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- PDB-4fqe: KdgM porin -

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Basic information

Entry
Database: PDB / ID: 4fqe
TitleKdgM porin
ComponentsOligogalacturonate-specific porin kdgM
KeywordsMEMBRANE PROTEIN / beta barrel / porin / outer membrane protein / oligogalacturonate specificity
Function / homology
Function and homology information


pectin metabolic process / oligosaccharide transport / voltage-gated monoatomic ion channel activity / porin activity / pore complex / cell outer membrane
Similarity search - Function
Oligogalacturonate-specific porin / Oligogalacturonate-specific porin protein (KdgM) / monomeric porin ompg / : / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-OCTANE / Oligogalacturonate-specific porin KdgM
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsHutter, C. / Peneff, C.M. / Wirth, C. / Schirmer, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the oligogalacturonate-specific KdgM porin.
Authors: Hutter, C.A. / Lehner, R. / Wirth, C.h. / Condemine, G. / Peneff, C. / Schirmer, T.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 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_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: Oligogalacturonate-specific porin kdgM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4219
Polymers25,5461
Non-polymers1,8758
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.856, 59.674, 51.564
Angle α, β, γ (deg.)90.000, 106.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Oligogalacturonate-specific porin kdgM


Mass: 25546.006 Da / Num. of mol.: 1 / Fragment: unp residues 21-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (bacteria) / Strain: 3937 / Gene: kdgM, Dda3937_03362 / Plasmid: pKSM717 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)omp8/pLys / References: UniProt: Q934G3
#2: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES, 22% MPD, 36mM digalacturonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.008 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionNumber: 61216
ReflectionResolution: 1.93→49.36 Å / Num. obs: 16187 / % possible obs: 99.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.78 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.4549
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.93-2.033.720.391.578662232999.93
2.03-2.163.770.310.798431223499.95
2.16-2.313.790.221.9879532101100
2.31-2.493.810.154.5374141946100
2.49-2.733.820.122.7268561796100
2.73-3.053.820.086.8362541639100
3.05-3.523.820.076.4454711433100
3.52-4.323.80.059.9346341221100
4.32-6.13.770.0317.983608957100
6.1-49.363.640.0318.76193353198.65

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16 2010/01/06data scaling
MAR345data collection
MOSFLMdata reduction
PHASERphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wjq

2wjq


Resolution: 1.93→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.628 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 790 4.9 %RANDOM
Rwork0.213 ---
all0.215 16172 --
obs0.215 16172 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.7 Å2 / Biso mean: 33.024 Å2 / Biso min: 5.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å2-1.63 Å2
2--0.76 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.93→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 129 66 1606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021598
X-RAY DIFFRACTIONr_bond_other_d0.0020.021220
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9852109
X-RAY DIFFRACTIONr_angle_other_deg0.77332936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7665174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35222.53279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36415249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.421513
X-RAY DIFFRACTIONr_chiral_restr0.0890.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02353
LS refinement shellResolution: 1.908→1.957 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 26 -
Rwork0.24 601 -
all-627 -
obs--52.42 %
Refinement TLS params.Method: refined / Origin x: 8.09 Å / Origin y: 1.541 Å / Origin z: 2.228 Å
111213212223313233
T0.0777 Å2-0.0024 Å20.0956 Å2-0.0482 Å20.016 Å2--0.3302 Å2
L1.1447 °2-0.0172 °20.0837 °2-1.8565 °20.2144 °2--0.032 °2
S-0.0369 Å °-0.009 Å °0.0328 Å °0.0926 Å °0.0314 Å °0.0269 Å °0.0097 Å °0.0085 Å °0.0055 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 217
2X-RAY DIFFRACTION1A301 - 308
3X-RAY DIFFRACTION1A401 - 466

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