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- PDB-4cbv: X-ray structure of full-length ComE from Streptococcus pneumoniae. -

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Basic information

Entry
Database: PDB / ID: 4cbv
TitleX-ray structure of full-length ComE from Streptococcus pneumoniae.
ComponentsCOME
KeywordsTRANSCRIPTION / NATURAL GENETIC TRANSFORMATION / TRANSCRIPTION FACTOR / REC DOMAIN
Function / homology
Function and homology information


phosphorelay signal transduction system / DNA binding
Similarity search - Function
LytTr DNA-binding domain / LytTr DNA-binding domain / LytTr DNA-binding domain / LytTR DNA-binding domain / LytTR-type HTH domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...LytTr DNA-binding domain / LytTr DNA-binding domain / LytTr DNA-binding domain / LytTR DNA-binding domain / LytTR-type HTH domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Accessory gene regulator protein A
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.39 Å
AuthorsBoudes, M. / Durand, D. / Graille, M. / van Tilbeurgh, H. / Quevillon-Cheruel, S.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural Insights Into the Dimerization of the Response Regulator Come from Streptococcus Pneumoniae.
Authors: Boudes, M. / Sanchez, D. / Graille, M. / Van Tilbeurgh, H. / Durand, D. / Quevillon-Cheruel, S.
History
DepositionOct 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COME
B: COME
C: COME
D: COME
E: COME
F: COME


Theoretical massNumber of molelcules
Total (without water)185,8676
Polymers185,8676
Non-polymers00
Water0
1
C: COME
D: COME


Theoretical massNumber of molelcules
Total (without water)61,9562
Polymers61,9562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-10.3 kcal/mol
Surface area25060 Å2
MethodPISA
2
E: COME
F: COME


Theoretical massNumber of molelcules
Total (without water)61,9562
Polymers61,9562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-10.3 kcal/mol
Surface area25220 Å2
MethodPISA
3
A: COME
B: COME


Theoretical massNumber of molelcules
Total (without water)61,9562
Polymers61,9562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-10.1 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.893, 135.004, 461.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
COME / RESPONSE REGULATOR


Mass: 30977.785 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q79CK7

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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: 3.75 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 7.5 / Details: 1.8M DL-MALIC ACID, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2010
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.4→45 Å / Num. obs: 71134 / % possible obs: 95.6 % / Observed criterion σ(I): 2.8 / Redundancy: 3.77 % / Biso Wilson estimate: 93.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9
Reflection shellResolution: 3.39→3.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.84 / % possible all: 87.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.39→37.95 Å / Cor.coef. Fo:Fc: 0.9049 / Cor.coef. Fo:Fc free: 0.8773 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.43
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 1897 5.04 %RANDOM
Rwork0.1964 ---
obs0.1978 37635 96.27 %-
Displacement parametersBiso mean: 114.46 Å2
Baniso -1Baniso -2Baniso -3
1--11.4772 Å20 Å20 Å2
2--11.4171 Å20 Å2
3---0.0601 Å2
Refinement stepCycle: LAST / Resolution: 3.39→37.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12732 0 0 0 12732
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812992HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9717470HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6267SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes378HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1813HARMONIC5
X-RAY DIFFRACTIONt_it12992HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.17
X-RAY DIFFRACTIONt_other_torsion3.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1703SEMIHARMONIC5
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_contact14349SEMIHARMONIC4
LS refinement shellResolution: 3.39→3.48 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2452 139 5.47 %
Rwork0.2209 2402 -
all0.2223 2541 -
obs--96.27 %
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)
16.24910.4909-1.85645.6074-2.37015.2802-0.1132-0.54370.0890.87380.1250.8833-0.1212-0.0777-0.0118-0.23650.0230.1756-0.2543-0.02330.162612.3107-10.786419.2359
22.93761.75190.23525.99730.41232.9514-0.09450.2768-0.3233-0.38240.2308-0.59810.0340.2076-0.1363-0.31850.0070.086-0.31-0.00650.283930.9489-19.9309-6.2906
33.9004-0.4719-0.05644.94890.0255.1441-0.2031-0.7954-0.22010.70270.0318-0.6182-0.1120.56080.1713-0.25670.0938-0.0676-0.21170.04620.066538.6273-9.714523.7758
46.3868-1.74462.40146.214-0.92473.93030.0425-0.02090.80680.2261-0.1158-0.3861-0.24870.25620.0734-0.33050.0342-0.0037-0.3679-0.05820.264462.1726-27.61396.3917
55.997-0.1448-0.64783.61030.13035.493-0.0681-0.4734-0.21780.0180.0055-0.24260.49220.37620.06260.30920.06910.10770.07560.1178-0.241925.3146-18.473854.5844
64.4925-1.2935-2.91455.8450.62443.56750.1009-0.44130.24410.53740.11950.1241-0.40690.0897-0.22040.58760.1320.14840.4039-0.0461-0.20739.7488-6.131680.5964
75.87350.0828-2.24453.5559-1.0196.5922-0.00310.07550.8420.2790.43040.1642-0.7357-0.2814-0.42730.50280.10490.25120.00520.13550.072314.64245.623550.235
84.5836-2.35091.03717.6075-3.10087.4176-0.07550.2810.26570.08310.08270.0291-0.0075-0.3417-0.00720.62570.23840.45080.41420.21260.0409-13.183916.181966.8364
92.0477-3.29950.17398.34751.15935.5082-0.03380.0144-0.58950.0495-0.1143-0.39810.26630.18870.14810.8870.19730.4352-0.03010.04180.178456.1331-7.296399.4339
102.28331.8084-0.73566.299-3.56964.7009-0.05110.5793-0.4382-0.0792-0.1106-0.16080.59220.10970.16170.71540.10660.45540.2350.0103-0.008353.54039.140671.2649
113.72070.00950.72186.4108-1.18272.3569-0.09850.2676-0.2026-0.1598-0.10340.31070.4259-0.48270.2020.5736-0.13060.30350.1539-0.019-0.229636.79111.615499.2017
123.12561.3917-1.94943.3081-1.19161.1504-0.04450.0589-0.0598-0.23680.13830.2948-0.1558-0.0119-0.09380.42370.15270.11580.49350.0777-0.246541.554340.059582.6246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 131}
2X-RAY DIFFRACTION2{A|141 - 251}
3X-RAY DIFFRACTION3{B|1 - 131}
4X-RAY DIFFRACTION4{B|141 - 251}
5X-RAY DIFFRACTION5{C|1 - 131}
6X-RAY DIFFRACTION6{C|141 - 249}
7X-RAY DIFFRACTION7{D|1 - 131}
8X-RAY DIFFRACTION8{D|141 - 250}
9X-RAY DIFFRACTION9{E|2 - 131}
10X-RAY DIFFRACTION10{E|141 - 249}
11X-RAY DIFFRACTION11{F|1 - 131}
12X-RAY DIFFRACTION12{F|141 - 256}

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