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- PDB-4hyl: The crystal structure of an anti-sigma-factor antagonist from Hal... -

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Basic information

Entry
Database: PDB / ID: 4hyl
TitleThe crystal structure of an anti-sigma-factor antagonist from Haliangium ochraceum DSM 14365
ComponentsStage II sporulation protein
KeywordsTRANSCRIPTION REGULATOR / structural genomics / PSI-Biology / protein structure initiative / Midwest Center For Structural Genomics / MCSG
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
Anti-sigma factor antagonist
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.751 Å
AuthorsTan, K. / Chhor, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of an anti-sigma-factor antagonist from Haliangium ochraceum DSM 14365
Authors: Tan, K. / Chhor, G. / Clancy, S. / Joachimiak, A.
History
DepositionNov 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stage II sporulation protein
B: Stage II sporulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,50510
Polymers25,9062
Non-polymers5998
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-35 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.466, 59.466, 65.599
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsExperimentally unknown. Chains A and B may form a dimer.

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Components

#1: Protein Stage II sporulation protein


Mass: 12953.056 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (bacteria) / Strain: DSM 14365 / Gene: Haliangium ochraceum, Hoch_4443 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D0LNN2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.58 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Ammonium Sulfate, 22%(w/v) PEG4000, 0.1M Sodium Avetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.75→26 Å / Num. all: 26011 / Num. obs: 26011 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 32
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1286 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.751→25.75 Å / σ(F): 1.96 / Phase error: 33.11 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 1329 5.11 %random
Rwork0.202 ---
obs0.2086 25983 99.55 %-
all-25983 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.994 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.8088 Å20 Å2-0 Å2
2--7.8088 Å20 Å2
3----15.6177 Å2
Refinement stepCycle: LAST / Resolution: 1.751→25.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 35 109 1891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081796
X-RAY DIFFRACTIONf_angle_d1.0752422
X-RAY DIFFRACTIONf_dihedral_angle_d14.973651
X-RAY DIFFRACTIONf_chiral_restr0.07290
X-RAY DIFFRACTIONf_plane_restr0.004305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7516-1.82170.45271300.38992764X-RAY DIFFRACTION95
1.8217-1.90460.4191350.38452749X-RAY DIFFRACTION95
1.9046-2.0050.36051380.35282762X-RAY DIFFRACTION95
2.005-2.13050.32921440.33112773X-RAY DIFFRACTION95
2.1305-2.29490.28261640.29762711X-RAY DIFFRACTION94
2.2949-2.52560.33231390.28912782X-RAY DIFFRACTION95
2.5256-2.89050.27211650.26832713X-RAY DIFFRACTION94
2.8905-3.63970.23361410.17742755X-RAY DIFFRACTION95
3.6397-23.97130.15681700.11442635X-RAY DIFFRACTION91
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)
10.164-0.16920.13460.4328-0.41060.6505-0.1733-0.11930.3192-0.1189-0.12760.12880.1346-0.2531-0.00520.4003-0.0563-0.01480.32330.00930.32747.11882.01419.9037
20.4333-0.3417-0.04040.3857-0.22270.47840.16430.1188-0.00340.2568-0.0886-0.24850.12680.0044-0.00010.26280.0231-0.02570.2330.0030.318913.81545.97136.1328
30.1355-0.11020.16330.2538-0.09950.1735-0.10730.03620.07180.30490.15590.0480.51920.468-0.00030.330.0912-0.00770.29740.04720.350116.9015-1.97927.2414
40.4589-0.02920.38560.0774-0.02020.29550.1324-0.20690.03710.2793-0.13530.01270.4734-0.5185-0.00090.4209-0.02-0.00130.23270.03970.26396.1-2.7031.7777
51.0794-0.276-0.4210.40460.48230.5943-0.023-0.063-0.08450.2203-0.33450.1142-0.72020.1546-0.01480.413-0.0723-0.07430.1850.08850.437715.357111.83220.9564
60.2059-0.13840.27070.1251-0.19430.27830.1608-0.1013-0.0748-0.17050.10320.04530.03720.34030.00050.29860.0429-0.02570.37760.01020.39717.5707-2.8843-3.3045
70.2510.07-0.17490.0173-0.0260.34550.0728-0.0110.04420.2307-0.1066-0.19750.4454-0.5108-0.07260.3314-0.0114-0.02010.19140.0290.30787.4241-1.5231-3.0622
80.10950.1529-0.05230.225-0.03290.07760.1335-0.49460.2479-0.2566-0.2841-0.0186-0.47770.5654-0.00050.4253-0.0946-0.04340.36920.08960.406713.836610.6389-10.4005
90.3298-0.20210.40021.05440.07140.56220.06320.05610.20020.0001-0.0259-0.008-0.1343-0.5800.25160.0680.0280.39440.02340.27223.02451.5939-5.7752
100.3591-0.0914-0.24460.0793-0.08510.42070.02630.11380.1146-0.87280.01550.00870.07420.4055-0.00350.3836-0.04460.00920.38860.01580.318828.7372-6.7916-31.8562
110.8169-0.1927-0.13650.05660.11350.9009-0.09070.17610.052-0.23190.0493-0.10750.01490.1635-0.00010.2802-0.0261-0.02220.2870.04550.328827.7006-4.6001-27.493
120.6886-0.2777-0.44660.17560.15880.45130.5392-0.01580.00920.0445-0.14790.02520.3614-0.81620.01430.3642-0.1275-0.12560.36060.00910.424218.3183-7.5219-27.0019
130.2163-0.19040.16720.2513-0.02140.342-0.03940.18570.13180.3496-0.0322-0.0423-0.04510.2366-0.00020.3002-0.0479-0.05380.30280.01640.329630.3207-5.4501-22.7398
140.0747-0.01660.08970.1129-0.11540.1540.3322-0.20990.06820.2365-0.3010.2965-0.5478-0.3114-0.00050.3110.05140.05810.3367-0.06310.409618.4557-3.2863-18.3401
150.2741-0.39090.13990.8711-0.65650.9696-0.08020.04410.10770.09220.0814-0.0678-0.1055-0.19390.00010.24310.0277-0.03170.33-0.01570.300728.2118-6.1098-13.4045
160.01170.00870.00680.04130.01890.0060.34930.1951-0.5520.00640.20780.1380.83180.0324-0.00090.42450.0662-0.12360.3544-0.01480.446131.9263-20.9903-19.8519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:10)
2X-RAY DIFFRACTION2chain 'A' and (resseq 11:24)
3X-RAY DIFFRACTION3chain 'A' and (resseq 25:35)
4X-RAY DIFFRACTION4chain 'A' and (resseq 36:47)
5X-RAY DIFFRACTION5chain 'A' and (resseq 48:53)
6X-RAY DIFFRACTION6chain 'A' and (resseq 54:69)
7X-RAY DIFFRACTION7chain 'A' and (resseq 70:80)
8X-RAY DIFFRACTION8chain 'A' and (resseq 81:90)
9X-RAY DIFFRACTION9chain 'A' and (resseq 91:111)
10X-RAY DIFFRACTION10chain 'B' and (resseq -2:8)
11X-RAY DIFFRACTION11chain 'B' and (resseq 9:24)
12X-RAY DIFFRACTION12chain 'B' and (resseq 25:40)
13X-RAY DIFFRACTION13chain 'B' and (resseq 41:53)
14X-RAY DIFFRACTION14chain 'B' and (resseq 54:69)
15X-RAY DIFFRACTION15chain 'B' and (resseq 70:101)
16X-RAY DIFFRACTION16chain 'B' and (resseq 102:112)

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