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- PDB-4lqe: Crystal Structure of MepB -

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Basic information

Entry
Database: PDB / ID: 4lqe
TitleCrystal Structure of MepB
ComponentsMepB
KeywordsDNA BINDING PROTEIN / Endonuclease
Function / homologyMepB-like / MepB-like / MepB-like superfamily / MepB-like / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Multidrug transporter / Uncharacterized protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFaham, S. / Agah, S.
CitationJournal: Protein Sci. / Year: 2014
Title: Structural characterization of MepB from Staphylococcus aureus reveals homology to endonucleases.
Authors: Agah, S. / Poulos, S. / Banchs, C. / Faham, S.
History
DepositionJul 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: MepB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3552
Polymers19,2591
Non-polymers961
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MepB
hetero molecules

A: MepB
hetero molecules

A: MepB
hetero molecules

A: MepB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4208
Polymers77,0364
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area10090 Å2
ΔGint-126 kcal/mol
Surface area29380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.645, 91.139, 100.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein MepB


Mass: 19258.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: MepB, SAV0335 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / References: UniProt: Q99WP1, UniProt: A0A0H3JPI4*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Bis-tris, pH 5.0, 2.3 M NH4SO4, 1% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 12092 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5 / Num. unique all: 969 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CRANKphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→23.04 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27938 595 4.9 %RANDOM
Rwork0.23587 ---
obs0.23804 11449 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.861 Å2
Baniso -1Baniso -2Baniso -3
1--4.64 Å20 Å20 Å2
2--5.77 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 5 74 1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221258
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9521705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2355150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9252562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89215210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.596153
X-RAY DIFFRACTIONr_chiral_restr0.0960.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021957
X-RAY DIFFRACTIONr_mcbond_it0.6581.5746
X-RAY DIFFRACTIONr_mcangle_it1.22121198
X-RAY DIFFRACTIONr_scbond_it1.8753512
X-RAY DIFFRACTIONr_scangle_it2.6484.5506
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 45 -
Rwork0.345 799 -
obs--95.05 %
Refinement TLS params.Method: refined / Origin x: 12.719 Å / Origin y: 13.763 Å / Origin z: 66.023 Å
111213212223313233
T0.1025 Å20.0014 Å20.0016 Å2-0.0522 Å2-0.0119 Å2--0.1043 Å2
L4.4019 °2-0.5987 °2-0.0777 °2-1.4699 °20.1303 °2--2.5017 °2
S0.0237 Å °-0.2141 Å °-0.1115 Å °0.0381 Å °0.0154 Å °0.0217 Å °-0.0301 Å °-0.2997 Å °-0.0391 Å °

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