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- PDB-3zq9: Structure of a Paenibacillus Polymyxa Xyloglucanase from Glycosid... -

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Basic information

Entry
Database: PDB / ID: 3zq9
TitleStructure of a Paenibacillus Polymyxa Xyloglucanase from Glycoside Hydrolase Family 44
ComponentsXYLOGLUCANASE
KeywordsHYDROLASE / GH44 / XYLOGLUCAN / ENDO-GLUCANASE
Function / homology
Function and homology information


substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase activity / cellulose binding / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Glycoside hydrolase family 26 / Carbohydrate binding module (family 35) / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain ...Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Glycoside hydrolase family 26 / Carbohydrate binding module (family 35) / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / CBM2/CBM3, carbohydrate-binding domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Chem-NOY / Cel44C
Similarity search - Component
Biological speciesPAENIBACILLUS POLYMYXA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsAriza, A. / Eklof, J.M. / Spadiut, O. / Offen, W.A. / Roberts, S.M. / Besenmatter, W. / Friis, E.P. / Skjot, M. / Wilson, K.S. / Brumer, H. / Davies, G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and Activity of Paenibacillus Polymyxa Xyloglucanase from Glycoside Hydrolase Family 44.
Authors: Ariza, A. / Eklof, J.M. / Spadiut, O. / Offen, W.A. / Roberts, S.M. / Besenmatter, W. / Friis, E.P. / Skjot, M. / Wilson, K.S. / Brumer, H. / Davies, G.
History
DepositionJun 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Other / Version format compliance
Revision 1.2Apr 25, 2012Group: Other
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 1.5Dec 20, 2023Group: 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XYLOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,74511
Polymers57,8861
Non-polymers85910
Water12,394688
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.610, 83.610, 157.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein XYLOGLUCANASE


Mass: 57886.160 Da / Num. of mol.: 1 / Fragment: RESIDUES 36-559 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PAENIBACILLUS POLYMYXA (bacteria) / Strain: GS01 / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): SHA273
References: UniProt: Q1A2D0, cellulase, xyloglucan-specific endo-beta-1,4-glucanase
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 697 molecules

#2: Chemical ChemComp-NOY / (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-2,3,4-TRIOL


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 164 TO ALA ENGINEERED RESIDUE IN CHAIN A, ARG 191 TO TYR
Has protein modificationY
Nonpolymer detailsBETA-D-GLUCOSE (GLC): GLUCOSE IS PART OF A DISACCHARIDE IN THIS STRUCTURE, WITH C1 GLUCOSE BOUND TO ...BETA-D-GLUCOSE (GLC): GLUCOSE IS PART OF A DISACCHARIDE IN THIS STRUCTURE, WITH C1 GLUCOSE BOUND TO O4 NOEUROMYCIN (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-2,3,4-TRIOL (NOY): O4 NOEUROMYCIN IS BOUND TO C1 BETA-D-GLUCOSE
Sequence detailsSEQUENCE IN DATABASE IS SEQUENCE 2 FROM PATENT US 6815192, WHICH IS FOR A XYLOGLUCANASE-BETA- ...SEQUENCE IN DATABASE IS SEQUENCE 2 FROM PATENT US 6815192, WHICH IS FOR A XYLOGLUCANASE-BETA-MANNANASE (CEL44C-MAN26A), AND THIS STRUCTURE IS FOR THE XYLOGLUCANASE PORTION. DISCREPANCIES WITH UNIPROT SEQUENCE Q1A2D0 MAY BE DUE TO SMALL VARIATIONS BETWEEN DIFFERENT STRAINS OF THE SAME ORGANISM.

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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 25% (W/V) PEG 3350, 0.2M LITHIUM SULPHATE, 0.1M HEPES PH 6.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→42.52 Å / Num. obs: 54053 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.3
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 11.3 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YKK

2ykk


Resolution: 1.86→22.23 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.755 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-6 AND 519-524 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.17122 2720 5 %RANDOM
Rwork0.13669 ---
obs0.13837 51240 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.16 Å20 Å2
2--0.33 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.86→22.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 50 688 4730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224314
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9495900
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71725.2200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60415719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5341515
X-RAY DIFFRACTIONr_chiral_restr0.1220.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213318
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
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 185 -
Rwork0.17 3220 -
obs--92.8 %

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