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- PDB-1okr: Three-dimensional structure of S.aureus methicillin-resistance re... -

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Basic information

Entry
Database: PDB / ID: 1okr
TitleThree-dimensional structure of S.aureus methicillin-resistance regulating transcriptional repressor MecI.
ComponentsMETHICILLIN RESISTANCE REGULATORY PROTEIN MECI
KeywordsBACTERIAL ANTIBIOTIC RESISTANCE / MECI PROTEIN / TRANSCRIPTIONAL REGULATORY ELEMENT / DNA-BINDING PROTEIN / WINGED HELIX PROTEIN
Function / homology
Function and homology information


response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Penicillinase repressor fold / Penicillinase repressor domain / BlaI transcriptional regulatory family / Penicillinase repressor / 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
Methicillin resistance regulatory protein MecI / Methicillin resistance regulatory protein MecI
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsGarcia-Castellanos, R. / Marrero, A. / Mallorqui-Fernandez, G. / Potempa, J. / Coll, M. / Gomis-Ruth, F.X.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Three-Dimensional Structure of Meci: Molecular Basis for Transcriptional Regulation of Staphylococcal Methicillin Resistance
Authors: Garcia-Castellanos, R. / Marrero, A. / Mallorqui-Fernandez, G. / Potempa, J. / Coll, M. / Gomis-Ruth, F.X.
History
DepositionJul 28, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 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: METHICILLIN RESISTANCE REGULATORY PROTEIN MECI
B: METHICILLIN RESISTANCE REGULATORY PROTEIN MECI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8445
Polymers29,6242
Non-polymers2203
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.050, 73.360, 74.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.882, -0.283, 0.376), (-0.136, -0.612, -0.779), (0.45, -0.739, 0.501)
Vector: 27.0601, 83.20142, 34.8589)

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Components

#1: Protein METHICILLIN RESISTANCE REGULATORY PROTEIN MECI / MECI


Mass: 14812.003 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: N315 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P26598, UniProt: P68261*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.1 Å3/Da / Density % sol: 60 %
Description: THE DATASETS ARE PART OF A 3-THREE WAVELENGTH MAD EXPERIMENT. THE WAVELENGTH OF THE NATIVE DATASET IS 0.97625 ANG. THE DATASET CONTAINS 14159 UNIQUE REFLECTIONS
Crystal growTemperature: 277 K / pH: 7.4 / Details: 20 MM TRIS-HCL PH 7.4, 0.2 M NACL AT 4 DEGREES.
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625,0.97915,0.97926, 0.96111
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.976251
20.979151
30.979261
40.961111
ReflectionResolution: 2.4→66.1 Å / Num. obs: 61498 / % possible obs: 96.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 5.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.4 / % possible all: 84.7
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 66.1 Å / Num. obs: 14159 / Num. measured all: 61498 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 84.7 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SOLVEphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MAD / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.895 / SU B: 9.736 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ADDITIONAL REFINEMENT WAS PERFORMED USING CNS 1.1.
RfactorNum. reflection% reflectionSelection details
Rfree0.298 753 5.3 %RANDOM
Rwork0.218 ---
obs0.222 13363 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.79 Å2
Baniso -1Baniso -2Baniso -3
1-4.79 Å20 Å20 Å2
2---0.88 Å20 Å2
3----3.91 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 13 69 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222097
X-RAY DIFFRACTIONr_bond_other_d0.0020.021883
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9542805
X-RAY DIFFRACTIONr_angle_other_deg0.8834436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1985240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
X-RAY DIFFRACTIONr_nbd_refined0.2190.2444
X-RAY DIFFRACTIONr_nbd_other0.230.22054
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.21314
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0970.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3340.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4991.51206
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.12221962
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.0173891
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.5274.5843
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
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.392 47
Rwork0.352 747
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)
10.88450.0457-0.70651.4398-0.23762.29440.08580.04460.03950.0803-0.06350.0754-0.4695-0.2594-0.02220.22830.0398-0.03520.27180.02460.29483.424835.161135.752
25.00899.16935.068312.13664.07397.4213-0.3795-0.5339-0.11250.81070.19970.491-0.72280.25480.17970.39540.0934-0.03850.36540.14630.14934.400443.515110.9188
31.693-0.89830.09051.31570.20170.90790.00810.07960.0312-0.17880.1439-0.1079-0.09270.1656-0.1520.28820.00020.05490.2585-0.00760.259927.501132.764728.3474
411.97990.8873-3.926911.7276-10.136835.20060.1442-0.14980.44680.30920.695-0.3942-0.99311.3631-0.83920.2484-0.00160.0270.32960.28020.283814.386449.060510.9806
5-79.549632.798653.2868-11.2005-21.6223-33.3035-0.30270.55832.77540.76660.7791-1.2063-0.21330.0105-0.47650.2977-0.00190.00250.29760.0010.294214.158636.105926.7793
6-0.4245-0.1139-0.06640.3115-0.21740.24190.0679-0.05440.0896-0.11090.0422-0.02530.0631-0.029-0.11010.25880.01850.01910.33690.00570.294116.994230.263929.2349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 108
2X-RAY DIFFRACTION2A109 - 123
3X-RAY DIFFRACTION3B1 - 108
4X-RAY DIFFRACTION4B109 - 122
5X-RAY DIFFRACTION5W201 - 202
6X-RAY DIFFRACTION6W203 - 271
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.56

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