid 99 through 110 )99 - 11089 - 100

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