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- PDB-4h5b: Crystal Structure of DR_1245 from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 4h5b
TitleCrystal Structure of DR_1245 from Deinococcus radiodurans
ComponentsDR_1245 protein
KeywordsUNKNOWN FUNCTION / Secretion chaperone-like fold
Function / homologyYope Regulator; Chain: A, - #70 / Putative sensory transduction regulator YbjN / Putative bacterial sensory transduction regulator / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta / BROMIDE ION / : / YbjN domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsNorais, C. / Servant, P. / Bouthier-de-la-Tour, C. / Coureux, P.D. / Ithurbide, S. / Vannier, F. / Guerin, P. / Dulberger, C.L. / Satyshur, K.A. / Keck, J.L. ...Norais, C. / Servant, P. / Bouthier-de-la-Tour, C. / Coureux, P.D. / Ithurbide, S. / Vannier, F. / Guerin, P. / Dulberger, C.L. / Satyshur, K.A. / Keck, J.L. / Armengaud, J. / Cox, M.M. / Sommer, S.
CitationJournal: Plos One / Year: 2013
Title: The Deinococcus radiodurans DR1245 Protein, a DdrB Partner Homologous to YbjN Proteins and Reminiscent of Type III Secretion System Chaperones.
Authors: Norais, C. / Servant, P. / Bouthier-de-la-Tour, C. / Coureux, P.D. / Ithurbide, S. / Vannier, F. / Guerin, P.P. / Dulberger, C.L. / Satyshur, K.A. / Keck, J.L. / Armengaud, J. / Cox, M.M. / Sommer, S.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: DR_1245 protein
B: DR_1245 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,82111
Polymers35,0492
Non-polymers7729
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-42 kcal/mol
Surface area15040 Å2
MethodPISA
2
A: DR_1245 protein
hetero molecules

B: DR_1245 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,82111
Polymers35,0492
Non-polymers7729
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-y+1,x-y,z-1/31
Buried area4080 Å2
ΔGint-37 kcal/mol
Surface area15520 Å2
MethodPISA
3
B: DR_1245 protein
hetero molecules

A: DR_1245 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,82111
Polymers35,0492
Non-polymers7729
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544x-y,x-1,z-1/61
Buried area2890 Å2
ΔGint-33 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.714, 91.714, 87.746
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DR_1245 protein


Mass: 17524.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: DR_1245 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RUY5

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Non-polymers , 5 types, 222 molecules

#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.7 M NH4(SO4)2, 27% w/v glycerol, 100 mM KBr, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.91983 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2010 / Details: Mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91983 Å / Relative weight: 1
ReflectionResolution: 2→45.9 Å / Num. obs: 28448 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.03 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→45.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.507 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.139 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 1441 5.1 %RANDOM
Rwork0.16368 ---
all0.1675 28448 --
obs0.16524 27007 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.394 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refine analyzeLuzzati coordinate error obs: 0.231 Å
Refinement stepCycle: LAST / Resolution: 2→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 42 213 2660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022602
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9583518
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.7824.777157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38215462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7821525
X-RAY DIFFRACTIONr_chiral_restr0.0990.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212007
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 118 -
Rwork0.21 1872 -
obs--96.56 %
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)
13.1324-0.48551.40291.6043-0.30581.3563-0.1281-0.11120.24220.07580.0024-0.0189-0.1606-0.02280.12560.09280.0064-0.01880.0723-0.01970.059361.182240.33577.5843
24.23230.81720.49742.770.2571.26030.00240.1352-0.18320.01180.0055-0.06620.1270.061-0.00790.09480.0041-0.01120.0284-0.01020.011760.437219.17947.2919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 145
2X-RAY DIFFRACTION2B5 - 141

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