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

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Basic information

Entry
Database: PDB / ID: 5mdr
TitleCrystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi in complex with chitohexaose
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: 1.9 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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
Revision 2.2Oct 16, 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
D: Chitoporin
E: Chitoporin
F: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,59145
Polymers235,1576
Non-polymers12,43339
Water31,4901748
1
A: Chitoporin
B: Chitoporin
C: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,25524
Polymers117,5793
Non-polymers6,67621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Chitoporin
E: Chitoporin
F: Chitoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,33621
Polymers117,5793
Non-polymers5,75718
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.552, 121.941, 147.155
Angle α, β, γ (deg.)90.00, 117.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

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
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Chitoporin


Mass: 39192.863 Da / Num. of mol.: 6
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-(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.: 6
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.: 15 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1748 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% (w/v) PEG 400, 0.05 M NaCl, 0.1 M sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.00727 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00727 Å / Relative weight: 1
ReflectionResolution: 1.9→130.02 Å / Num. obs: 357447 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.056 / Net I/σ(I): 11
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 1.8 / Rpim(I) all: 0.598 / % possible all: 99.5

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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: 1.9→130.02 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.082 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1835 3476 1 %RANDOM
Rwork0.17196 ---
obs0.17206 353937 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.555 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0 Å2-0.27 Å2
2--1.71 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.9→130.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15990 0 729 1748 18467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217144
X-RAY DIFFRACTIONr_bond_other_d0.0060.0214930
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.97723202
X-RAY DIFFRACTIONr_angle_other_deg1.113334375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9765.0632051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91324.828903
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.201152240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1981578
X-RAY DIFFRACTIONr_chiral_restr0.0940.22329
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219888
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024206
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_it0.8121.7598183
X-RAY DIFFRACTIONr_mcbond_other0.8121.7598182
X-RAY DIFFRACTIONr_mcangle_it1.2922.63210220
X-RAY DIFFRACTIONr_mcangle_other1.2912.63210221
X-RAY DIFFRACTIONr_scbond_it1.7432.3538961
X-RAY DIFFRACTIONr_scbond_other1.7432.3538962
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7043.42712983
X-RAY DIFFRACTIONr_long_range_B_refined7.96418.45820808
X-RAY DIFFRACTIONr_long_range_B_other7.96418.46120809
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)
11A381540.02
12B381540.02
21A380400.03
22C380400.03
31A379660.04
32D379660.04
41A382080.03
42E382080.03
51A382220.02
52F382220.02
61B379800.03
62C379800.03
71B380820.03
72D380820.03
81B381240.03
82E381240.03
91B382220.01
92F382220.01
101C380720.03
102D380720.03
111C380000.04
112E380000.04
121C380240.03
122F380240.03
131D379120.04
132E379120.04
141D379880.03
142F379880.03
151E381580.03
152F381580.03
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 308 -
Rwork0.265 26074 -
obs--99.4 %
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)
11.4634-0.59521.42746.8654-4.73454.6170.0546-0.151-0.0225-0.07-0.0602-0.22380.2036-0.02730.00550.30010.0048-0.00970.2569-0.01550.3382-7.3553-24.605858.6711
20.8533-0.189600.599-0.30671.17270.02590.1722-0.0599-0.1741-0.0698-0.06640.14890.13580.04390.11010.02930.02320.1387-0.0120.0159-2.7313.877434.4113
34.4092-2.33221.28112.9578-0.98332.10450.3217-0.0231-0.5795-0.2252-0.04740.34640.5075-0.0127-0.27440.1806-0.0431-0.0370.0644-0.01120.0998-14.8266-6.5457.5418
41.2715-0.0610.10110.37410.08091.02140.0123-0.1331-0.00410.09350.01690.15880.0109-0.2-0.02920.0716-0.01150.05290.14440.0170.0752-25.01525.860568.9419
54.31484.75850.088910.20131.37630.58790.06930.0045-0.13960.2019-0.06410.07480.0286-0.0941-0.00520.3010.02070.010.25420.00750.31210.0501-24.55156.5474
61.07420.20350.24270.3289-0.03611.28320.0219-0.08370.03490.1361-0.0758-0.1258-0.02840.23530.05390.0849-0.0061-0.04050.17570.0430.076115.31327.020470.2589
71.2989-0.842-0.98846.41222.53992.52810.0766-0.12380.0233-0.1191-0.03620.1832-0.20890.0388-0.04040.3039-0.0142-0.00560.24510.01620.328611.417187.588125.0884
81.0611-0.00030.17170.34470.09531.1317-0.00560.22250.011-0.1427-0.01350.00630.04660.05150.01910.11970.01250.01050.1470.00780.00336.014655.90195.3728
91.7832-2.16960.611811.7612-3.92149.1541-0.15090.01520.3518-0.0336-0.0234-0.1974-0.4744-0.2290.17430.4278-0.01070.01690.2727-0.01710.3795.946387.849630.5352
101.4171-0.1160.14190.3892-0.2271.09580.0322-0.04590.05740.052-0.0907-0.1908-0.0310.23540.05850.0617-0.0391-0.03390.15450.02240.100829.111659.041138.059
111.79310.4462-0.09713.9177-3.5365.6914-0.0159-0.0790.31260.3441-0.1141-0.0134-0.69280.05210.130.10750.0003-0.00960.102-0.06960.10063.294568.982538.3465
120.9610.2857-0.02720.5577-0.0151.02460.0395-0.17680.09260.154-0.04570.112-0.0912-0.13270.00630.06870.00420.04020.1373-0.0370.0364-11.880557.869941.6247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 17
2X-RAY DIFFRACTION2A18 - 350
3X-RAY DIFFRACTION3B10 - 37
4X-RAY DIFFRACTION4B38 - 350
5X-RAY DIFFRACTION5C10 - 17
6X-RAY DIFFRACTION6C18 - 350
7X-RAY DIFFRACTION7D10 - 17
8X-RAY DIFFRACTION8D18 - 350
9X-RAY DIFFRACTION9E10 - 17
10X-RAY DIFFRACTION10E18 - 350
11X-RAY DIFFRACTION11F10 - 38
12X-RAY DIFFRACTION12F39 - 350

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