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- PDB-5mds: Crystal structure of outer membrane expressed Chitoporin VhChip f... -

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Basic information

Entry
Database: PDB / ID: 5mds
TitleCrystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi in complex with chitotetraose
ComponentsChitoporin
KeywordsSUGAR BINDING PROTEIN / outer membrane protein Vibrio harveyi porin channel
Function / homologyGram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin domain superfamily / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / Chitoporin
Function and homology information
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0996
Polymers115,6073
Non-polymers2,4923
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15220 Å2
ΔGint-1 kcal/mol
Surface area40460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.010, 145.047, 55.158
Angle α, β, γ (deg.)90.00, 94.80, 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: 0 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 10 - 350 / Label seq-ID: 10 - 350

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: 38535.668 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
#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


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE

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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: 71.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28% (w/v) PEG 400, 0.2 M sodium acetate, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→125.35 Å / Num. obs: 56059 / % possible obs: 93.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.081 / Net I/σ(I): 8.4
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 1.1 / Rpim(I) all: 0.699 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MDO

5mdo


Resolution: 2.6→125.35 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / SU B: 29.25 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24749 1652 2.9 %RANDOM
Rwork0.22126 ---
obs0.22201 54404 93.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.644 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å2-1.36 Å2
2---0.79 Å20 Å2
3----1.27 Å2
Refinement stepCycle: 1 / Resolution: 2.6→125.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7995 0 171 0 8166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.028382
X-RAY DIFFRACTIONr_bond_other_d0.0020.027230
X-RAY DIFFRACTIONr_angle_refined_deg2.0851.94911379
X-RAY DIFFRACTIONr_angle_other_deg1.038316623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72151020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63424.834453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.183151203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1621539
X-RAY DIFFRACTIONr_chiral_restr0.1090.21134
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022100
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_it0.9622.2544089
X-RAY DIFFRACTIONr_mcbond_other0.9622.2544088
X-RAY DIFFRACTIONr_mcangle_it1.5783.3785106
X-RAY DIFFRACTIONr_mcangle_other1.5783.3785107
X-RAY DIFFRACTIONr_scbond_it1.7512.654293
X-RAY DIFFRACTIONr_scbond_other1.7522.6524294
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6993.9396274
X-RAY DIFFRACTIONr_long_range_B_refined3.82326.739160
X-RAY DIFFRACTIONr_long_range_B_other3.82526.7449161
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A220640.03
12B220640.03
21A221140.02
22C221140.02
31B221400.02
32C221400.02
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 117 -
Rwork0.369 4059 -
obs--94.72 %
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)
11.9680.0330.03082.1535-0.26011.29530.0415-0.1129-0.17760.1474-0.0914-0.19340.11880.29550.04980.06580.0347-0.14250.16190.00240.820298.7438-7.705726.0954
25.63885.4723-0.31816.26385.83053.4684-0.00580.03070.1050.467-0.31260.58910.2697-0.23990.31840.46540.0129-0.06520.5889-0.00280.543119.5035-1.621337.2143
31.358-0.4234-0.10071.43020.17551.29910.01030.1803-0.0303-0.1097-0.0582-0.1423-0.03450.44710.0480.0723-0.04-0.12130.3589-0.00510.8959110.52532.262218.5563
41.91290.2756-0.08892.10850.221.5646-0.0026-0.065-0.13010.3092-0.09170.16060.1725-0.16220.09430.1457-0.0543-0.06370.0310.00090.822665.4591-11.73626.1514
55.2463-6.62323.763116.0255-3.00333.1026-0.00720.18240.0148-0.0388-0.01060.0229-0.01590.23470.01780.5704-0.0508-0.00370.6410.11070.604560.4352-32.758237.4321
62.74250.36441.10360.89520.05293.5798-0.00250.1267-0.2972-0.0782-0.0408-0.05260.6134-0.13410.04320.3801-0.0716-0.05070.0288-0.03880.785368.2539-26.988718.7816
71.9806-0.17310.2462.06040.03321.1506-0.0078-0.09170.21340.2094-0.0330.0969-0.2110.00640.04070.18640.0059-0.06660.0073-0.00220.794178.631519.132925.9958
816.07913.7796-5.40033.8855-5.60568.0931-0.5033-0.1285-1.01320.08810.0953-0.2877-0.0869-0.17260.4080.6033-0.0230.07370.4797-0.09830.663463.084134.085537.1231
91.10360.2935-0.49552.6187-0.52142.2290.0780.15480.1841-0.0491-0.09620.2327-0.3735-0.24630.01820.18940.1264-0.08890.10110.00590.871364.052424.256718.5336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 225
2X-RAY DIFFRACTION2A226 - 230
3X-RAY DIFFRACTION3A231 - 350
4X-RAY DIFFRACTION4B10 - 225
5X-RAY DIFFRACTION5B226 - 230
6X-RAY DIFFRACTION6B231 - 350
7X-RAY DIFFRACTION7C10 - 225
8X-RAY DIFFRACTION8C226 - 230
9X-RAY DIFFRACTION9C231 - 350

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