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- PDB-8qvs: Crystal structure of Ompk36 GD at 3500 eV based on a combination ... -

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Basic information

Entry
Database: PDB / ID: 8qvs
TitleCrystal structure of Ompk36 GD at 3500 eV based on a combination of spherical harmonics and analytical absorption corrections
ComponentsOmpK36
KeywordsMEMBRANE PROTEIN / long-wavelength x-ray diffraction
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsDuman, R. / Wagner, A. / Beis, K. / Wong, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: J.Appl.Crystallogr. / Year: 2024
Title: Ray-tracing analytical absorption correction for X-ray crystallography based on tomographic reconstructions.
Authors: Lu, Y. / Duman, R. / Beilsten-Edmands, J. / Winter, G. / Basham, M. / Evans, G. / Kamps, J.J.A.G. / Orville, A.M. / Kwong, H.S. / Beis, K. / Armour, W. / Wagner, A.
History
DepositionOct 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OmpK36
B: OmpK36
C: OmpK36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2709
Polymers114,6933
Non-polymers5766
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-142 kcal/mol
Surface area40290 Å2
Unit cell
Length a, b, c (Å)232.078, 74.700, 91.350
Angle α, β, γ (deg.)90.00, 112.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein OmpK36 / OmpK36 porin / Outer membrane protein C


Mass: 38231.062 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ompK36, ompC_2, DDJ63_09115, NCTC13443_05288 / Production host: Escherichia coli (E. coli) / References: UniProt: D6QLY1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.19 Å3/Da / Density % sol: 61.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Lithium sulfate, 0.1M sodium citrate pH 5.6 and 12% PEG4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.54 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 3.54 Å / Relative weight: 1
ReflectionResolution: 2.34→107.43 Å / Num. obs: 60652 / % possible obs: 98.86 % / Redundancy: 11 % / CC1/2: 0.998 / Net I/σ(I): 24.92
Reflection shellResolution: 2.34→2.424 Å / Num. unique obs: 5634 / CC1/2: 0.878

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→107.43 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.965 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23277 3261 5.4 %RANDOM
Rwork0.19262 ---
obs0.19473 57401 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.852 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å20.15 Å2
2---2.48 Å20 Å2
3---1.97 Å2
Refinement stepCycle: 1 / Resolution: 2.34→107.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8119 0 10 196 8325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0118302
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167200
X-RAY DIFFRACTIONr_angle_refined_deg1.451.65911245
X-RAY DIFFRACTIONr_angle_other_deg0.5121.58716482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85451034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.436536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.427101233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022189
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3723.8154148
X-RAY DIFFRACTIONr_mcbond_other3.3723.8154148
X-RAY DIFFRACTIONr_mcangle_it4.7516.8385178
X-RAY DIFFRACTIONr_mcangle_other4.7516.8395179
X-RAY DIFFRACTIONr_scbond_it4.3594.354154
X-RAY DIFFRACTIONr_scbond_other4.3524.3464147
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6327.7776056
X-RAY DIFFRACTIONr_long_range_B_refined8.08437.119012
X-RAY DIFFRACTIONr_long_range_B_other8.07537.119000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.4 Å
RfactorNum. reflection% reflection
Rfree0.278 245 -
Rwork0.262 3827 -
obs--89.79 %

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