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- PDB-2bnl: The structure of the N-terminal domain of RsbR -

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Basic information

Entry
Database: PDB / ID: 2bnl
TitleThe structure of the N-terminal domain of RsbR
ComponentsMODULATOR PROTEIN RSBR
KeywordsSTRESS-RESPONSE / STRESS RESPONSE / PHOSPHORYLATION
Function / homology
Function and homology information


oxygen binding / heme binding
Similarity search - Function
RsbS co-antagonist protein RsbRA N-terminal domain / Rsbr N terminal / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / Globin/Protoglobin / Globins / Globin-like / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RsbT co-antagonist protein RsbRA
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMurray, J.W. / Delumeau, O. / Lewis, R.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of a Nonheme Globin in Environmental Stress Signaling.
Authors: Murray, J.W. / Delumeau, O. / Lewis, R.J.
History
DepositionMar 28, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MODULATOR PROTEIN RSBR
B: MODULATOR PROTEIN RSBR
C: MODULATOR PROTEIN RSBR
D: MODULATOR PROTEIN RSBR
E: MODULATOR PROTEIN RSBR
F: MODULATOR PROTEIN RSBR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8799
Polymers97,8106
Non-polymers693
Water14,250791
1
A: MODULATOR PROTEIN RSBR
B: MODULATOR PROTEIN RSBR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6263
Polymers32,6032
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: MODULATOR PROTEIN RSBR
D: MODULATOR PROTEIN RSBR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6263
Polymers32,6032
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: MODULATOR PROTEIN RSBR
F: MODULATOR PROTEIN RSBR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6263
Polymers32,6032
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)136.062, 136.062, 113.296
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 136
2116B1 - 136
3116C1 - 136
4116D1 - 136
5116E1 - 136
6116F1 - 136

NCS oper:
IDCodeMatrixVector
1given(0.42321, -0.89735, 0.12512), (-0.8885, -0.43808, -0.13658), (0.17737, -0.05337, -0.9827)145.28452, 228.84772, -14.81048
2given(0.53964, 0.82318, 0.17652), (0.84167, -0.52268, -0.13562), (-0.01938, 0.22176, -0.97491)-63.73373, 201.23291, -26.1363
3given(-0.52929, 0.84757, 0.0383), (-0.84817, -0.52973, 0.00143), (0.0215, -0.03173, 0.99927)-65.59531, 200.93973, -12.74161
4given(-0.99888, -0.0292, 0.03722), (-0.03026, 0.99914, -0.02822), (-0.03636, -0.02932, -0.99891)70.91087, 42.5564, 21.62604
5given(-0.40159, -0.91172, -0.08653), (0.90787, -0.40874, 0.09327), (-0.1204, -0.0411, 0.99187)139.89409, 144.87776, -25.49308

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Components

#1: Protein
MODULATOR PROTEIN RSBR


Mass: 16301.636 Da / Num. of mol.: 6 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P42409
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPOSITIVE REGULATOR OF SIGMA-B ACTIVITY IN SALT AND HEAT STRESS
Sequence detailsSEQUENCE FROM RESIDUES 3-136.

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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: 2.97 Å3/Da / Density % sol: 58.28 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: EQUAL VOLUMES OF 1.8M SODIUM MALONATE PH 8.0 AND 10MG/ML N-RSBR PROTEIN IN A HANGING DROP ABOVE A WELL OF 1.8M SODIUM MALONATE PH 8.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97889
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 2→22.25 Å / Num. obs: 80643 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 21.05 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 3.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 13.11 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.24 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→22.24 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.449 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.198 4050 5 %RANDOM
Rwork0.154 ---
obs0.157 76557 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→22.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6484 0 3 791 7278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0226600
X-RAY DIFFRACTIONr_bond_other_d0.0010.025803
X-RAY DIFFRACTIONr_angle_refined_deg2.1121.9448938
X-RAY DIFFRACTIONr_angle_other_deg1.065313572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8645767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.80626.246357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.591151222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6561519
X-RAY DIFFRACTIONr_chiral_restr0.1440.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021280
X-RAY DIFFRACTIONr_nbd_refined0.2360.21618
X-RAY DIFFRACTIONr_nbd_other0.1780.25975
X-RAY DIFFRACTIONr_nbtor_refined0.1940.23354
X-RAY DIFFRACTIONr_nbtor_other0.0950.23648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2631
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1320.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2650.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4191.53880
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.53426284
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.26732854
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5594.52654
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2018 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.445
2Bloose positional0.485
3Cloose positional0.385
4Dloose positional0.495
5Eloose positional0.445
6Floose positional0.565
1Aloose thermal2.0610
2Bloose thermal2.5110
3Cloose thermal2.3510
4Dloose thermal2.7610
5Eloose thermal2.3610
6Floose thermal2.2410
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 287
Rwork0.164 5555
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)
11.6767-0.35840.94222.2545-0.51331.19560.1313-0.1467-0.0583-0.04080.03170.1476-0.0584-0.1217-0.163-0.0661-0.02270.0385-0.03610.0271-0.070833.74151.469-5.2885
21.69420.4983-0.60092.48460.35260.61850.1109-0.01020.2464-0.0897-0.06680.19240.0285-0.1335-0.0441-0.0592-0.0207-0.0233-0.02440.0207-0.064223.3741133.3655-12.6748
32.52240.7009-0.55271.7692-0.6940.6715-0.13630.0594-0.1947-0.05410.06430.00230.08060.07820.072-0.06150.00280.0131-0.0497-0.0184-0.062110.3892109.80723.6028
42.43540.8212-0.36011.7540.50040.9471-0.10010.1286-0.12150.04420.1743-0.13210.0643-0.0485-0.0742-0.05230.0132-0.0129-0.0386-0.0158-0.0933-10.5172110.06911.1623
52.30290.14570.33622.9686-0.20371.16680.13970.1507-0.05160.17740.0188-0.146-0.11680.0245-0.1586-0.0339-0.01220.032-0.08470.016-0.086534.7773110.678822.4206
61.9934-0.1649-0.44531.8175-0.92851.25840.09860.06960.17490.068-0.0802-0.0565-0.00930.1647-0.0183-0.0306-0.0284-0.0122-0.04960.0074-0.093446.315593.303929.856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 136
2X-RAY DIFFRACTION2B3 - 136
3X-RAY DIFFRACTION3C3 - 136
4X-RAY DIFFRACTION4D3 - 136
5X-RAY DIFFRACTION5E3 - 136
6X-RAY DIFFRACTION6F3 - 136

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