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

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Basic information

Entry
Database: PDB / ID: 5mdq
TitleCrystal structure of outer membrane expressed Chitoporin VhChip from Vibrio harveyi
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 / monoatomic ion transmembrane transport / cell outer membrane / metal ion binding / Chitoporin
Function and homology information
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)115,6766
Polymers115,6073
Non-polymers693
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14140 Å2
ΔGint-87 kcal/mol
Surface area40230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)255.730, 148.639, 54.364
Angle α, β, γ (deg.)90.00, 94.94, 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: ASP / Beg label comp-ID: ASP / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 1 - 350 / Label seq-ID: 1 - 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 4.45 Å3/Da / Density % sol: 72.37 %
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: I02 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→49.15 Å / Num. obs: 66687 / % possible obs: 95.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.078 / Net I/σ(I): 12.2
Reflection shellRedundancy: 4.1 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.1 / Rpim(I) all: 0.58 / % possible all: 97.5

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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: 2.5→128.39 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.921 / SU B: 22.653 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.22 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24093 2089 3.1 %RANDOM
Rwork0.23013 ---
obs0.23048 64598 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.574 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å20.48 Å2
2--0.59 Å20 Å2
3---0.53 Å2
Refinement stepCycle: 1 / Resolution: 2.5→128.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8169 0 3 38 8210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.028376
X-RAY DIFFRACTIONr_bond_other_d0.0090.027245
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.92111346
X-RAY DIFFRACTIONr_angle_other_deg1.362316629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28151047
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81324.935462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.443151227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.921539
X-RAY DIFFRACTIONr_chiral_restr0.1160.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210068
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022121
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_it0.9211.6444197
X-RAY DIFFRACTIONr_mcbond_other0.9211.6444196
X-RAY DIFFRACTIONr_mcangle_it1.5382.4665241
X-RAY DIFFRACTIONr_mcangle_other1.5382.4665242
X-RAY DIFFRACTIONr_scbond_it1.2261.7614179
X-RAY DIFFRACTIONr_scbond_other1.2261.7614179
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0062.5996105
X-RAY DIFFRACTIONr_long_range_B_refined3.27213.4899222
X-RAY DIFFRACTIONr_long_range_B_other3.25113.4789218
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)
11A380740.03
12B380740.03
21A379480.04
22C379480.04
31B379960.03
32C379960.03
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 150 -
Rwork0.351 4930 -
obs--97.45 %
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)
12.6577-1.61542.51061.7498-0.973610.62880.0592-0.1480.24090.4241-0.0915-0.2018-0.41170.1960.03230.4224-0.065-0.07450.2636-0.00550.283770.203812.120937.6178
20.89230.06450.1813.37180.64511.429-0.03630.0255-0.21680.07780.0175-0.35460.3838-0.36350.01880.2145-0.1341-0.05980.125-0.02150.325169.3614-19.499522.9718
31.15370.48040.43612.7020.82584.77590.0510.045-0.3551-0.15820.1577-0.81330.6363-0.0426-0.20870.2415-0.068-0.00230.0284-0.04850.674881.8378-24.899219.7898
41.7868-1.51473.96457.6098-6.162810.31240.33450.0256-0.33810.3229-0.313-1.79520.92980.2313-0.02150.72350.0341-0.47560.1868-0.1531.08899.81774.281237.4547
51.79430.22250.19612.3442-0.08511.2737-0.0662-0.07150.0882-0.01080.0643-0.3102-0.3998-0.25610.00180.18580.0826-0.12150.0535-0.0170.341375.394219.919525.9041
61.0758-0.09970.13442.4384-0.03372.2008-0.00950.17550.1258-0.24250.03660.1269-0.4701-0.5814-0.02710.21350.1362-0.15440.2204-0.01770.31762.0220.206118.391
71.39610.7908-0.12073.3078-0.07121.4586-0.06520.0091-0.49980.06420.1419-1.5740.13030.1932-0.07670.06140.0094-0.1180.0699-0.17081.3063100.2532-5.363325.7455
81.5910.94080.15796.96280.40540.0319-0.00750.1584-0.18080.44230.0344-0.37770.0270.032-0.0270.1270.02570.05680.5016-0.11140.9413119.43931.479227.7604
92.11570.2368-0.49441.4826-0.26712.8155-0.20550.3151-0.5033-0.25420.2206-1.4077-0.0890.3958-0.01510.1667-0.13480.13990.1952-0.29811.8201110.43578.386318.1025
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION2A19 - 298
3X-RAY DIFFRACTION3A299 - 350
4X-RAY DIFFRACTION4B1 - 18
5X-RAY DIFFRACTION5B19 - 240
6X-RAY DIFFRACTION6B241 - 350
7X-RAY DIFFRACTION7C1 - 220
8X-RAY DIFFRACTION8C221 - 242
9X-RAY DIFFRACTION9C243 - 350

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