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- PDB-4q7e: Non-phosphorylated HemR Receiver Domain from Leptospira biflexa -

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Basic information

Entry
Database: PDB / ID: 4q7e
TitleNon-phosphorylated HemR Receiver Domain from Leptospira biflexa
ComponentsResponse regulator of a two component regulatory system
KeywordsSIGNALING PROTEIN / Response Regulator / DNA BINDING PROTEIN
Function / homologyResponse regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesLeptospira biflexa serovar Patoc (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.441 Å
AuthorsMorero, N.R. / Buschiazzo, A.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: HemR is an OmpR/PhoB-like response regulator from Leptospira, which simultaneously effects transcriptional activation and repression of key haem metabolism genes.
Authors: Morero, N.R. / Botti, H. / Nitta, K.R. / Carrion, F. / Obal, G. / Picardeau, M. / Buschiazzo, A.
History
DepositionApr 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator of a two component regulatory system
B: Response regulator of a two component regulatory system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2718
Polymers29,7022
Non-polymers5686
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-47 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.446, 62.963, 66.977
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Response regulator of a two component regulatory system


Mass: 14851.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira biflexa serovar Patoc (bacteria)
Strain: Patoc / Gene: LBF_1368 / Production host: Escherichia coli (E. coli) / References: UniProt: B0SGG3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2M ammonium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 1, 2012
RadiationMonochromator: Varimax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.441→66.977 Å / Num. all: 40835 / Num. obs: 40835 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 14.68 Å2 / Rsym value: 0.033 / Net I/σ(I): 22.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.44-1.523.10.213.61857559880.2193.5
1.52-1.613.30.1345.81991160830.134100
1.61-1.723.30.0898.61912457410.089100
1.72-1.863.40.06112.31807953430.061100
1.86-2.043.40.04117.3948327790.04156.1
2.04-2.283.50.03320.51186434220.03376.9
2.28-2.634.60.03717.21761038420.03795.8
2.63-3.2270.03518.92373933920.035100
3.22-4.565.60.02724.11512326810.027100
4.56-35.8474.80.02322.6754615640.02399.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.14data extraction
MAR345dtbdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.441→35.847 Å / FOM work R set: 0.9055 / SU ML: 0.13 / σ(F): 1.21 / Phase error: 16.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1846 2000 2.6 %RANDOM
Rwork0.1403 ---
all0.1415 76984 --
obs0.1415 -90.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.08 Å2 / Biso mean: 21.17 Å2 / Biso min: 6.18 Å2
Refinement stepCycle: LAST / Resolution: 1.441→35.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 32 280 2336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122325
X-RAY DIFFRACTIONf_angle_d1.4653167
X-RAY DIFFRACTIONf_chiral_restr0.095333
X-RAY DIFFRACTIONf_plane_restr0.008427
X-RAY DIFFRACTIONf_dihedral_angle_d14.531923
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.441-1.4770.23331170.1814741485880
1.477-1.5170.271420.159459156057100
1.517-1.56160.19861620.13958476009100
1.5616-1.6120.17711600.122558726032100
1.612-1.66960.23851870.116359116098100
1.6696-1.73650.16361410.107558816022100
1.7365-1.81550.13961830.10258636046100
1.8155-1.91120.22231240.10544141426598
1.9112-2.0310.2347720.11373583365598
2.031-2.18780.19211400.118658966036100
2.1878-2.40790.1703960.12863661375762
2.4079-2.75620.17421590.153358826041100
2.7562-3.47210.16591440.157159056049100
3.4721-35.85840.18491730.155358866059100

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