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- PDB-3uqz: X-ray structure of DNA processing protein A (DprA) from Streptoco... -

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Basic information

Entry
Database: PDB / ID: 3uqz
TitleX-ray structure of DNA processing protein A (DprA) from Streptococcus pneumoniae
ComponentsDNA processing protein DprA
KeywordsDNA BINDING PROTEIN / SAM and Rossmann Fold / DNA processing protein A
Function / homology
Function and homology information


DNA-mediated transformation
Similarity search - Function
DNA processing protein A, sterile alpha motif domain / DNA processing protein A sterile alpha motif domain / DNA recombination-mediator protein A / DNA recombination-mediator protein A / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative DNA processing protein DprA / Putative DNA processing protein DprA
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsQuevillon-Cheruel, S. / Brooks, M.A. / Li de la Sierra-Gallay, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure-function analysis of pneumococcal DprA protein reveals that dimerization is crucial for loading RecA recombinase onto DNA during transformation.
Authors: Quevillon-Cheruel, S. / Campo, N. / Mirouze, N. / Mortier-Barriere, I. / Brooks, M.A. / Boudes, M. / Durand, D. / Soulet, A.L. / Lisboa, J. / Noirot, P. / Martin, B. / van Tilbeurgh, H. / ...Authors: Quevillon-Cheruel, S. / Campo, N. / Mirouze, N. / Mortier-Barriere, I. / Brooks, M.A. / Boudes, M. / Durand, D. / Soulet, A.L. / Lisboa, J. / Noirot, P. / Martin, B. / van Tilbeurgh, H. / Noirot-Gros, M.F. / Claverys, J.P. / Polard, P.
History
DepositionNov 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA processing protein DprA
B: DNA processing protein DprA
C: DNA processing protein DprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8707
Polymers96,4863
Non-polymers3844
Water2,972165
1
A: DNA processing protein DprA
hetero molecules

B: DNA processing protein DprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6125
Polymers64,3242
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_553-x+1/2,y,-z-5/41
Buried area2060 Å2
ΔGint-55 kcal/mol
Surface area25340 Å2
MethodPISA
2
C: DNA processing protein DprA
hetero molecules

C: DNA processing protein DprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5164
Polymers64,3242
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_553-x+1/2,y,-z-5/41
Buried area1880 Å2
ΔGint-49 kcal/mol
Surface area24790 Å2
MethodPISA
3
B: DNA processing protein DprA
hetero molecules

A: DNA processing protein DprA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6125
Polymers64,3242
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_553-x+1/2,y,-z-5/41
Unit cell
Length a, b, c (Å)300.240, 300.240, 78.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein DNA processing protein DprA


Mass: 32162.021 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SP_1266 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97QF0, UniProt: A0A0H2UQA6*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.57 Å3/Da / Density % sol: 73.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 1M LiSO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 110.933
SYNCHROTRONSOLEIL PROXIMA 120.9796
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDFeb 29, 2008
ADSC QUANTUM 315r2CCDMay 10, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSADMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
20.97961
ReflectionResolution: 2.7→41.8 Å / Num. all: 49479 / Num. obs: 47450 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 67.24 Å2
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.464 / % possible all: 92.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→41.76 Å / Cor.coef. Fo:Fc: 0.9161 / Cor.coef. Fo:Fc free: 0.8921 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 2421 5.11 %RANDOM
Rwork0.2193 ---
obs0.2206 47388 --
all-48729 --
Displacement parametersBiso mean: 58.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.1161 Å20 Å20 Å2
2--2.1161 Å20 Å2
3----4.2323 Å2
Refine analyzeLuzzati coordinate error obs: 0.402 Å
Refinement stepCycle: LAST / Resolution: 2.7→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6542 0 20 165 6727
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096682HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.139017HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2357SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes176HARMONIC2
X-RAY DIFFRACTIONt_gen_planes962HARMONIC5
X-RAY DIFFRACTIONt_it6682HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion21.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion851SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7663SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3008 180 5.54 %
Rwork0.2591 3072 -
all0.2614 3252 -

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