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- PDB-4ija: Structure of S. aureus methicillin resistance factor MecR2 -

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Basic information

Entry
Database: PDB / ID: 4ija
TitleStructure of S. aureus methicillin resistance factor MecR2
ComponentsXylR protein
KeywordsPROTEIN BINDING / ROK family protein
Function / homology
Function and homology information


D-xylose metabolic process / DNA-binding transcription factor activity
Similarity search - Function
ROK family signature. / ROK family / ROK family / MarR family / MarR-type HTH domain / ATPase, nucleotide binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A ...ROK family signature. / ROK family / ROK family / MarR family / MarR-type HTH domain / ATPase, nucleotide binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / XylR protein / XylR protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsArede, P. / Botelho, T. / Guevara, T. / Uson, I. / Oliveira, D.C. / Gomis-Ruth, F.X.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure-Function Studies of the Staphylococcal Methicillin Resistance Antirepressor MecR2.
Authors: Arede, P. / Botelho, T. / Guevara, T. / Uson, I. / Oliveira, D.C. / Gomis-Ruth, F.X.
History
DepositionDec 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: XylR protein
B: XylR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,99213
Polymers90,1882
Non-polymers80411
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-16 kcal/mol
Surface area32020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.470, 73.220, 157.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein XylR protein


Mass: 45094.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: HU25 / Gene: mecR2, SA0041, xylR / Plasmid: pCri8a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99XE2, UniProt: A0A0H3JS71*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: Crystals suitable for structure analysis were obtained at 5.4mg/ml protein concentration in 20 mM Tris-HCl, 200 mM NaCl, pH7.4 by using 0.2M NaCl, 20% PEG 1000, 0.1M KH2PO4/Na2HPO4, pH6.2 as ...Details: Crystals suitable for structure analysis were obtained at 5.4mg/ml protein concentration in 20 mM Tris-HCl, 200 mM NaCl, pH7.4 by using 0.2M NaCl, 20% PEG 1000, 0.1M KH2PO4/Na2HPO4, pH6.2 as reservoir solution. Crystals were cryo-protected with reservoir solution supplemented with 30% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→49.22 Å / Num. all: 45671 / Num. obs: 45488 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 19.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.716 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→49.22 Å / Cor.coef. Fo:Fc: 0.9461 / Cor.coef. Fo:Fc free: 0.9275 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 762 1.68 %RANDOM
Rwork0.1904 ---
all0.191 46195 --
obs0.191 45433 --
Displacement parametersBiso mean: 49.15 Å2
Baniso -1Baniso -2Baniso -3
1--7.252 Å20 Å20 Å2
2--3.6788 Å20 Å2
3---3.5732 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5813 0 45 278 6136
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2835SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes191HARMONIC2
X-RAY DIFFRACTIONt_gen_planes814HARMONIC5
X-RAY DIFFRACTIONt_it5939HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion802SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7174SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5939HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8019HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion3.07
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2634 56 1.71 %
Rwork0.2115 3228 -
all0.2124 3284 -
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)
11.20531.4599-0.15183.2698-0.49313.99290.03380.1450.2059-0.06180.16870.0584-0.54510.0691-0.20240.1926-0.00540.0242-0.11430.02530.072527.915874.769127.4258
21.81110.26310.0742.0335-0.1122.30950.0668-0.32960.11020.496-0.08630.3902-0.064-0.18730.01950.17060.01420.124-0.0685-0.01780.050715.099354.852945.8083
31.3791-0.13740.23161.4999-0.10561.282-0.04030.0139-0.11510.13910.07290.07450.216-0.0993-0.03270.0738-0.01620.0409-0.12730.0316-0.013818.010133.559428.0105
41.86160.376-1.31343.00880.22511.68650.01820.08520.19050.0176-0.01480.18320.0531-0.1389-0.00340.0365-0.0051-0.0047-0.11250.007-0.015821.738956.253533.7564
53.1113-2.3948-0.7229.33673.49672.9540.0556-0.04370.510.2520.1638-0.0432-0.2797-0.16-0.21940.1503-0.0478-0.2237-0.22360.09450.37811.858175.32662.4487
62.2527-0.66051.91651.6669-0.96112.38390.06610.55330.2078-0.2265-0.2069-0.09420.18360.54460.14080.0480.0229-0.01910.13010.11950.02319.606949.1328-10.1819
72.5169-0.85231.32081.7388-1.19882.5150.2163-0.2065-0.4589-0.26340.17610.57460.5782-0.5536-0.39240.1572-0.1563-0.1070.08250.12860.2118-0.922435.043210.9355
82.4845-1.4463-1.36724.5938-3.08081.8736-0.0783-0.15870.25740.38280.0234-0.1038-0.1824-0.08070.05490.0774-0.0005-0.12470.05130.07860.07152.722555.91580.5159
90.5607-0.01740.06540.7443-0.23960.88480.02770.07230.10680.04350.03130.1330.0488-0.0176-0.05910.09490.00170.0441-0.04440.03220.121817.604348.602122.7248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|-1 - 51 A|59 - 68}A-1 - 51
2X-RAY DIFFRACTION1{A|-1 - 51 A|59 - 68}A59 - 68
3X-RAY DIFFRACTION2{A|69 - 151 A|159 - 177}A69 - 151
4X-RAY DIFFRACTION2{A|69 - 151 A|159 - 177}A159 - 177
5X-RAY DIFFRACTION3{A|178 - 345}A178 - 345
6X-RAY DIFFRACTION4{A|346 - 376}A346 - 376
7X-RAY DIFFRACTION5{B|3 - 50 B|64 - 68}B3 - 50
8X-RAY DIFFRACTION5{B|3 - 50 B|64 - 68}B64 - 68
9X-RAY DIFFRACTION6{B|69 - 177}B69 - 177
10X-RAY DIFFRACTION7{B|178 - 345}B178 - 345
11X-RAY DIFFRACTION8{B|346 - 376}B346 - 376
12X-RAY DIFFRACTION9{A|501 - 793 B|401 - 585}A501 - 793
13X-RAY DIFFRACTION9{A|501 - 793 B|401 - 585}B401 - 585

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