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- PDB-3i42: Structure of response regulator receiver domain (CheY-like) from ... -

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Basic information

Entry
Database: PDB / ID: 3i42
TitleStructure of response regulator receiver domain (CheY-like) from Methylobacillus flagellatus
ComponentsResponse regulator receiver domain protein (CheY-like)Response regulator
KeywordsStructural Genomics / Unknown function / CheY-like / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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 receiver domain protein (CheY-like)
Similarity search - Component
Biological speciesMethylobacillus flagellatus KT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsRamagopal, U.A. / Morano, C. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of response regulator receiver domain (CheY-like) from Methylobacillus flagellatus
Authors: Ramagopal, U.A. / Morano, C. / Burley, S.K. / Almo, S.C.
History
DepositionJul 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator receiver domain protein (CheY-like)


Theoretical massNumber of molelcules
Total (without water)14,1521
Polymers14,1521
Non-polymers00
Water1629
1
A: Response regulator receiver domain protein (CheY-like)

A: Response regulator receiver domain protein (CheY-like)


Theoretical massNumber of molelcules
Total (without water)28,3042
Polymers28,3042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area910 Å2
ΔGint-11 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.998, 81.998, 33.291
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Response regulator receiver domain protein (CheY-like) / Response regulator


Mass: 14152.095 Da / Num. of mol.: 1 / Fragment: residues 19-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus flagellatus KT (bacteria)
Gene: Mfla_1736 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1H0I3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris HCl pH 7.0, 0.2M NaCl, 1M Na-citrate dihydrate, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 7121 / Num. obs: 7121 / % possible obs: 99.4 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.104 / Χ2: 1.102 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.15-2.236.60.5876730.90895.1
2.23-2.328.10.5296940.85100
2.32-2.429.60.5026950.882100
2.42-2.5510.50.3817190.943100
2.55-2.71110.3087000.969100
2.71-2.92110.237171.062100
2.92-3.2110.90.1347111.101100
3.21-3.6810.70.0917261.324100
3.68-4.6310.10.0697261.3499.9
4.63-509.60.0617601.4899.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→35.51 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.201 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.784 / SU B: 6.568 / SU ML: 0.169 / SU R Cruickshank DPI: 0.244 / SU Rfree: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 336 4.7 %RANDOM
Rwork0.205 ---
obs0.207 7110 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 410.51 Å2 / Biso mean: 43.65 Å2 / Biso min: 19.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20.74 Å20 Å2
2--1.47 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.15→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 0 9 914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022920
X-RAY DIFFRACTIONr_angle_refined_deg1.461.991243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5335116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.8252640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75815158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.773152
X-RAY DIFFRACTIONr_chiral_restr0.0920.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021681
X-RAY DIFFRACTIONr_mcbond_it1.091.5461
X-RAY DIFFRACTIONr_mcangle_it2.0672728
X-RAY DIFFRACTIONr_scbond_it2.6313250
X-RAY DIFFRACTIONr_scangle_it4.5744.5233
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 30 -
Rwork0.252 451 -
all-481 -
obs--92.5 %

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