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- PDB-2qf4: High resolution structure of the major periplasmic domain from th... -

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Basic information

Entry
Database: PDB / ID: 2qf4
TitleHigh resolution structure of the major periplasmic domain from the cell shape-determining filament MreC (orthorhombic form)
ComponentsCell shape determining protein MreC
KeywordsSTRUCTURAL PROTEIN / filament a-lytic protease fold
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 / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cell shape-determining protein MreC
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsLovering, A.L. / Strynadka, N.C.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: High-resolution Structure of the Major Periplasmic Domain from the Cell Shape-determining Filament MreC.
Authors: Lovering, A.L. / Strynadka, N.C.
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
A: Cell shape determining protein MreC
B: Cell shape determining protein MreC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7376
Polymers36,4552
Non-polymers2824
Water7,909439
1
A: Cell shape determining protein MreC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4144
Polymers18,2271
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell shape determining protein MreC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3242
Polymers18,2271
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.247, 70.362, 89.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell shape determining protein MreC


Mass: 18227.457 Da / Num. of mol.: 2 / Fragment: Major Periplasmic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: mreC / Plasmid: pET41 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8DMY2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na Acetate pH 4.6, 0.2M Ammonium sulfate, 12.5% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→55.385 Å / Num. obs: 99707 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 8.3
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.6 / Num. unique all: 14257 / Rsym value: 0.472 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→55.385 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.045 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.167 4983 5 %RANDOM
Rwork0.144 ---
all0.145 ---
obs0.145 99637 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.2→55.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 17 439 2954
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222620
X-RAY DIFFRACTIONr_bond_other_d0.0020.021650
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9663549
X-RAY DIFFRACTIONr_angle_other_deg3.13134153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.215339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72826.577111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78415493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1841511
X-RAY DIFFRACTIONr_chiral_restr0.1390.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022877
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02432
X-RAY DIFFRACTIONr_nbd_refined0.2240.2410
X-RAY DIFFRACTIONr_nbd_other0.1960.21822
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21291
X-RAY DIFFRACTIONr_nbtor_other0.0960.21495
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.269
X-RAY DIFFRACTIONr_mcbond_it2.0241.52133
X-RAY DIFFRACTIONr_mcbond_other0.6981.5697
X-RAY DIFFRACTIONr_mcangle_it2.44822734
X-RAY DIFFRACTIONr_scbond_it3.66231036
X-RAY DIFFRACTIONr_scangle_it4.9144.5813
X-RAY DIFFRACTIONr_rigid_bond_restr1.83734985
X-RAY DIFFRACTIONr_sphericity_free7.1693439
X-RAY DIFFRACTIONr_sphericity_bonded3.97334251
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 346 -
Rwork0.249 6779 -
obs-7125 97.42 %

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