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- PDB-2j5u: MreC Lysteria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 2j5u
TitleMreC Lysteria monocytogenes
ComponentsMREC PROTEIN
KeywordsCELL SHAPE REGULATION / BACTERIAL CELL SHAPE DETERMINING PROTEIN MREC
Function / homology
Function and homology information


regulation of cell shape / plasma membrane
Similarity search - Function
Rod shape-determining protein MreC, domain 1 / Rod shape-determining protein MreC, domain 2 / : / Cell/Rod shape-determining protein MreC, domain 1 / Rod shape-determining protein MreC / Cell/Rod shape-determining protein MreC, domain 2 / Rod shape-determining protein MreC, barrel core / Single helix bin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Thrombin, subunit H ...Rod shape-determining protein MreC, domain 1 / Rod shape-determining protein MreC, domain 2 / : / Cell/Rod shape-determining protein MreC, domain 1 / Rod shape-determining protein MreC / Cell/Rod shape-determining protein MreC, domain 2 / Rod shape-determining protein MreC, barrel core / Single helix bin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Thrombin, subunit H / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Cell shape-determining protein MreC
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
Authorsvan den Ent, F. / Leaver, M. / Bendezu, F. / Errington, J. / de Boer, P. / Lowe, J.
CitationJournal: Mol.Microbiol. / Year: 2006
Title: Dimeric Structure of the Cell Shape Protein Mrec and its Functional Implications.
Authors: Van Den Ent, F. / Leaver, M. / Bendezu, F. / Errington, J. / De Boer, P. / Lowe, J.
History
DepositionSep 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MREC PROTEIN
B: MREC PROTEIN


Theoretical massNumber of molelcules
Total (without water)55,2582
Polymers55,2582
Non-polymers00
Water00
1
A: MREC PROTEIN
B: MREC PROTEIN
x 12


Theoretical massNumber of molelcules
Total (without water)663,09224
Polymers663,09224
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_556-x,-x+y,-z+11
crystal symmetry operation11_456-x+y-1,y,-z+11
crystal symmetry operation5_455y-1,-x+y,z1
crystal symmetry operation6_665x-y+1,x+1,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11
crystal symmetry operation7_466y-1,x+1,-z+11
crystal symmetry operation3_465-x+y-1,-x+1,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation8_676x-y+1,-y+2,-z+11
crystal symmetry operation12_576x,x-y+2,-z+11
crystal symmetry operation4_575-x,-y+2,z1
MethodPQS
Unit cell
Length a, b, c (Å)162.954, 162.954, 95.391
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999932, -0.011239, 0.003138), (0.010826, -0.793178, 0.608894), (-0.004354, 0.608886, 0.793246)
Vector: 174.4428, -1.514, 0.7045)

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Components

#1: Protein MREC PROTEIN


Mass: 27628.818 Da / Num. of mol.: 2 / Fragment: RESIDUES 50-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8Y6Y4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.16 Å3/Da / Density % sol: 70.17 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 26161 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 77.168 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.5→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2658 1303 4.9 %RANDOM
Rwork0.2449 ---
obs0.2449 26160 99.3 %-
Solvent computationBsol: 41.2095 Å2 / ksol: 0.33611 e/Å3
Displacement parametersBiso mean: 75.588 Å2
Baniso -1Baniso -2Baniso -3
1--12.258 Å2-12.659 Å20 Å2
2---12.258 Å20 Å2
3---24.515 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 0 0 3142
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.469
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.53 Å / Rfactor Rfree error: 0.0129 / Total num. of bins used: 26
RfactorNum. reflection% reflection
Rfree0.569 44 4.98 %
Rwork0.432 937 -
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2PROTEIN_REP.PARAM

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