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- PDB-5ocr: Crystal structure of the kappa-carrageenase zobellia_236 from Zob... -

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Basic information

Entry
Database: PDB / ID: 5ocr
TitleCrystal structure of the kappa-carrageenase zobellia_236 from Zobellia galactanivorans
ComponentsKappa-carrageenase
KeywordsHYDROLASE / Glycoside hydrolase 16 / kappa-carrageenase / beta-jellyroll / marine polysaccharidase
Function / homology
Function and homology information


kappa-carrageenase / kappa-carrageenase activity / carbohydrate metabolic process
Similarity search - Function
Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Kappa-carrageenase, family GH16 / Kappa-carrageenase
Similarity search - Component
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsCzjzek, M. / Matard-Mann, M. / Michel, G. / Jeudy, A. / Larocque, R.
Funding support France, 2items
OrganizationGrant numberCountry
ANRT2014/0684 France
French National Research AgencyANR-10-BTBR-04 France
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural insights into marine carbohydrate degradation by family GH16 kappa-carrageenases.
Authors: Matard-Mann, M. / Bernard, T. / Leroux, C. / Barbeyron, T. / Larocque, R. / Prechoux, A. / Jeudy, A. / Jam, M. / Nyvall Collen, P. / Michel, G. / Czjzek, M.
History
DepositionJul 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 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 / pdbx_struct_conn_angle / 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 / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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_symmetry / _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: Kappa-carrageenase
B: Kappa-carrageenase
C: Kappa-carrageenase
D: Kappa-carrageenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,78718
Polymers134,0404
Non-polymers74714
Water14,052780
1
A: Kappa-carrageenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6514
Polymers33,5101
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kappa-carrageenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7435
Polymers33,5101
Non-polymers2334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kappa-carrageenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7435
Polymers33,5101
Non-polymers2334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kappa-carrageenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6514
Polymers33,5101
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.960, 83.040, 85.710
Angle α, β, γ (deg.)72.56, 88.34, 89.48
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 30 - 307 / Label seq-ID: 9 - 286

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999971, -0.00751, 0.000829), (0.007414, 0.996487, 0.083418), (-0.001452, -0.08341, 0.996514)-1.01273, 25.16297, -41.46136
3given(0.99985, 0.016276, -0.005857), (0.015738, -0.996468, -0.082488), (-0.007179, 0.082384, -0.996575)-20.7817, 9.6117, 44.72337
4given(0.999821, 0.018552, -0.003754), (0.01856, -0.999826, 0.002096), (-0.003714, -0.002166, -0.999991)-20.26209, 34.57153, 2.9206

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Components

#1: Protein
Kappa-carrageenase /


Mass: 33510.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The discrepancies to the coordinate file are due to sequencing errors of the Uniprot entry (the sequence was deposited in early sequencing days). The GenBank sequence CAZ94309.1 is part of a ...Details: The discrepancies to the coordinate file are due to sequencing errors of the Uniprot entry (the sequence was deposited in early sequencing days). The GenBank sequence CAZ94309.1 is part of a more recent genome sequencing project - and that has the exact same sequence as our crystal structure
Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Gene: cgkA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O84907, UniProt: G0L921*PLUS, kappa-carrageenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 780 / 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: 2.22 Å3/Da / Density % sol: 44.7 % / Description: rather thin, long and rectangular plates
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 27-29 % PEG 3350, 100 mM MES buffer at pH 6.5, 0.3 M NaNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2016
RadiationMonochromator: optical mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.61→81.7 Å / Num. obs: 132172 / % possible obs: 93.9 % / Redundancy: 1.98 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/av σ(I): 11.97 / Net I/σ(I): 11.97
Reflection shellResolution: 1.61→1.7 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 20564 / CC1/2: 0.771 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DYP

