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- PDB-8quq: Crystal structure of Ompk36 GD at 3500 eV based on spherical harm... -

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Basic information

Entry
Database: PDB / ID: 8quq
TitleCrystal structure of Ompk36 GD at 3500 eV based on spherical harmonics 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 16, 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

Downloads & links

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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
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-141 kcal/mol
Surface area40310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.078, 74.700, 91.350
Angle α, β, γ (deg.)90.000, 112.209, 90.000
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.2 Å3/Da / Density % sol: 61.51 %
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 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 3.54 Å / Relative weight: 1
ReflectionResolution: 2.34→107.4 Å / Num. obs: 60662 / % possible obs: 98.85 % / Redundancy: 11 % / CC1/2: 0.997 / Net I/σ(I): 16.42
Reflection shellResolution: 2.34→2.42 Å / Num. unique obs: 5634 / CC1/2: 0.896

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→107.4 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.88 / SU ML: 0.158 / Cross valid method: FREE R-VALUE / ESU R: 0.285 / ESU R Free: 0.222
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2437 3261 5.376 %
Rwork0.2023 57401 -
all0.205 --
obs-60662 98.758 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.225 Å2-0 Å20.43 Å2
2---2.735 Å20 Å2
3---1.619 Å2
Refinement stepCycle: LAST / Resolution: 2.34→107.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8099 0 30 198 8327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0118302
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167200
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.65911245
X-RAY DIFFRACTIONr_angle_other_deg0.5031.58716482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88951034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.285536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.356101233
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.87310465
X-RAY DIFFRACTIONr_chiral_restr0.0650.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022189
X-RAY DIFFRACTIONr_nbd_refined0.1810.21352
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.26539
X-RAY DIFFRACTIONr_nbtor_refined0.1850.23996
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.24574
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2359
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.217
X-RAY DIFFRACTIONr_nbd_other0.1840.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.25
X-RAY DIFFRACTIONr_mcbond_it3.4714.0114148
X-RAY DIFFRACTIONr_mcbond_other3.474.0114148
X-RAY DIFFRACTIONr_mcangle_it4.9027.1845178
X-RAY DIFFRACTIONr_mcangle_other4.9027.1845179
X-RAY DIFFRACTIONr_scbond_it4.2424.5074154
X-RAY DIFFRACTIONr_scbond_other4.2354.5024147
X-RAY DIFFRACTIONr_scangle_it6.4588.0886067
X-RAY DIFFRACTIONr_scangle_other6.4488.086056
X-RAY DIFFRACTIONr_lrange_it7.97239.069035
X-RAY DIFFRACTIONr_lrange_other7.96839.069025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.40.3182450.313827X-RAY DIFFRACTION89.7905
2.4-2.4650.3072020.2924061X-RAY DIFFRACTION97.3732
2.465-2.5370.3242110.2763994X-RAY DIFFRACTION98.3396
2.537-2.6150.3152280.2463866X-RAY DIFFRACTION98.7934
2.615-2.7010.2912240.2193787X-RAY DIFFRACTION99.184
2.701-2.7950.2512050.2043665X-RAY DIFFRACTION99.7423
2.795-2.9010.2581840.1963589X-RAY DIFFRACTION99.947
2.901-3.0190.2492390.1953388X-RAY DIFFRACTION100
3.019-3.1530.2521910.1883302X-RAY DIFFRACTION99.9714
3.153-3.3070.2422190.1953091X-RAY DIFFRACTION100
3.307-3.4860.2221690.192998X-RAY DIFFRACTION100
3.486-3.6970.2891380.2242873X-RAY DIFFRACTION100
3.697-3.9520.2361440.1962690X-RAY DIFFRACTION100
3.952-4.2680.1861240.1692501X-RAY DIFFRACTION100
4.268-4.6750.1491190.1422325X-RAY DIFFRACTION100
4.675-5.2250.211030.1732081X-RAY DIFFRACTION100
5.225-6.0310.2821200.2041842X-RAY DIFFRACTION100
6.031-7.3810.226740.2231594X-RAY DIFFRACTION100
7.381-10.4130.214730.1891225X-RAY DIFFRACTION100
10.413-107.40.294490.278701X-RAY DIFFRACTION100

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