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- PDB-3nhm: Crystal structure of a response regulator from Myxococcus xanthus -

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Basic information

Entry
Database: PDB / ID: 3nhm
TitleCrystal structure of a response regulator from Myxococcus xanthus
ComponentsResponse regulator
KeywordsSIGNALING PROTEIN / Protein Structure Initiative II(PSI II) / NYSGXRC / Structural Genomics / New York SGX Research Center for Structural Genomics
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 speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsPalani, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a response regulator from Myxococcus xanthus
Authors: Palani, K. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 1.3Sep 6, 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
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator
B: Response regulator


Theoretical massNumber of molelcules
Total (without water)29,3802
Polymers29,3802
Non-polymers00
Water2,468137
1
A: Response regulator


Theoretical massNumber of molelcules
Total (without water)14,6901
Polymers14,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Response regulator


Theoretical massNumber of molelcules
Total (without water)14,6901
Polymers14,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.616, 40.408, 99.617
Angle α, β, γ (deg.)90.00, 102.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Response regulator /


Mass: 14690.192 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Strain: DK 1622 / Gene: MXAN_5889 / Plasmid: BC - pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1CZZ7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.89 Å3/Da / Density % sol: 35.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Potassium Thiocyanate, 30% Polyethylene Glycol Monomethyl Ether 2000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2010 / Details: MIRRORS
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.19→48.67 Å / Num. all: 11270 / Num. obs: 11270 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.8
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.5 / Num. unique all: 954 / % possible all: 84.3

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
ARP/wARPmodel building
Cootmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GT7

3gt7


Resolution: 2.19→48.67 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 68091.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 553 5.2 %RANDOM
Rwork0.23 ---
all0.249 11270 --
obs0.23 10640 92.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.4495 Å2 / ksol: 0.386516 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å25.84 Å2
2---3.68 Å20 Å2
3---3.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.19→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 0 137 1879
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.8
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.19→2.33 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 70 4.4 %
Rwork0.25 1511 -
obs-1511 83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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