1dyp


Resolution: 1.66→81.74 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.274 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20599 5682 4.7 %RANDOM
Rwork0.16807 ---
obs0.16986 114681 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.029 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20.2 Å2-0.32 Å2
2--0 Å2-0.4 Å2
3----1.33 Å2
Refinement stepCycle: 1 / Resolution: 1.66→81.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9208 0 44 780 10032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0210044
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.91613748
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.42451246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49125.164550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.909151694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2261539
X-RAY DIFFRACTIONr_chiral_restr0.1670.21370
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217991
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1075medium positional0.170.5
B1075medium positional0.150.5
C1075medium positional0.160.5
D1075medium positional0.160.5
A1088loose positional0.285
B1088loose positional0.275
C1088loose positional0.265
D1088loose positional0.265
A1075medium thermal3.032
B1075medium thermal2.252
C1075medium thermal2.82
D1075medium thermal2.332
A1088loose thermal3.2910
B1088loose thermal310
C1088loose thermal3.0510
D1088loose thermal3.0310
LS refinement shellResolution: 1.658→1.701 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 463 -
Rwork0.252 8422 -
obs--93.79 %
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)
10.1859-0.1014-0.09440.06310.03940.39070.0008-0.0191-0.0041-0.01080.0191-0.0122-0.0362-0.0068-0.020.1136-0.00490.00960.12610.00580.14490.774-3.271-0.035
20.847-0.1136-0.32641.7077-0.2390.23660.1055-0.11460.17210.0336-0.0779-0.0449-0.12990.0447-0.02760.15850.00080.03130.08880.00230.1492.54117.528-5.844
30.3980.0032-0.02110.00310.00880.85210.06090.0051-0.01610.01180.0138-0.0071-0.0015-0.0231-0.07460.1170.0075-0.00260.12110.0020.1271.516-31.82238.923
41.40420.92640.16021.8977-0.5150.63550.1427-0.06760.15140.2936-0.12030.0239-0.2791-0.0114-0.02230.19370.0180.05240.06590.00870.11613.483-10.62534.85
50.08270.06710.04690.10730.32561.59-0.03020.0073-0.0045-0.0301-0.00660.0066-0.0502-0.06010.03670.11140.0129-0.00950.1278-0.00810.123421.6599.55245.529
62.1742-1.48910.04991.9014-0.45432.1902-0.01980.2728-0.0592-0.1558-0.23050.01980.64490.06160.25020.3070.00280.00060.03890.00370.090623.842-11.62449.609
70.33650.01210.03120.14090.17580.78510.0230.00080.03540.02890.0203-0.02640.0384-0.0133-0.04330.11260.0009-0.00680.1115-0.00040.139320.31138.2732.778
80.787-0.15090.30450.7987-0.76671.05840.09930.0307-0.045-0.2021-0.0571-0.02590.4623-0.0016-0.04220.347-0.0013-0.08670.03940.00140.101622.54217.5118.7
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 66
2X-RAY DIFFRACTION1A74 - 95
3X-RAY DIFFRACTION1A107 - 266
4X-RAY DIFFRACTION1A291 - 307
5X-RAY DIFFRACTION2A67 - 73
6X-RAY DIFFRACTION2A96 - 106
7X-RAY DIFFRACTION2A267 - 290
8X-RAY DIFFRACTION3B30 - 66
9X-RAY DIFFRACTION3B74 - 95
10X-RAY DIFFRACTION3B107 - 266
11X-RAY DIFFRACTION3B291 - 307
12X-RAY DIFFRACTION4B67 - 73
13X-RAY DIFFRACTION4B96 - 106
14X-RAY DIFFRACTION4B267 - 290
15X-RAY DIFFRACTION5C30 - 66
16X-RAY DIFFRACTION5C74 - 95
17X-RAY DIFFRACTION5C107 - 266
18X-RAY DIFFRACTION5C291 - 307
19X-RAY DIFFRACTION6C67 - 73
20X-RAY DIFFRACTION6C96 - 106
21X-RAY DIFFRACTION6C267 - 290
22X-RAY DIFFRACTION7D30 - 66
23X-RAY DIFFRACTION7D74 - 95
24X-RAY DIFFRACTION7D107 - 266
25X-RAY DIFFRACTION7D291 - 307
26X-RAY DIFFRACTION8D67 - 73
27X-RAY DIFFRACTION8D96 - 106
28X-RAY DIFFRACTION8D267 - 290

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