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- PDB-5mdp: Crystal structure of in vitro folded Chitoporin VhChip from Vibri... -

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Basic information

Entry
Database: PDB / ID: 5mdp
TitleCrystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi (crystal form II)
ComponentsChitoporin
KeywordsSUGAR BINDING PROTEIN / outer membrane protein / Vibrio harveyi / porin channel
Function / homology
Function and homology information


porin activity / cell outer membrane / monoatomic ion transmembrane transport / metal ion binding
Similarity search - Function
Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsZahn, M. / van den Berg, B.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for chitin acquisition by marine Vibrio species.
Authors: Aunkham, A. / Zahn, M. / Kesireddy, A. / Pothula, K.R. / Schulte, A. / Basle, A. / Kleinekathofer, U. / Suginta, W. / van den Berg, B.
History
DepositionNov 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / 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
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitoporin
B: Chitoporin
C: Chitoporin


Theoretical massNumber of molelcules
Total (without water)117,5793
Polymers117,5793
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-68 kcal/mol
Surface area41360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)254.761, 147.031, 53.759
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 10 - 350 / Label seq-ID: 12 - 352

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Chitoporin


Mass: 39192.863 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: chiP / Production host: Escherichia coli (E. coli) / References: UniProt: L0RVU0
Has protein modificationY

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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: 4.31 Å3/Da / Density % sol: 71.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28% (w/v) PEG 400, 0.5 M potassium iodide, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.08→29.21 Å / Num. obs: 34933 / % possible obs: 95.7 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.1 / Net I/σ(I): 6.6
Reflection shellResolution: 3.08→3.23 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.41 / Rpim(I) all: 0.385 / % possible all: 38.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MDO

5mdo


Resolution: 3.08→127.2 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.913 / SU B: 50.469 / SU ML: 0.356 / Cross valid method: THROUGHOUT / ESU R: 1.766 / ESU R Free: 0.374 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23977 1731 5 %RANDOM
Rwork0.21699 ---
obs0.2181 33200 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70.514 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å2-0 Å2-2.13 Å2
2---1.74 Å20 Å2
3---0.59 Å2
Refinement stepCycle: 1 / Resolution: 3.08→127.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7995 0 0 0 7995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.028202
X-RAY DIFFRACTIONr_bond_other_d0.0070.027098
X-RAY DIFFRACTIONr_angle_refined_deg2.171.93411112
X-RAY DIFFRACTIONr_angle_other_deg1.256316281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7785.0341023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.06824.845452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.537151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1121539
X-RAY DIFFRACTIONr_chiral_restr0.1050.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029843
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022082
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_it0.4231.2114089
X-RAY DIFFRACTIONr_mcbond_other0.4231.2114088
X-RAY DIFFRACTIONr_mcangle_it0.7531.8155106
X-RAY DIFFRACTIONr_mcangle_other0.7531.8155107
X-RAY DIFFRACTIONr_scbond_it0.4761.2534113
X-RAY DIFFRACTIONr_scbond_other0.4761.2534113
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7831.8626006
X-RAY DIFFRACTIONr_long_range_B_refined1.4919.869316
X-RAY DIFFRACTIONr_long_range_B_other1.4919.8599317
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A38486
12B38486
21A38390
22C38390
31B38356
32C38356
LS refinement shellResolution: 3.078→3.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 102 -
Rwork0.35 2351 -
obs--89.72 %
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)
11.46070.16150.09452.0947-0.70931.72010.0827-0.1436-0.13680.2008-0.1478-0.21350.00540.35310.06510.0984-0.0079-0.11170.4037-0.00391.3884-28.9272-2.766227.3173
21.1925-0.04750.69512.46840.03391.7733-0.01020.0155-0.0071-0.0586-0.1429-0.32840.020.86850.15310.0109-0.0114-0.00030.67490.06161.5983-12.53910.654919.6491
31.8593-0.5201-0.81670.67421.08133.83850.02320.12780.1778-0.14-0.0388-0.2051-0.29720.32420.01560.279-0.10280.00950.44590.011.2033-23.308311.293618.6039
41.793-0.04740.03572.03390.09171.33710.0015-0.1706-0.180.2916-0.05990.0160.256-0.14410.05840.163-0.0419-0.05890.26390.03031.2585-56.8586-13.73827.7444
51.809-0.95531.26231.8556-1.17644.20070.0971-0.0038-0.1664-0.1072-0.1395-0.01460.8421-0.27710.04230.4468-0.1543-0.04910.2496-0.02181.2356-59.0384-29.009218.1309
61.32630.77760.14841.5221-0.62062.02780.0250.0542-0.3602-0.24370.0519-0.38010.20340.2059-0.07690.26660.0681-0.07160.2292-0.05981.394-46.0678-24.364819.1428
71.59980.08180.15721.56420.18981.39950.0204-0.25720.16070.1916-0.0182-0.0144-0.2356-0.0463-0.00220.2182-0.0118-0.03960.2698-0.03161.2533-51.04517.267127.4519
80.49860.0206-0.20021.85170.42131.31210.08470.05380.2226-0.0887-0.09750.1394-0.5693-0.2890.01280.26070.1406-0.0960.31740.02911.3609-64.013224.401719.1753
93.10030.6045-0.30391.63180.80880.74710.1150.4920.061-0.1299-0.17150.1556-0.1287-0.47450.05640.25360.1215-0.14370.463-0.01351.3168-63.143413.642513.3644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 184
2X-RAY DIFFRACTION2A185 - 301
3X-RAY DIFFRACTION3A302 - 350
4X-RAY DIFFRACTION4B10 - 205
5X-RAY DIFFRACTION5B206 - 301
6X-RAY DIFFRACTION6B302 - 350
7X-RAY DIFFRACTION7C10 - 203
8X-RAY DIFFRACTION8C204 - 319
9X-RAY DIFFRACTION9C320 - 350

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