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- PDB-3uz0: Crystal Structure of SpoIIIAH and SpoIIQ Complex -

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Basic information

Entry
Database: PDB / ID: 3uz0
TitleCrystal Structure of SpoIIIAH and SpoIIQ Complex
Components
  • Stage II sporulation protein Q
  • Stage III sporulation protein AH
KeywordsTRANSPORT PROTEIN / Hybrid Transporter / Sporulation / Membrane
Function / homology
Function and homology information


endospore-forming forespore / sporulation resulting in formation of a cellular spore / metalloendopeptidase activity / membrane / plasma membrane
Similarity search - Function
Stage III sporulation protein AH-like / Stage III sporulation protein AH-like / Stage III sporulation protein AH-like superfamily / SpoIIIAH-like protein / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich ...Stage III sporulation protein AH-like / Stage III sporulation protein AH-like / Stage III sporulation protein AH-like superfamily / SpoIIIAH-like protein / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Helix Hairpins / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Stage III sporulation protein AH / Stage II sporulation protein Q
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.82 Å
AuthorsMaehigashi, T. / Meisner, J. / Dunham, C.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the basal components of a bacterial transporter.
Authors: Meisner, J. / Maehigashi, T. / Andre, I. / Dunham, C.M. / Moran, C.P.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stage III sporulation protein AH
B: Stage II sporulation protein Q
C: Stage III sporulation protein AH
D: Stage II sporulation protein Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3427
Polymers63,0534
Non-polymers2883
Water48627
1
A: Stage III sporulation protein AH
B: Stage II sporulation protein Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6233
Polymers31,5272
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-17 kcal/mol
Surface area13320 Å2
MethodPISA
2
C: Stage III sporulation protein AH
D: Stage II sporulation protein Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7194
Polymers31,5272
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-25 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.370, 64.490, 176.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Stage III sporulation protein AH


Mass: 14764.911 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: JH642 / Gene: spoIIIAH, BSU24360 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P49785
#2: Protein Stage II sporulation protein Q


Mass: 16761.836 Da / Num. of mol.: 2 / Fragment: UNP residues 73-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: JH642 / Gene: spoIIQ, ywnI, BSU36550 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P71044
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2.8M Ammonium sulfate, 10mM Mg acetate, 50 mM MES, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2011 / Details: MIRRORS
RadiationMonochromator: KOHZU DIAMOND MONOCHROMATOR / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→36.4 Å / Num. obs: 36350 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 12.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: SAD / Resolution: 2.82→36.4 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 28.6 / Stereochemistry target values: MLHL / Details: BIJVOET PAIRS MERGED PRIOR TO THE REFINEMENT
RfactorNum. reflection% reflection
Rfree0.27 1253 7.11 %
Rwork0.208 --
obs0.213 17632 98.8 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.86 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0106 Å20 Å2-0 Å2
2--4.7374 Å2-0 Å2
3----3.7268 Å2
Refinement stepCycle: LAST / Resolution: 2.82→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 15 27 3892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013904
X-RAY DIFFRACTIONf_angle_d1.3925290
X-RAY DIFFRACTIONf_dihedral_angle_d17.0061406
X-RAY DIFFRACTIONf_chiral_restr0.091631
X-RAY DIFFRACTIONf_plane_restr0.005689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.93290.36121400.26211720X-RAY DIFFRACTION96
2.9329-3.06630.3951350.27041786X-RAY DIFFRACTION98
3.0663-3.22790.35911330.27171774X-RAY DIFFRACTION98
3.2279-3.430.33091360.24651790X-RAY DIFFRACTION99
3.43-3.69460.2951410.2121813X-RAY DIFFRACTION99
3.6946-4.06590.2561380.18591819X-RAY DIFFRACTION100
4.0659-4.65330.19281380.151843X-RAY DIFFRACTION100
4.6533-5.85870.2191410.18921872X-RAY DIFFRACTION100
5.8587-36.42810.2871510.22881962X-RAY DIFFRACTION99

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