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- PDB-4qtp: Crystal Structure of an Anti-sigma Factor Antagonist from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 4qtp
TitleCrystal Structure of an Anti-sigma Factor Antagonist from Mycobacterium paratuberculosis
ComponentsAnti-sigma factor antagonist
KeywordsPROTEIN BINDING / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / STAS domain / Anti-sigma factor antagonist
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
CITRIC ACID / Anti-sigma factor antagonist
Similarity search - Component
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsDranow, D.M. / Clifton, M.C. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of an Anti-sigma Factor Antagonist from Mycobacterium paratuberculosis
Authors: Dranow, D.M. / Clifton, M.C. / Edwards, T.E. / Lorimer, D.
History
DepositionJul 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 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 / 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 / _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 / _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: Anti-sigma factor antagonist
B: Anti-sigma factor antagonist
C: Anti-sigma factor antagonist
D: Anti-sigma factor antagonist
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,79224
Polymers59,9404
Non-polymers1,85220
Water7,188399
1
A: Anti-sigma factor antagonist
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4556
Polymers14,9851
Non-polymers4705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anti-sigma factor antagonist
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3935
Polymers14,9851
Non-polymers4084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Anti-sigma factor antagonist
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5508
Polymers14,9851
Non-polymers5657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Anti-sigma factor antagonist
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3935
Polymers14,9851
Non-polymers4084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.170, 58.300, 58.900
Angle α, β, γ (deg.)69.660, 78.610, 78.940
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERARGARGAA2 - 11624 - 138
21SERSERARGARGBB2 - 11624 - 138
12SERSERARGARGAA2 - 11624 - 138
22SERSERARGARGCC2 - 11624 - 138
13ALAALAARGARGAA3 - 11625 - 138
23ALAALAARGARGDD3 - 11625 - 138
14LEULEUASPASPBB1 - 11723 - 139
24LEULEUASPASPCC1 - 11723 - 139
15ALAALAARGARGBB3 - 11625 - 138
25ALAALAARGARGDD3 - 11625 - 138
16ALAALAARGARGCC3 - 11625 - 138
26ALAALAARGARGDD3 - 11625 - 138

NCS ensembles :
ID
1
2
3
4
5
6
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein
Anti-sigma factor antagonist


Mass: 14984.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: ATCC BAA-968 / K-10 / Gene: MAP_0380 / Production host: Escherichia coli (E. coli) / References: UniProt: Q744G1
#2: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: JCSG(a3): 20% PEG-3350, 200mM ammonium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 55656 / Num. obs: 54310 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.227 Å2 / Rmerge(I) obs: 0.052 / Χ2: 0.975 / Net I/σ(I): 19.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.950.4413.1215874399596.3
1.95-20.3464.0515501390196.7
2-2.060.2834.9114893374896.8
2.06-2.120.2266.3314421364097
2.12-2.190.1777.8814077355497.1
2.19-2.270.1519.2313809348297
2.27-2.360.12810.7413182332997.5
2.36-2.450.10712.8112807323997.5
2.45-2.560.08615.3612186308197.7
2.56-2.690.06819.2211693295797.9
2.69-2.830.05822.2811073280498.2
2.83-30.04626.710538267098.1
3-3.210.0430.110016254198.3
3.21-3.470.0338.919234234898.3
3.47-3.80.02545.678342211998.8
3.8-4.250.02250.357799198498.7
4.25-4.910.01954.136827173198.8
4.91-6.010.0251.135688144898.6
6.01-8.50.0251.884440113198.9
8.50.01760.85227360897.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.42 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1829 / WRfactor Rwork: 0.1564 / FOM work R set: 0.8671 / SU B: 4.031 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1109 / SU Rfree: 0.1069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1932 2603 5 %RANDOM
Rwork0.1659 ---
obs0.1672 52225 93.99 %-
all-54828 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.53 Å2 / Biso mean: 24.449 Å2 / Biso min: 7.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.03 Å2-0.01 Å2
2---0.09 Å20.43 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 122 399 3842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193554
X-RAY DIFFRACTIONr_bond_other_d0.0090.023457
X-RAY DIFFRACTIONr_angle_refined_deg1.5412.0214863
X-RAY DIFFRACTIONr_angle_other_deg1.42337991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4715483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.46424.766107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99415513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0091513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213936
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02629
X-RAY DIFFRACTIONr_mcbond_it1.4931.6251887
X-RAY DIFFRACTIONr_mcbond_other1.4931.6231886
X-RAY DIFFRACTIONr_mcangle_it2.5072.4132361
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A68520.07
12B68520.07
21A64290.13
22C64290.13
31A63780.13
32D63780.13
41B64590.13
42C64590.13
51B63680.13
52D63680.13
61C65850.04
62D65850.04
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 173 -
Rwork0.245 3295 -
all-3468 -
obs--83.99 %
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)
10.5011-0.5595-0.44611.61650.27120.9225-0.0221-0.00020.03770.09690.01340.09840.0587-0.01490.00870.0269-0.0111-0.0120.0726-0.01430.115112.035516.152853.8212
23.3495-1.2341.66023.48730.89968.02970.2739-0.17690.5709-0.0245-0.0462-0.1906-0.4311-0.1225-0.22760.1105-0.03880.04670.0621-0.02390.237315.639427.810854.4867
30.3603-0.6656-0.29531.31780.58711.6193-0.03240.0216-0.00160.07690.0276-0.01640.09380.08320.00480.0233-0.0104-0.00680.0901-0.01620.101141.103931.228564.8299
43.42161.7443-1.48029.3855-0.76343.88020.28380.4294-0.3263-0.5251-0.3009-0.04590.2061-0.02450.01710.13760.0444-0.05380.1811-0.06050.089537.727326.643453.9188
50.0854-0.2537-0.12581.6993-0.68771.7076-0.00690.0178-0.03020.19720.07480.0611-0.2097-0.1169-0.06790.0822-0.0008-0.00140.0633-0.01150.088218.214-1.103870.5144
66.0649-1.09521.59867.42392.104922.2053-0.32370.11290.27310.93850.4370.5886-1.6129-0.8221-0.11330.37610.20580.19620.15950.11910.19067.03773.236780.0794
70.1145-0.1845-0.24831.334-0.56782.2851-0.0101-0.04220.0184-0.1567-0.0518-0.02780.31250.09070.06190.08110.0013-0.01210.06060.01030.083234.999121.59485.6509
83.9245-0.3664-4.81063.8329-1.85577.5498-0.2552-0.263-0.0259-0.5134-0.1011-0.3561.09090.45890.35630.8150.1150.17050.04860.04540.103641.835312.586190.0744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 97
2X-RAY DIFFRACTION2A98 - 117
3X-RAY DIFFRACTION3B1 - 97
4X-RAY DIFFRACTION4B98 - 117
5X-RAY DIFFRACTION5C1 - 107
6X-RAY DIFFRACTION6C108 - 117
7X-RAY DIFFRACTION7D67
8X-RAY DIFFRACTION8D98 - 117

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