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- PDB-7kpo: High Resolution Crystal Structure of the DNA-binding Domain from ... -

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Basic information

Entry
Database: PDB / ID: 7kpo
TitleHigh Resolution Crystal Structure of the DNA-binding Domain from the Sensor Histidine Kinase ChiS from Vibrio cholerae
ComponentsResponse regulator
KeywordsDNA BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / DNA-binding Domain / Histidine Kinase
Function / homology
Function and homology information


phosphorelay response regulator activity / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / membrane => GO:0016020 / nucleotide binding / plasma membrane
Similarity search - Function
HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain ...HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / Histidine kinase / Histidine kinase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.28 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: High Resolution Crystal Structure of the DNA-binding Domain from the Sensor Histidine Kinase ChiS from Vibrio cholerae.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4338
Polymers12,8501
Non-polymers5827
Water3,603200
1
A: Response regulator
hetero molecules

A: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,86516
Polymers25,7002
Non-polymers1,16514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3040 Å2
ΔGint-89 kcal/mol
Surface area12730 Å2
MethodPISA
2
A: Response regulator
hetero molecules

A: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,86516
Polymers25,7002
Non-polymers1,16514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area3090 Å2
ΔGint-84 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.912, 78.606, 72.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Response regulator /


Mass: 12850.206 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Gene: GTF71_10845, GTF73_11165, GTF74_11165, GTF75_11330 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: A0A6M4V2D1, UniProt: Q9KUA1*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 59.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 6.3 mg/ml, 0.01M Tris pH 8.3; Screen: Classics II (G2), 0.2M Lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2019 / Details: Be
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.28→30 Å / Num. obs: 38590 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Rsym value: 0.076 / Χ2: 1.576 / Net I/σ(I): 28.3
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1866 / CC1/2: 0.637 / CC star: 0.882 / Rpim(I) all: 0.386 / Rrim(I) all: 0.854 / Rsym value: 0.757 / Χ2: 1.002 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.28→25.97 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.262 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1803 1885 4.9 %RANDOM
Rwork0.1443 ---
obs0.146 36482 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.95 Å2 / Biso mean: 18.571 Å2 / Biso min: 9.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.28→25.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 38 228 1148
Biso mean--31.77 31.77 -
Num. residues----107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131049
X-RAY DIFFRACTIONr_bond_other_d0.0010.017982
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.6631429
X-RAY DIFFRACTIONr_angle_other_deg0.3621.5812292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8055133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.7220.67859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.54115191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4121511
X-RAY DIFFRACTIONr_chiral_restr0.0550.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0520.021171
X-RAY DIFFRACTIONr_gen_planes_other0.0470.02230
X-RAY DIFFRACTIONr_rigid_bond_restr1.64532030
LS refinement shellResolution: 1.28→1.313 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 138 -
Rwork0.214 2634 -
all-2772 -
obs--98.33 %
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)
14.26391.11691.13041.8021-0.41481.4541-0.0241-0.0298-0.08720.0664-0.033-0.18570.05680.05080.05710.02450.0028-0.00790.0168-0.01140.036710.210733.707236.6363
21.40940.27170.44053.1173-1.33752.2515-0.0059-0.0999-0.10480.19520.08640.226-0.0052-0.2462-0.08050.0225-0.01270.02290.05060.00240.0328-7.748622.67336.4625
31.4637-0.76850.07941.39230.77992.9598-0.0414-0.0645-0.05290.20690.0420.04040.1041-0.0531-0.00060.0424-0.00160.00080.0120.00030.03642.890225.573142.4164
40.6703-0.00970.33291.9265-0.59381.7425-0.01410.013-0.0252-0.1092-0.01060.02960.0213-0.02860.02460.01770.0001-0.00940.0181-0.0050.0095-0.463628.583224.9865
59.6281-2.27893.4493.7884-1.61514.2352-0.03450.05830.0501-0.14070.0698-0.2430.14750.1365-0.03530.03220.0122-0.00280.0239-0.00950.028113.361431.292728.0848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1022 - 1038
2X-RAY DIFFRACTION2A1039 - 1070
3X-RAY DIFFRACTION3A1079 - 1092
4X-RAY DIFFRACTION4A1093 - 1119
5X-RAY DIFFRACTION5A1120 - 1128

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