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- PDB-6vpw: 1.90 Angstrom Resolution Crystal Structure Chemotaxis protein Che... -

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Basic information

Entry
Database: PDB / ID: 6vpw
Title1.90 Angstrom Resolution Crystal Structure Chemotaxis protein CheX from Vibrio vulnificus
ComponentsChemotaxis protein CheX
KeywordsSIGNALING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyCheY-P phosphatase CheX-like / Chemotaxis phosphatase CheX-like domain / Chemotaxis phosphatase CheX / CheC-like superfamily / chemotaxis / Chemotaxis protein CheX
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Wiersum, G. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.90 Angstrom Resolution Crystal Structure Chemotaxis protein CheX from Vibrio vulnificus
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Wiersum, G. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chemotaxis protein CheX
B: Chemotaxis protein CheX


Theoretical massNumber of molelcules
Total (without water)33,7112
Polymers33,7112
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, 3h2d
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-14 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.093, 44.093, 143.062
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Chemotaxis protein CheX /


Mass: 16855.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (strain CMCP6) (bacteria)
Strain: CMCP6 / Gene: VV1_1397 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A3Q0L3P3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 10.4 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, Screen: Classics II (D7), 0.1M Bis-Tris pH 6.5, 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: Jul 24, 2019 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 21375 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.028 / Rrim(I) all: 0.063 / Rsym value: 0.056 / Χ2: 1.009 / Net I/σ(I): 25
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1065 / CC1/2: 0.823 / CC star: 0.95 / Rpim(I) all: 0.397 / Rrim(I) all: 0.887 / Rsym value: 0.791 / Χ2: 0.995 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h2d

3h2d


Resolution: 1.9→28.58 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.746 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.15
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 1027 4.8 %RANDOM
Rwork0.1741 ---
obs0.1766 20315 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.79 Å2 / Biso mean: 40.315 Å2 / Biso min: 20.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2--1.06 Å20 Å2
3----2.12 Å2
Refinement stepCycle: final / Resolution: 1.9→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 0 101 2365
Biso mean---41.29 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132339
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172221
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.6343154
X-RAY DIFFRACTIONr_angle_other_deg0.3221.5725170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5575307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.33923.084107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57515428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2951513
X-RAY DIFFRACTIONr_chiral_restr0.0570.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0560.022647
X-RAY DIFFRACTIONr_gen_planes_other0.0530.02460
LS refinement shellResolution: 1.902→1.951 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 75 -
Rwork0.267 1473 -
all-1548 -
obs--99.55 %
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)
13.3671-0.6231-1.36564.2039-0.81661.59560.1453-0.25270.20470.24750.1892-0.1794-0.26180.2215-0.33460.2578-0.07050.05560.1563-0.06570.128114.161716.9314.9214
22.1396-0.49480.31751.7628-1.16994.29130.1035-0.122-0.32430.07820.1047-0.02780.00760.0861-0.20820.11370.0386-0.04040.0626-0.0030.072517.3585.8529-0.2454
32.4091-0.201-0.50981.22610.48422.64640.13630.0337-0.01220.11040.105-0.0956-0.14470.1281-0.24130.18020.0062-0.00290.05490.00830.042213.880112.1304-3.1167
41.20330.4940.72492.82210.63163.7128-0.02860.45010.0878-0.17430.1742-0.1119-0.06420.0027-0.14560.2442-0.00510.04610.3194-0.04360.216718.79912.3406-29.1565
56.3105-0.69910.47141.7216-0.47532.4259-0.09330.30550.1814-0.00430.0589-0.3335-0.17550.2120.03440.0149-0.0160.0010.1157-0.0650.100224.11327.0617-19.5601
61.85-0.7094-0.24022.29690.43964.1949-0.01730.1212-0.0054-0.06450.0788-0.1815-0.12780.0595-0.06150.0076-0.01230.01160.0664-0.04680.041319.0085.9917-20.0674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 35
2X-RAY DIFFRACTION2A36 - 83
3X-RAY DIFFRACTION3A84 - 153
4X-RAY DIFFRACTION4B-1 - 29
5X-RAY DIFFRACTION5B30 - 78
6X-RAY DIFFRACTION6B79 - 153

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