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- PDB-3hdv: Crystal structure of response regulator receiver protein from Pse... -

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Basic information

Entry
Database: PDB / ID: 3hdv
TitleCrystal structure of response regulator receiver protein from Pseudomonas putida
ComponentsResponse regulator
Keywordstranscription regulator / Response regulator / PSI-II / 11224l / Structural Genomics / 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
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsBagaria, A. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of response regulator receiver protein from Pseudomonas putida
Authors: Bagaria, A. / Burley, S.K. / Swaminathan, S.
History
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Response regulator
B: Response regulator
C: Response regulator
D: Response regulator


Theoretical massNumber of molelcules
Total (without water)60,9604
Polymers60,9604
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-32 kcal/mol
Surface area23830 Å2
MethodPISA
2
A: Response regulator
C: Response regulator


Theoretical massNumber of molelcules
Total (without water)30,4802
Polymers30,4802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-11 kcal/mol
Surface area12330 Å2
MethodPISA
3
B: Response regulator
D: Response regulator


Theoretical massNumber of molelcules
Total (without water)30,4802
Polymers30,4802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-11 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.769, 140.436, 48.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailstetramer

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Components

#1: Protein
Response regulator


Mass: 15240.009 Da / Num. of mol.: 4 / Fragment: Response Regulator
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP_0355, PP0355 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q88QX9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 0.1M HEPES pH7.5, 0.8M Potassium Sodium Tartarate tetrahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111)CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→44.5 Å / Num. obs: 45411 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.09→44.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.178 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2304 5.1 %RANDOM
Rwork0.205 ---
obs0.207 43315 99.6 %-
all-45411 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.95 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.09→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 0 243 3978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223767
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8752.0085095
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.94524.088159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85615712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.6371535
X-RAY DIFFRACTIONr_chiral_restr0.1260.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022711
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21722
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22570
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3721.52517
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.03523858
X-RAY DIFFRACTIONr_scbond_it3.44931423
X-RAY DIFFRACTIONr_scangle_it4.9994.51237
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 187 -
Rwork0.252 2958 -
obs--95.33 %

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