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

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Basic information

Entry
Database: PDB / ID: 6fhj
TitleStructural dynamics and catalytic properties of a multi-modular xanthanase, native.
Componentsprotein,protein
KeywordsHYDROLASE / endo-xanthanase / xanthan degradation / novel CBM
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process / metal ion binding
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 / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
MALONATE ION / DI(HYDROXYETHYL)ETHER / Protein,protein
Similarity search - Component
Biological speciesPaenibacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 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 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1May 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein,protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,72013
Polymers109,1001
Non-polymers61912
Water14,034779
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-58 kcal/mol
Surface area36630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.350, 103.350, 212.500
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,protein


Mass: 109100.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The last domain is ill defined, the fragments that could be fit into density are described as UNK.,The last domain is ill defined, the fragments that could be fit into density are described as UNK.
Source: (gene. exp.) Paenibacillus (bacteria) / Strain: sp. 62047 / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A3F2YM16*PLUS

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Non-polymers , 6 types, 791 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MLI / MALONATE ION


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


Mass: 18.015 Da / Num. of mol.: 779 / 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: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PACT condition E12, 20 percent PEG3350, sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.04→27.5 Å / Num. obs: 84289 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.8
Reflection shellResolution: 2.04→2.09 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.6 / CC1/2: 0.878

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.04→27.5 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.268 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21047 4202 5 %RANDOM
Rwork0.17978 ---
obs0.18133 80028 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.273 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.04→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7432 0 30 780 8242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.027660
X-RAY DIFFRACTIONr_bond_other_d0.0020.026626
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.93610475
X-RAY DIFFRACTIONr_angle_other_deg0.984315360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8725979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63224.866337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.575151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.321523
X-RAY DIFFRACTIONr_chiral_restr0.0930.21182
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021579
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_it0.561.8323925
X-RAY DIFFRACTIONr_mcbond_other0.5611.8323924
X-RAY DIFFRACTIONr_mcangle_it0.8682.7434901
X-RAY DIFFRACTIONr_mcangle_other0.8682.7434902
X-RAY DIFFRACTIONr_scbond_it0.6631.883733
X-RAY DIFFRACTIONr_scbond_other0.6631.8793731
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0222.7955574
X-RAY DIFFRACTIONr_long_range_B_refined4.51822.738769
X-RAY DIFFRACTIONr_long_range_B_other4.51822.7298769
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 280 -
Rwork0.197 5846 -
obs--99.9 %
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)
11.3176-0.27950.37792.1149-1.70372.06040.0538-0.1941-0.35760.0967-0.1637-0.18710.26030.02350.110.2082-0.0158-0.04420.12010.06830.151893.90017.811124.4939
20.72270.17550.09351.344-0.21040.58320.0086-0.10820.04510.24860.0028-0.0633-0.1229-0.0085-0.01140.07990.0192-0.01750.0301-0.01580.012288.514737.65814.8571
31.923-0.0923-1.06070.97790.28031.19370.0499-0.01740.00660.08230.02260.034-0.0648-0.0831-0.07250.02630.0015-0.00350.03960.01160.046973.473711.88880.9973
41.84441.1004-0.37433.0651-0.56561.42950.18550.1340.34670.256-0.0075-0.0487-0.65550.3416-0.1780.4124-0.14490.12920.2358-0.04630.1574100.535526.7718-24.9726
50.97990.1449-1.02881.1318-0.84463.5406-0.16020.1717-0.3133-0.19190.0162-0.10740.3649-0.01790.14410.0813-0.02020.02230.0815-0.0590.162581.6707-4.7514-13.9945
63.52410.2475-0.13672.2723-0.68263.2206-0.0272-0.2241-0.22730.29580.00120.17940.3695-0.40670.02590.2341-0.06790.04280.22970.05130.257862.3757-9.861712.0468
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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