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- PDB-2b4a: Crystal structure of a response regulator receiver domain protein... -

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Basic information

Entry
Database: PDB / ID: 2b4a
TitleCrystal structure of a response regulator receiver domain protein (bh3024) from bacillus halodurans c-125 at 2.42 A resolution
ComponentsBH3024
KeywordsSIGNALING PROTEIN / Flavodoxin-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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 speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.42 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of BH3024 protein (10175646) from BACILLUS HALODURANS at 2.42 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: 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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BH3024
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7433
Polymers15,6191
Non-polymers1242
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.003, 39.003, 172.741
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein BH3024


Mass: 15618.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: 10175646 / Plasmid: HK100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K8I2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.54 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.2
Details: 0.2M NaCl, 10.0% PEG-8000, 0.1M Na, K-Phosphate, pH 6.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2005 / Details: flat mirror
RadiationMonochromator: Single Crystal Si(333) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.36→28.94 Å / Num. obs: 5994 / % possible obs: 98 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.36-2.4284.83.80.711.13690.71
2.42-2.4991.17.90.6061.33730.606
2.49-2.5698.38.70.5141.54120.514
2.56-2.6410010.60.4421.74000.442
2.64-2.7310012.70.38423870.384
2.73-2.8210012.60.3012.53800.301
2.82-2.9310012.90.2532.93640.253
2.93-3.0510012.60.23.73550.2
3.05-3.1810012.60.1345.23350.134
3.18-3.3410012.50.1215.73330.121
3.34-3.5210012.20.1036.23200.103
3.52-3.7310012.20.0926.42940.092
3.73-3.9910011.80.0935.32910.093
3.99-4.3110012.10.0688.52690.068
4.31-4.7299.911.80.053112440.053
4.72-5.2899.811.50.04911.82240.049
5.28-6.0999.910.90.05111.82150.051
6.09-7.461009.30.05510.61850.055
7.46-10.5599.59.80.04412.41510.044
10.55-28.9489.77.80.03813.5930.038

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0013refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: molecular replacement
Starting model: 1kgs

1kgs


Resolution: 2.42→28.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 16.654 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. HIS 87 AND GLU 88 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 257 4.6 %RANDOM
Rwork0.182 ---
all0.185 ---
obs-5309 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.123 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--0.68 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.42→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 8 25 922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021912
X-RAY DIFFRACTIONr_bond_other_d0.0010.02589
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9661237
X-RAY DIFFRACTIONr_angle_other_deg0.99531455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0175114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4182536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54515150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.805152
X-RAY DIFFRACTIONr_chiral_restr0.1040.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02165
X-RAY DIFFRACTIONr_nbd_refined0.2110.2158
X-RAY DIFFRACTIONr_nbd_other0.1950.2558
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2455
X-RAY DIFFRACTIONr_nbtor_other0.0940.2455
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.22
X-RAY DIFFRACTIONr_mcbond_it2.3723602
X-RAY DIFFRACTIONr_mcbond_other0.4433228
X-RAY DIFFRACTIONr_mcangle_it3.8155940
X-RAY DIFFRACTIONr_scbond_it6.3098347
X-RAY DIFFRACTIONr_scangle_it8.32611297
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 19 -
Rwork0.289 326 -
obs--89.15 %
Refinement TLS params.Method: refined / Origin x: 28.6778 Å / Origin y: 16.2032 Å / Origin z: 73.4553 Å
111213212223313233
T-0.0405 Å20.002 Å2-0.0099 Å2-0.1811 Å2-0.1066 Å2--0.0432 Å2
L6.7271 °2-1.3427 °2-3.4635 °2-2.1846 °22.6625 °2--7.2576 °2
S0.2299 Å °0.2097 Å °0.0733 Å °0.0225 Å °0.0664 Å °-0.0196 Å °-0.2541 Å °0.0259 Å °-0.2963 Å °
Refinement TLS groupSelection: all

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