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- PDB-4xrf: Crystal structure of MepR like protein complexed with pseudoligands -

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Basic information

Entry
Database: PDB / ID: 4xrf
TitleCrystal structure of MepR like protein complexed with pseudoligands
ComponentsTranscriptional regulator, MarR family
KeywordsTRANSCRIPTION / WINGED HELIX TURN HELIX TRANSCRIPTION FACTOR
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / 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
LAURIC ACID / ISOQUINOLINE / NICKEL (II) ION / PHOSPHATE ION / Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 Å
AuthorsHong, M. / Kim, M.I. / Cho, M.U.
CitationJournal: to be published
Title: Crystal structure of MepR like protein complexed with pseudoligands
Authors: Hong, M. / Kim, M.I. / Cho, M.U.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,58011
Polymers16,5311
Non-polymers1,04810
Water1,18966
1
A: Transcriptional regulator, MarR family
hetero molecules

A: Transcriptional regulator, MarR family
hetero molecules

A: Transcriptional regulator, MarR family
hetero molecules

A: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,31844
Polymers66,1254
Non-polymers4,19340
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area17640 Å2
ΔGint-283 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.172, 111.172, 67.368
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-203-

PO4

21A-208-

PO4

31A-322-

HOH

DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -X+Y, Y, -Z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transcriptional regulator, MarR family / MepR-like transcription factor


Mass: 16531.305 Da / Num. of mol.: 1 / Fragment: UNP residues 5-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31) (bacteria)
Strain: ATCC 14579 / DSM 31 / Gene: BC_0657 / Plasmid: pET49b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q81HX3

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Non-polymers , 7 types, 76 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ISQ / ISOQUINOLINE


Mass: 129.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7N
#4: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.63 Å3/Da / Density % sol: 66.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1M phosphate citrate, 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97958 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 8, 2014 / Details: certical focusing toroidal, rhodium coated
RadiationMonochromator: DCM Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 13502 / % possible obs: 99.1 % / Redundancy: 20.6 % / Rmerge(I) obs: 0.094 / Χ2: 5.479 / Net I/av σ(I): 83.969 / Net I/σ(I): 16.8 / Num. measured all: 277710
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.16-2.218.10.3376462.33798.9
2.2-2.2420.80.3316742.706100
2.24-2.2821.50.2846603.058100
2.28-2.3321.30.276693.215100
2.33-2.3821.50.2396513.71100
2.38-2.4321.20.2296653.831100
2.43-2.4921.40.2156843.873100
2.49-2.5621.40.1936514.157100
2.56-2.6421.30.1766814.537100
2.64-2.7221.10.1576675.258100
2.72-2.8221.30.1456725.376100
2.82-2.9321.20.136746.036100
2.93-3.0621.20.1216736.745100
3.06-3.2321.10.1086817.154100
3.23-3.43210.1036778.309100
3.43-3.6920.80.0916938.746100
3.69-4.0620.50.0826929.197100
4.06-4.6519.70.0696987.85599.3
4.65-5.8619.30.0637147.08899.7
5.86-5015.90.0566805.98586.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata reduction
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→26.72 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.708 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 670 5 %RANDOM
Rwork0.2131 12815 --
obs0.2144 12822 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.63 Å2 / Biso mean: 45.695 Å2 / Biso min: 20.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.43 Å20 Å2
2---0.43 Å20 Å2
3---1.4 Å2
Refinement stepCycle: final / Resolution: 2.16→26.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 62 69 1287
Biso mean--60.49 52 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191235
X-RAY DIFFRACTIONr_angle_refined_deg1.782.0171661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0795147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.24124.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41215235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.581159
X-RAY DIFFRACTIONr_chiral_restr0.0850.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02877
X-RAY DIFFRACTIONr_mcbond_it0.9451.447576
X-RAY DIFFRACTIONr_mcangle_it1.6522.154720
X-RAY DIFFRACTIONr_scbond_it1.6442.037658
LS refinement shellResolution: 2.162→2.219 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 53 -
Rwork0.255 912 -
all-965 -
obs--98.37 %
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)
12.8910.9093-0.91071.09090.41651.3144-0.3032-0.0447-0.18250.05060.2634-0.10710.22390.10870.03980.46420.05310.03440.3267-0.03160.0293-46.361-14.1680.175
22.3344-0.0474-0.57733.14660.86273.2166-0.32210.3066-0.1307-0.39190.4494-0.2799-0.09850.1105-0.12720.4871-0.11040.12820.4662-0.16810.0955-35.234-9.713-15.843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 34
2X-RAY DIFFRACTION1A35 - 53
3X-RAY DIFFRACTION1A99 - 146
4X-RAY DIFFRACTION2A54 - 98

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