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- PDB-1kgs: Crystal Structure at 1.50 A of an OmpR/PhoB Homolog from Thermoto... -

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Basic information

Entry
Database: PDB / ID: 1kgs
TitleCrystal Structure at 1.50 A of an OmpR/PhoB Homolog from Thermotoga maritima
ComponentsDNA BINDING RESPONSE REGULATOR D
KeywordsDNA BINDING PROTEIN / DNA-binding protein / alph-beta sandwich / winged-helix / helix-turn-helix / response regulator
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / metal ion binding / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Response regulator
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsBuckler, D.R. / Zhou, Y. / Stock, A.M.
CitationJournal: Structure / Year: 2002
Title: Evidence of intradomain and interdomain flexibility in an OmpR/PhoB homolog from Thermotoga maritima.
Authors: Buckler, D.R. / Zhou, Y. / Stock, A.M.
History
DepositionNov 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA BINDING RESPONSE REGULATOR D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8277
Polymers26,4781
Non-polymers3486
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.570, 71.267, 54.605
Angle α, β, γ (deg.)90.00, 106.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA BINDING RESPONSE REGULATOR D / DRRD


Mass: 26478.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: DRRD / Plasmid: pDrrD / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9WYN0
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein at 12-25 mg/ml in 0.0125 M tris(hydroxymethyl)amino methane (TRIS) pH 8.0, 0.50 M NaCl; precipitating solution: 20% (w/v) PEG 3350, 0.10 M 2-(N-Morpholino)ethanesulfonic acid (MES) ...Details: Protein at 12-25 mg/ml in 0.0125 M tris(hydroxymethyl)amino methane (TRIS) pH 8.0, 0.50 M NaCl; precipitating solution: 20% (w/v) PEG 3350, 0.10 M 2-(N-Morpholino)ethanesulfonic acid (MES) pH 6.5, 0.20 M potassium thiocyanate (KSCN), VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: matrix screening kits
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMMES11pH6.5
210 %PEG335011
3200 mMKSCN11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9640, 0.9796, 0.9797
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2001 / Details: parabolic collimating mirror
RadiationMonochromator: double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9641
20.97961
30.97971
ReflectionResolution: 1.5→20 Å / Num. all: 40628 / Num. obs: 40466 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 7.5
Reflection shellResolution: 1.5→1.57 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 5 / Num. unique all: 5891 / Rsym value: 0.139 / % possible all: 100
Reflection shell
*PLUS
Lowest resolution: 1.58 Å / % possible obs: 100 % / Num. unique obs: 5891

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.612 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: BABINET MODEL WITH MASK / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.072 / Stereochemistry target values: Engh & Huber
Details: Maximum likelihood target and experimental phases as Hendrickson-Lattman coefficients used throughout refinement. TLS refinement performed for last stages where each subdomain defined as ...Details: Maximum likelihood target and experimental phases as Hendrickson-Lattman coefficients used throughout refinement. TLS refinement performed for last stages where each subdomain defined as separate group. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20984 2026 5 %RANDOM
Rwork0.17911 ---
all0.1806 40628 --
obs0.1806 40466 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.834 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0.22 Å2
2--0.33 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 18 206 1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221758
X-RAY DIFFRACTIONr_bond_other_d0.0010.021674
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9852360
X-RAY DIFFRACTIONr_angle_other_deg1.83433866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5463213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75615339
X-RAY DIFFRACTIONr_chiral_restr0.1050.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021889
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02339
X-RAY DIFFRACTIONr_nbd_refined0.2320.3355
X-RAY DIFFRACTIONr_nbd_other0.1940.31553
X-RAY DIFFRACTIONr_nbtor_other0.1970.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.5164
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0370.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.357
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.527
X-RAY DIFFRACTIONr_mcbond_it1.031.51084
X-RAY DIFFRACTIONr_mcangle_it1.77121739
X-RAY DIFFRACTIONr_scbond_it2.9453674
X-RAY DIFFRACTIONr_scangle_it4.5264.5621
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.227 140
Rwork0.19 2816
obs-2816
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)
10.4011-0.00440.00560.4675-0.18710.6133-0.00890.0105-0.019-0.0250.0140.01230.0133-0.0094-0.0050.00140.0034-0.00210.0088-0.00260.018121.29228.90244.608
20.2711-0.04230.11210.167-0.07840.89940.0097-0.00780.01430.0071-0.01120.0062-0.022-0.00050.00160.027700.0010.02830.00380.028521.26740.35176.167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1222 - 122
2X-RAY DIFFRACTION2AA127 - 225127 - 225
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.65
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.227 / Rfactor Rwork: 0.19

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