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- PDB-3ilh: Crystal structure of Two component response regulator from Cytoph... -

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Basic information

Entry
Database: PDB / ID: 3ilh
TitleCrystal structure of Two component response regulator from Cytophaga hutchinsonii
ComponentsTwo component response regulator
Keywordstranscription regulator / NYSGXRC / PSI-II / two component response regulator / Protein structure Initiative / structural genomics / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


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
Two component response regulator / Two component response regulator
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
AuthorsSyed Ibrahim, B. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Two component response regulator from Cytophaga hutchinsonii
Authors: Syed Ibrahim, B. / Burley, S.K. / Swaminathan, S.
History
DepositionAug 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.3Feb 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: Two component response regulator


Theoretical massNumber of molelcules
Total (without water)16,5991
Polymers16,5991
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Two component response regulator

A: Two component response regulator


Theoretical massNumber of molelcules
Total (without water)33,1982
Polymers33,1982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1140 Å2
ΔGint-12 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.671, 63.671, 158.388
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Two component response regulator


Mass: 16598.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / Gene: narL, CHU_1356 / Plasmid: TOP10 INVITROGEN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q11VD8, UniProt: A0A6N4SQL8*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 298 K / pH: 4.5
Details: 0.1M Sodium Acetate trihydrate, pH4.5, 3.0M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2009 / Details: MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 6499 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 55.9 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 9.8
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 47.9 % / Rmerge(I) obs: 0.81 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.59→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.558 / SU ML: 0.228 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.458 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 300 4.6 %RANDOM
Rwork0.232 ---
obs0.235 6160 99.9 %-
all-6499 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20.38 Å20 Å2
2--0.76 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 0 14 1062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0390.0221068
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.2911.9551452
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5625132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.57325.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.79715190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.563155
X-RAY DIFFRACTIONr_chiral_restr0.1960.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02800
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2990.2488
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3410.2724
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0420.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7511.5693
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.84421081
X-RAY DIFFRACTIONr_scbond_it4.5313439
X-RAY DIFFRACTIONr_scangle_it6.9924.5371
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.503 30 -
Rwork0.238 441 -
obs--99.16 %

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