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- PDB-6fcg: Crystal structure of an endo-laminarinase from Formosa Hel1_33_131 -

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Basic information

Entry
Database: PDB / ID: 6fcg
TitleCrystal structure of an endo-laminarinase from Formosa Hel1_33_131
ComponentsGlycoside hydrolase, GH17 family
KeywordsHYDROLASE / Glycoside hydrolase / GH17 / bacteria / laminarinase
Function / homologyGlycoside hydrolase family 17 / Glycosyl hydrolases family 17 / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / Glycoside hydrolase, GH17 family
Function and homology information
Biological speciesFormosa sp. Hel1_33_131 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBecker, S. / Robb, C.S. / Hehemann, J.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: ISME J / Year: 2018
Title: Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms.
Authors: Unfried, F. / Becker, S. / Robb, C.S. / Hehemann, J.H. / Markert, S. / Heiden, S.E. / Hinzke, T. / Becher, D. / Reintjes, G. / Kruger, K. / Kappelmann, L. / Hahnke, R.L. / Fischer, T. / ...Authors: Unfried, F. / Becker, S. / Robb, C.S. / Hehemann, J.H. / Markert, S. / Heiden, S.E. / Hinzke, T. / Becher, D. / Reintjes, G. / Kruger, K. / Kappelmann, L. / Hahnke, R.L. / Fischer, T. / Harder, J. / Teeling, H. / Fuchs, B. / Barbeyron, T. / Amann, R.I. / Schweder, T.
History
DepositionDec 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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.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: Glycoside hydrolase, GH17 family
B: Glycoside hydrolase, GH17 family
C: Glycoside hydrolase, GH17 family
D: Glycoside hydrolase, GH17 family
E: Glycoside hydrolase, GH17 family
F: Glycoside hydrolase, GH17 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,7998
Polymers293,7196
Non-polymers802
Water15,547863
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15000 Å2
ΔGint-71 kcal/mol
Surface area89040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.336, 149.143, 107.217
Angle α, β, γ (deg.)90.00, 103.35, 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: 0 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: 38 - 430 / Label seq-ID: 38 - 430

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
Glycoside hydrolase, GH17 family /


Mass: 48953.215 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Formosa sp. Hel1_33_131 (bacteria) / Gene: FORMB_24720 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D7Y259
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 863 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.03M Magnesium Chloride 0.1M MOPS pH 7 9% PEG8000 15% Ethyleneglycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2017
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→104.32 Å / Num. obs: 87396 / % possible obs: 99.7 % / Redundancy: 5.2 % / Net I/σ(I): 6.9
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4421 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wtp

4wtp


Resolution: 2.6→104.32 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.151 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 1.151 / ESU R Free: 0.308 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23881 4247 4.9 %RANDOM
Rwork0.20461 ---
obs0.20629 83120 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.096 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å2-0.44 Å2
2---0.69 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: 1 / Resolution: 2.6→104.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18826 0 2 863 19691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01919318
X-RAY DIFFRACTIONr_bond_other_d0.0080.0217890
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.92826184
X-RAY DIFFRACTIONr_angle_other_deg1.689341192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44152352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43824.693927
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.045153245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6551566
X-RAY DIFFRACTIONr_chiral_restr0.0930.22771
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222038
X-RAY DIFFRACTIONr_gen_planes_other0.0060.024608
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_it1.6232.4869426
X-RAY DIFFRACTIONr_mcbond_other1.6242.4869425
X-RAY DIFFRACTIONr_mcangle_it2.6033.72811772
X-RAY DIFFRACTIONr_mcangle_other2.6023.72811773
X-RAY DIFFRACTIONr_scbond_it2.3272.79892
X-RAY DIFFRACTIONr_scbond_other2.3272.79892
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.833.94114412
X-RAY DIFFRACTIONr_long_range_B_refined5.15519.47822212
X-RAY DIFFRACTIONr_long_range_B_other5.12519.49422068
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)
11A490240.05
12B490240.05
21A464020.1
22C464020.1
31A472220.09
32D472220.09
41A468120.09
42E468120.09
51A471920.09
52F471920.09
61B465140.1
62C465140.1
71B472040.09
72D472040.09
81B470280.09
82E470280.09
91B470480.09
92F470480.09
101C470240.09
102D470240.09
111C492200.05
112E492200.05
121C465840.1
122F465840.1
131D473700.09
132E473700.09
141D490000.06
142F490000.06
151E471220.09
152F471220.09
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 343 -
Rwork0.308 6102 -
obs--99.86 %

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