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- PDB-3f43: Crystal structure of a putative anti-sigma factor antagonist (tm1... -

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Basic information

Entry
Database: PDB / ID: 3f43
TitleCrystal structure of a putative anti-sigma factor antagonist (tm1081) from thermotoga maritima at 1.59 A resolution
ComponentsPutative anti-sigma factor antagonist TM1081
KeywordsTRANSCRIPTION / Stas domain / spoiiaa-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


anti-sigma factor antagonist activity
Similarity search - Function
Anti-sigma factor antagonist / STAS domain / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Putative anti-sigma factor antagonist TM_1081
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.59 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative anti-sigma factor antagonist TM1081 (TM1081) from THERMOTOGA MARITIMA at 1.59 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: 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: Putative anti-sigma factor antagonist TM1081
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0886
Polymers14,6371
Non-polymers4515
Water2,180121
1
A: Putative anti-sigma factor antagonist TM1081
hetero molecules

A: Putative anti-sigma factor antagonist TM1081
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,17612
Polymers29,2752
Non-polymers90210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2940 Å2
ΔGint-82 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.700, 49.700, 113.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative anti-sigma factor antagonist TM1081


Mass: 14637.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1081, TM_1081 / Plasmid: MH4a / Production host: Escherichia Coli (E. coli) / Strain (production host): HK200 / References: UniProt: Q9X0H0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH.

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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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.67
Details: 38.0% polyethylene glycol 400, 0.2M magnesium chloride, 0.1M citric acid pH 5.67, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97967
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979671
ReflectionResolution: 1.59→29.881 Å / Num. obs: 19931 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.628 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.05
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.59-1.650.7251.5139503793199.4
1.65-1.710.5572.1123533342199.2
1.71-1.790.4212.7137613688199
1.79-1.880.2874.1132073498199.6
1.88-20.1786.4142103746199.8
2-2.160.11210.1144283789199.6
2.16-2.370.09714.4159743541199.8
2.37-2.720.10218.5235133729199.8
2.72-3.420.07126.52779436321100
3.42-29.8810.05333.3283973702199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.59→29.881 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.187 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.084
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (4). CL IONS AND PEG 400 FRAGMENTS (1PE AND PEG) FROM CRYSTALLIZATION SOLUTION WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1013 5.1 %RANDOM
Rwork0.178 ---
obs0.179 19865 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.55 Å2 / Biso mean: 29.405 Å2 / Biso min: 12.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--0.76 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 1.59→29.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 26 121 1088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221053
X-RAY DIFFRACTIONr_bond_other_d0.010.02723
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9691417
X-RAY DIFFRACTIONr_angle_other_deg1.10831777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4235129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61524.54544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67615184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.932153
X-RAY DIFFRACTIONr_chiral_restr0.1020.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021139
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02207
X-RAY DIFFRACTIONr_nbd_refined0.2360.2207
X-RAY DIFFRACTIONr_nbd_other0.1690.2688
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2524
X-RAY DIFFRACTIONr_nbtor_other0.0870.2498
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.214
X-RAY DIFFRACTIONr_mcbond_it2.2883682
X-RAY DIFFRACTIONr_mcbond_other0.483248
X-RAY DIFFRACTIONr_mcangle_it2.96651026
X-RAY DIFFRACTIONr_scbond_it4.9778459
X-RAY DIFFRACTIONr_scangle_it7.34211391
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 62 -
Rwork0.25 1349 -
all-1411 -
obs--99.65 %
Refinement TLS params.Method: refined / Origin x: 9.4423 Å / Origin y: 25.7872 Å / Origin z: 7.1158 Å
111213212223313233
T-0.0615 Å2-0.0164 Å2-0.0122 Å2--0.0637 Å20.0016 Å2---0.0871 Å2
L1.353 °2-0.332 °2-0.9063 °2-2.3557 °20.9479 °2--2.1388 °2
S0.0478 Å °0.0067 Å °0.1553 Å °0.0579 Å °-0.0207 Å °-0.0215 Å °-0.049 Å °-0.1785 Å °-0.0271 Å °

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