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- PDB-1ylf: X-ray crystal structure of BC1842 protein from Bacillus cereus, a... -

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Basic information

Entry
Database: PDB / ID: 1ylf
TitleX-ray crystal structure of BC1842 protein from Bacillus cereus, a member of the Rrf2 family of putative transcription regulators.
ComponentsRRF2 family protein
KeywordsTRANSCRIPTION REGULATOR / structural genomics / RRF2 family / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DNA-binding transcription factor activity / regulation of DNA-templated transcription / cytosol
Similarity search - Function
Transcription regulator Rrf2 / Iron-dependent Transcriptional regulator / Rrf2-type HTH domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsOsipiuk, J. / Wu, R. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of BC1842 protein from Bacillus cereus, a member of the Rrf2 family of putative transcription regulators.
Authors: Osipiuk, J. / Wu, R. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionJan 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 21, 2022Group: 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). THE AUTHORS STATE THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RRF2 family protein
B: RRF2 family protein
C: RRF2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7798
Polymers50,6023
Non-polymers1775
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RRF2 family protein
B: RRF2 family protein
C: RRF2 family protein
hetero molecules

A: RRF2 family protein
B: RRF2 family protein
C: RRF2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,55916
Polymers101,2046
Non-polymers35510
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area12960 Å2
ΔGint-195 kcal/mol
Surface area34370 Å2
MethodPISA
3
A: RRF2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9032
Polymers16,8671
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: RRF2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9744
Polymers16,8671
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
C: RRF2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9032
Polymers16,8671
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.080, 73.080, 157.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RRF2 family protein


Mass: 16867.393 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: Bacillus cereus / Strain: ATCC 14579 / DSM 31 / Gene: BC1842 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q81EX1
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.5 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Na Cl, 25% PEG 3350, Tris_Cl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97917 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 22, 2003
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 17581 / Num. obs: 17282 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17 % / Rmerge(I) obs: 0.101 / Rsym value: 0.068 / Χ2: 1.761 / Net I/σ(I): 25.2
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.02 / Num. unique all: 1190 / Rsym value: 0.469 / Χ2: 0.875 / % possible all: 83.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
CNSphasing
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACT1.401data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.93 / SU B: 12.057 / SU ML: 0.133 / SU R Cruickshank DPI: 0.364 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R- FACTORS, R-WORK AND R-FREE, ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1564 -random
Rwork0.217 ---
all0.216 17222 --
obs0.216 17222 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.119 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0.29 Å20 Å2
2---0.57 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 5 40 2768
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01627550.022
X-RAY DIFFRACTIONr_angle_refined_deg1.47437271.97
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7743475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.22211125.315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20350215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4771115
X-RAY DIFFRACTIONr_chiral_restr0.0924610.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00519720.02
X-RAY DIFFRACTIONr_nbd_refined0.23612050.2
X-RAY DIFFRACTIONr_nbtor_refined0.31619530.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.14840.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2261090.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.24360.2
X-RAY DIFFRACTIONr_mcbond_it0.90117941.5
X-RAY DIFFRACTIONr_mcangle_it1.51528362
X-RAY DIFFRACTIONr_scbond_it2.59610523
X-RAY DIFFRACTIONr_scangle_it3.8268914.5
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 85 -
Rwork0.274 1016 -
obs-1016 83.07 %
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)
12.52720.84090.3085.218-1.13172.39970.2360.089-0.2610.0436-0.16660.19690.0726-0.1203-0.0694-0.1140.0236-0.0488-0.0365-0.0529-0.077133.467416.34847.4527
25.74210.9351.05612.94010.96434.0547-0.0552-0.36930.01190.06460.012-0.1109-0.05890.20420.0432-0.1760.01240.0291-0.0088-0.0019-0.063953.858553.95693.6232
32.14140.0522-1.07592.11331.83397.75260.21740.05360.1954-0.18190.0389-0.0205-0.3141-0.0928-0.2563-0.05190.04540.1175-0.0954-0.0301-0.074128.950538.9339-30.8128
42.9352-1.68272.58491.0017-1.35422.71620.09570.044-0.2819-0.07320.01580.05030.21360.0582-0.1115-0.02350.01870.01820.0230.002-0.054124.49632.5644-0.0517
53.60373.2535-4.26765.2345-5.08545.7257-0.0991-0.0018-0.1040.14230.0556-0.288-0.0095-0.02170.0435-0.07660.0210.0084-0.0012-0.0406-0.076533.725743.42359.053
61.14530.14260.72619.84996.18385.5487-0.14050.10780.0143-0.39220.04890.0698-0.0683-0.05650.0917-0.07420.05740.03390.02940.0081-0.032327.391246.2664-11.4775
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 868 - 89
22BB7 - 8610 - 89
33CC6 - 869 - 89
44AA105 - 142108 - 145
55BB103 - 140106 - 143
66CC106 - 143109 - 146

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