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- PDB-7vu3: Chitoporin from Serratia marcescens in-complex with chitohexaose -

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Basic information

Entry
Database: PDB / ID: 7vu3
TitleChitoporin from Serratia marcescens in-complex with chitohexaose
ComponentsChitoporin
KeywordsMEMBRANE PROTEIN / Outer membrane protein Chitoporin
Function / homologyOuter membrane porin, bacterial / outer membrane porin, OprD family / Porin domain superfamily / membrane => GO:0016020 / Chitoporin
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAmornloetwattana, R. / Robinson, R.C. / van den Berg, B. / Suginta, W.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: To Be Published
Title: Chitoporin from Serratia marcescens in-complex with chitohexaose
Authors: Amornloetwattana, R. / Robinson, R.C. / van den Berg, B. / Suginta, W.
History
DepositionNov 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8148
Polymers49,0051
Non-polymers2,8097
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint7 kcal/mol
Surface area19730 Å2
Unit cell
Length a, b, c (Å)73.240, 73.240, 213.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-687-

HOH

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Components

#1: Protein Chitoporin / Outer membrane porin / OprD family


Mass: 49004.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: chiP, AR325_08275, HMI62_06020 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0QBS3
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1237.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 19% (w/v) PEG 1500, 0.2 M Ammonium phosphate monobasic, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.7→71.15 Å / Num. obs: 15892 / % possible obs: 94.9 % / Redundancy: 6.3 % / CC1/2: 0.966 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.074 / Rrim(I) all: 0.189 / Net I/σ(I): 8.7 / Num. measured all: 100353 / Scaling rejects: 286
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.836.50.9651309820000.5690.4141.057392.5
8.96-71.155.40.07330375580.8930.0420.08612.899

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
PHENIXmodel building
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VU2

7vu2


Resolution: 2.7→69.28 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1578 9.99 %
Rwork0.2073 14212 -
obs0.212 15790 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.73 Å2 / Biso mean: 49.8684 Å2 / Biso min: 14.77 Å2
Refinement stepCycle: final / Resolution: 2.7→69.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 236 89 3797
Biso mean--91.86 41.43 -
Num. residues----435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.790.30271380.29071234137293
2.79-2.890.33241340.25531218135292
2.89-30.28331390.23671243138293
3-3.140.26771370.23761238137592
3.14-3.30.29681390.22351247138693
3.3-3.510.24621400.20951253139393
3.51-3.780.28191410.19771282142394
3.78-4.160.23621440.18481293143795
4.16-4.770.21651470.15461331147896
4.77-60.24051550.18841397155299
6-69.280.23191640.23621476164097
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3311-0.3320.01462.0239-0.46910.4970.03170.0155-0.0888-0.0970.22460.3365-0.0713-0.2208-0.25450.2309-0.0068-0.010.30210.05250.2994-37.769-2.014-10.26
21.9522-0.50550.32242.1289-0.85440.5508-0.0178-0.0393-0.03250.0847-0.0179-0.1552-0.134-0.0507-0.0020.2343-0.0072-0.00830.19220.05810.1961-18.5090.302-6.651
30.4539-0.36110.66832.43080.2481.2633-0.0449-0.05520.03680.02020.09490.1876-0.1131-0.05690.05410.2967-0.0045-0.00230.23890.03640.2258-23.2519.515-12.768
41.217-0.01550.1111.9742-0.56060.7469-0.0427-0.03650.15290.25020.12090.0983-0.0827-0.2693-0.01110.24520.0127-0.02760.29850.01720.2073-32.30716.142-10.87
50.0103-0.0110.00040.0117-0.00260.0081-0.22260.2140.03460.09690.12370.1025-0.06720.0317-0.00010.94120.1720.06880.6749-0.1740.8127-31.2436.307-15.231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:141 )A1 - 141
2X-RAY DIFFRACTION2( CHAIN A AND RESID 142:288 )A142 - 288
3X-RAY DIFFRACTION3( CHAIN A AND RESID 289:336 )A289 - 336
4X-RAY DIFFRACTION4( CHAIN A AND RESID 337:435 )A337 - 435
5X-RAY DIFFRACTION5( CHAIN U AND RESID 1:6 )U1 - 6

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