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- PDB-6fhn: Structural dynamics and catalytic properties of a multi-modular x... -

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Basic information

Entry
Database: PDB / ID: 6fhn
TitleStructural dynamics and catalytic properties of a multi-modular xanthanase (Pt derivative)
Componentsprotein
KeywordsHYDROLASE / endo-xanthanase / xanthan degradation / novel CBM / platinum derivative
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process
Similarity search - Function
Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
MALONATE ION / : / THIOCYANATE ION / Protein
Similarity search - Component
Biological speciesPaenibacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMoroz, O.V. / Jensen, P.F. / McDonald, S.P. / McGregor, N. / Blagova, E. / Comamala, G. / Segura, D.R. / Anderson, L. / Vasu, S.M. / Rao, V.P. ...Moroz, O.V. / Jensen, P.F. / McDonald, S.P. / McGregor, N. / Blagova, E. / Comamala, G. / Segura, D.R. / Anderson, L. / Vasu, S.M. / Rao, V.P. / Giger, L. / Monrad, R.N. / Svendsen, A. / Nielsen, J.E. / Henrissat, B. / Davies, G.J. / Brumer, H. / Rand, K. / Wilson, K.S.
CitationJournal: Acs Catalysis / Year: 2018
Title: Structural Dynamics and Catalytic Properties of a Multimodular Xanthanase
Authors: Moroz, O.V. / Jensen, P.F. / McDonald, S.P. / McGregor, N. / Blagova, E. / Comamala, G. / Segura, D.R. / Anderson, L. / Vasu, S.M. / Rao, V.P. / Giger, L. / Monrad, R.N. / Svendsen, A. / ...Authors: Moroz, O.V. / Jensen, P.F. / McDonald, S.P. / McGregor, N. / Blagova, E. / Comamala, G. / Segura, D.R. / Anderson, L. / Vasu, S.M. / Rao, V.P. / Giger, L. / Monrad, R.N. / Svendsen, A. / Nielsen, J.E. / Henrissat, B. / Davies, G.J. / Brumer, H. / Rand, K. / Wilson, K.S.
History
DepositionJan 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Category: pdbx_seq_map_depositor_info / reflns_shell
Item: _pdbx_seq_map_depositor_info.one_letter_code_mod / _reflns_shell.Rmerge_I_obs
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_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.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.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,29616
Polymers109,1001
Non-polymers1,19615
Water14,826823
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-108 kcal/mol
Surface area36210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.270, 103.270, 210.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein protein


Mass: 109100.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The last domain is very poorly defined, some fragments are described as UNK residues
Source: (gene. exp.) Paenibacillus sp. (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A3F2YM17*PLUS

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Non-polymers , 8 types, 838 molecules

#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 823 / 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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20-22% PEG3350, 0.1M Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2→52.29 Å / Num. obs: 88513 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Net I/σ(I): 16
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.5 / CC1/2: 0.876 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2→52.29 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.073 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20976 4435 5 %RANDOM
Rwork0.17272 ---
obs0.17458 84008 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0.21 Å20 Å2
2---0.42 Å20 Å2
3---1.37 Å2
Refinement stepCycle: 1 / Resolution: 2→52.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7433 0 43 825 8301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.027727
X-RAY DIFFRACTIONr_bond_other_d0.0020.026710
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.93810589
X-RAY DIFFRACTIONr_angle_other_deg0.994315566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17451001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.124.792336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.873151105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2511524
X-RAY DIFFRACTIONr_chiral_restr0.10.21206
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218813
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021595
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_it0.7322.2673946
X-RAY DIFFRACTIONr_mcbond_other0.7192.2663943
X-RAY DIFFRACTIONr_mcangle_it1.0593.3934928
X-RAY DIFFRACTIONr_mcangle_other1.0593.3934929
X-RAY DIFFRACTIONr_scbond_it0.8892.3353779
X-RAY DIFFRACTIONr_scbond_other0.8882.3343777
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3373.4725648
X-RAY DIFFRACTIONr_long_range_B_refined5.41528.8549294
X-RAY DIFFRACTIONr_long_range_B_other5.34427.9069050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 314 -
Rwork0.205 6145 -
obs--99.97 %
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)
11.6880.0831-0.0442.5656-1.23962.84910.0651-0.2412-0.41740.267-0.3132-0.33940.24690.23090.24810.1661-0.0133-0.09040.12020.12690.218593.68437.966824.2919
20.88990.3646-0.00191.7488-0.37060.69580.087-0.13030.04450.3956-0.0721-0.0965-0.16780.0572-0.01490.1245-0.0237-0.03040.0238-0.0090.022488.211837.623714.7444
32.2167-0.1677-1.21391.40410.39411.58610.02980.0365-0.01020.09560.04170.03190.0017-0.0789-0.07160.01320.0017-0.00680.01080.0020.054573.404211.86751.0312
41.97241.0904-0.43282.6537-0.16681.40410.11670.11980.22540.1712-0.0317-0.0643-0.35380.302-0.0850.3033-0.10220.0980.2356-0.01750.1438100.306926.7853-24.7322
51.384-0.0021-1.42771.4019-0.39443.4592-0.09910.2188-0.2789-0.14450.0284-0.09170.32840.03890.07070.09130.0002-0.00390.0831-0.06570.156281.6587-4.6229-13.7618
63.488-0.03360.92832.1479-0.20613.3890.0376-0.4182-0.37250.6141-0.12870.26020.4374-0.34270.0910.3822-0.09370.08350.18980.05160.333562.3899-9.773412.1426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 95
2X-RAY DIFFRACTION2A96 - 559
3X-RAY DIFFRACTION3A560 - 657
4X-RAY DIFFRACTION4A658 - 814
5X-RAY DIFFRACTION5A815 - 918
6X-RAY DIFFRACTION6A919 - 3000

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