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- PDB-3da3: Crystal Structure of Colicin M, A Novel Phosphatase Specifically ... -

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Basic information

Entry
Database: PDB / ID: 3da3
TitleCrystal Structure of Colicin M, A Novel Phosphatase Specifically Imported by Escherichia Coli
ComponentsColicin-M
KeywordsANTIBIOTIC / Colicin / Phosphatase / Xray / Dimer / three functional domains / Antimicrobial / Bacteriocin / Plasmid / TonB box
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium
Similarity search - Function
de novo design (two linked rop proteins) - #280 / Colicin M, catalytic domain / Colicin M / Colicin M / de novo design (two linked rop proteins) / Beta-Lactamase / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsZeth, K. / Albrecht, R. / Romer, C. / Braun, V.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of colicin M, a novel phosphatase specifically imported by Escherichia coli
Authors: Zeth, K. / Romer, C. / Patzer, S.I. / Braun, V.
History
DepositionMay 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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: Colicin-M
B: Colicin-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8744
Polymers60,8252
Non-polymers492
Water2,594144
1
A: Colicin-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4372
Polymers30,4121
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Colicin-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4372
Polymers30,4121
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-38 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.880, 119.880, 96.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 2 - 271 / Label seq-ID: 2 - 271

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Colicin-M


Mass: 30412.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P05820
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 20% PEG 3350, 0.2M potassium nitrate, 0.1mM CaCl2, 0.1mM pyrophosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 23282 / % possible obs: 93.2 % / Observed criterion σ(I): 2.7 / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.175 / Net I/σ(I): 8
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3858 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→19.98 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.841 / SU B: 11.561 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.432 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29468 1183 5 %RANDOM
Rwork0.23503 ---
all0.24 23282 --
obs0.23802 22199 94.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.076 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4134 0 2 144 4280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224236
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9525762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9165538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31124.302172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90415676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6151514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023208
X-RAY DIFFRACTIONr_nbd_refined0.2180.22110
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22932
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.210
X-RAY DIFFRACTIONr_mcbond_it0.4321.52750
X-RAY DIFFRACTIONr_mcangle_it0.75524326
X-RAY DIFFRACTIONr_scbond_it0.92531695
X-RAY DIFFRACTIONr_scangle_it1.4334.51436
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2067 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.260.5
medium thermal0.412
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 123 -
Rwork0.28 1874 -
obs--100 %

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