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- PDB-2i6f: Receiver domain from Myxococcus xanthus social motility protein FrzS -

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Basic information

Entry
Database: PDB / ID: 2i6f
TitleReceiver domain from Myxococcus xanthus social motility protein FrzS
ComponentsResponse regulator FrzS
KeywordsSIGNALING PROTEIN / Social motility / signaling / receiver domain / two-component
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Response regulator homolog / Response regulator FrzS
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEchols, N. / Fraser, J. / Merlie, J. / Zusman, D. / Alber, T.
CitationJournal: Mol.Microbiol. / Year: 2007
Title: An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS.
Authors: Fraser, J.S. / Merlie, J.P. / Echols, N. / Weisfield, S.R. / Mignot, T. / Wemmer, D.E. / Zusman, D.R. / Alber, T.
History
DepositionAug 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Response regulator FrzS
B: Response regulator FrzS
C: Response regulator FrzS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2017
Polymers41,0603
Non-polymers1424
Water4,792266
1
A: Response regulator FrzS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7222
Polymers13,6871
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Response regulator FrzS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7573
Polymers13,6871
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Response regulator FrzS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7222
Polymers13,6871
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.479, 142.479, 37.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Response regulator FrzS


Mass: 13686.523 Da / Num. of mol.: 3 / Fragment: Receiver domain (residues 1-124)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: frzS / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21+ / References: UniProt: Q1D4U9, UniProt: O68522*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2005
RadiationMonochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 30067 / Num. obs: 30067 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 25 Å2 / Net I/σ(I): 6.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 4230 / Rsym value: 0.64 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2gkg

2gkg


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.59 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.182 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25369 1518 5.1 %RANDOM
Rwork0.21991 ---
obs0.22167 30067 98.5 %-
all-30067 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 4 266 2936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222713
X-RAY DIFFRACTIONr_bond_other_d0.0010.022571
X-RAY DIFFRACTIONr_angle_refined_deg0.8261.9833675
X-RAY DIFFRACTIONr_angle_other_deg0.67135962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8075362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55525.088114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97115453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1051518
X-RAY DIFFRACTIONr_chiral_restr0.0480.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023075
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
X-RAY DIFFRACTIONr_nbd_refined0.1790.2532
X-RAY DIFFRACTIONr_nbd_other0.1480.22566
X-RAY DIFFRACTIONr_nbtor_refined0.1520.21341
X-RAY DIFFRACTIONr_nbtor_other0.0750.21630
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2206
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1360.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.224
X-RAY DIFFRACTIONr_mcbond_it0.1851.51908
X-RAY DIFFRACTIONr_mcbond_other0.0251.5756
X-RAY DIFFRACTIONr_mcangle_it0.31622857
X-RAY DIFFRACTIONr_scbond_it0.4143965
X-RAY DIFFRACTIONr_scangle_it0.6744.5817
LS refinement shellResolution: 1.9→2.002 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.354 229 -
Rwork0.35 3977 -
obs-3977 97.81 %
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)
11.8971-0.4052-0.1651.08670.07622.02130.0536-0.05580.0570.02090.0235-0.0265-0.184-0.0471-0.0771-0.04370.015-0.0074-0.08180.0132-0.0456134.158190.11441.7682
21.7747-0.6541-0.33792.2539-0.1271.58030.04080.0316-0.0066-0.0698-0.05680.0551-0.0927-0.08550.016-0.07370.0747-0.0127-0.0266-0.0168-0.0759108.328194.113121.4326
34.539-0.29681.52085.84450.52151.6395-0.105-0.55650.85160.2501-0.15040.667-0.2118-0.30750.2554-0.0877-0.00550.0487-0.0479-0.15680.2233141.3783113.57658.5706
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1244 - 127
2X-RAY DIFFRACTION2BB3 - 1236 - 126
3X-RAY DIFFRACTION3CC3 - 1206 - 123

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