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- PDB-3da4: Crystal Structure of Colicin M, a Novel Phosphatase Specifically ... -

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Basic information

Entry
Database: PDB / ID: 3da4
TitleCrystal Structure of Colicin M, a Novel Phosphatase Specifically Imported by Escherichia Coli
ComponentsColicin-M
KeywordsANTIBIOTIC / Colicin M / Phosphatase / 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
NITRATE ION / Colicin-M
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.0Jul 29, 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 1.3Nov 1, 2023Group: 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 / pdbx_initial_refinement_model / 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)61,2777
Polymers60,9672
Non-polymers3105
Water11,548641
1
A: Colicin-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7325
Polymers30,4841
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Colicin-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5462
Polymers30,4841
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.490, 108.750, 224.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUILEILEAA4 - 1304 - 130
21LEULEUILEILEBB4 - 1304 - 130
12LYSLYSPROPROAA180 - 260180 - 260
22LYSLYSPROPROBB180 - 260180 - 260

NCS ensembles :
ID
1
2

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Components

#1: Protein Colicin-M


Mass: 30483.541 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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M N-(2-acetamido) iminodiacetate, 12% PEG 6000, 0.2M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 67044 / % possible obs: 97.7 % / Observed criterion σ(I): 2.4 / Redundancy: 5.6 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 9.9
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.4 / Num. unique all: 10264 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DA3

3da3


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.659 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26134 4692 7 %RANDOM
Rwork0.21838 ---
all0.23 67044 --
obs0.22136 62343 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.698 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 20 641 4801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224258
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9545789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07824.335173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29715677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4051514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023236
X-RAY DIFFRACTIONr_nbd_refined0.2550.24119
X-RAY DIFFRACTIONr_nbtor_refined0.3410.23197
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2873
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.2217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.252
X-RAY DIFFRACTIONr_mcbond_it0.7111.52723
X-RAY DIFFRACTIONr_mcangle_it1.17224334
X-RAY DIFFRACTIONr_scbond_it1.96731698
X-RAY DIFFRACTIONr_scangle_it2.9584.51454
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1508medium positional0.090.5
2324medium positional0.130.5
1464loose positional0.335
2303loose positional0.25
1508medium thermal0.612
2324medium thermal0.62
1464loose thermal110
2303loose thermal1.3610
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 321 -
Rwork0.285 4274 -
obs--100 %

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