[English] 日本語
Yorodumi
- PDB-3zxk: Engineering the active site of a GH43 glycoside hydrolase generat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zxk
TitleEngineering the active site of a GH43 glycoside hydrolase generates a biotechnologically significant enzyme that displays both endo- xylanase and exo-arabinofuranosidase activity
ComponentsHIAXHD3
KeywordsHYDROLASE / SUGAR BINDING PROTEIN
Function / homologyGlycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Jelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesHUMICOLA INSOLENS (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsMcKee, L.S. / Pena, M.J. / Rogowski, A. / Jackson, A. / Lewis, R.J. / York, W.S. / Krogh, K.B.R.M. / Vikso-Nielsen, A. / Skjot, M. / Gilbert, H.J. / Marles-Wright, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Introducing Endo-Xylanase Activity Into an Exo-Acting Arabinofuranosidase that Targets Side Chains.
Authors: Mckee, L.S. / Pena, M.J. / Rogowski, A. / Jackson, A. / Lewis, R.J. / York, W.S. / Krogh, K.B.R.M. / Vikso-Nielsen, A. / Skjot, M. / Gilbert, H.J. / Marles-Wright, J.
History
DepositionAug 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Other
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIAXHD3
B: HIAXHD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,6446
Polymers121,0752
Non-polymers1,5704
Water18,3031016
1
A: HIAXHD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3223
Polymers60,5371
Non-polymers7852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HIAXHD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3223
Polymers60,5371
Non-polymers7852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.380, 52.970, 146.870
Angle α, β, γ (deg.)90.00, 101.69, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein HIAXHD3


Mass: 60537.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMICOLA INSOLENS (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: non-reducing end alpha-L-arabinofuranosidase
#2: Polysaccharide alpha-L-arabinofuranose-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-2[DXylpb1-4]DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a212h-1b_1-5][a211h-1a_1-4]/1-1-2-1/a4-b1_b2-c1_b4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-L-Araf]{}[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1016 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGENBANK SEQUENCE REF CAL81199. D43A MUTATION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.3 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5 22.5 % (W/V) PEG4000 0.1 M NACL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Type: APS / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: May 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→33.68 Å / Num. obs: 177611 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 8.08 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.2
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 9.8 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZXJ

3zxj


Resolution: 1.44→33.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.897 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20725 8835 5 %RANDOM
Rwork0.16649 ---
obs0.16853 167521 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.592 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.44→33.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8338 0 104 1016 9458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028753
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.93811954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88851079
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.7422.22419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.424151245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2731585
X-RAY DIFFRACTIONr_chiral_restr0.180.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216887
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_restr2.33738753
X-RAY DIFFRACTIONr_sphericity_free30.3335297
X-RAY DIFFRACTIONr_sphericity_bonded8.03459207
LS refinement shellResolution: 1.437→1.474 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 624 -
Rwork0.243 11554 -
obs--93.76 %
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)
10.47230.0208-0.13480.03010.00810.29020.012-0.0085-0.0090.0139-0.004300.00550.006-0.00770.0131-0.0018-0.00080.0009-0.00160.014613.139-11.708317.0563
20.2487-0.0899-0.08970.38870.17040.55540.01660.00520.0111-0.0282-0.01980.0045-0.0384-0.03120.00320.00810.00150.00060.0023-0.00060.01450.1018-3.650113.284
30.1748-0.0998-0.07830.14560.09340.2153-0.0042-0.0424-0.00040.02450.00340.0225-0.0052-0.00180.00090.0179-0.00560.0020.0172-0.00030.01933.2095-7.256931.0468
40.4059-0.0282-0.08330.9345-0.34520.8915-0.00660.0196-0.0415-0.03370.0140.02250.097-0.0441-0.00740.0108-0.0039-0.00260.0056-0.00690.016124.5414-22.50599.1536
50.275-0.0325-0.0620.15910.10550.3166-0.0019-0.0219-0.00260.00830.0031-0.01920.00670.0269-0.00120.0112-0.0007-0.00050.0056-0.00090.015136.2067-13.537617.4522
60.4883-0.1130.09430.11470.05810.13280.004-0.00620.01450.0039-0.0063-0.01590.0093-0.00270.00220.0174-0.00260.00150.01080.00020.014237.6767-32.252455.5432
70.428-0.0145-0.08540.26380.10.5318-0.00280.02660.028-0.01380.0075-0.0151-0.02040.0243-0.00460.0057-0.0037-0.00220.00450.00260.015750.7267-28.145947.8919
80.5001-0.0182-0.03560.11240.06030.1723-0.0160.001-0.06520.00830.0136-0.00750.03840.01930.00240.02270.0028-0.00360.0065-0.00220.021847.5508-46.227450.4238
90.0806-0.0324-0.06350.6259-0.0050.8112-0.0017-0.05240.02340.06240.0069-0.0272-0.00090.0178-0.00520.008-0.0003-0.00260.0358-0.01190.024726.3798-25.226966.9069
100.2326-0.0439-0.03430.25430.05480.1575-0.0050.0062-0.00140.00710.00070.01440.0063-0.02040.00430.0111-0.0021-0.00250.0147-0.00060.015614.5895-32.730957.5231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 108
2X-RAY DIFFRACTION2A109 - 242
3X-RAY DIFFRACTION3A243 - 341
4X-RAY DIFFRACTION4A342 - 376
5X-RAY DIFFRACTION5A377 - 557
6X-RAY DIFFRACTION6B29 - 108
7X-RAY DIFFRACTION7B109 - 242
8X-RAY DIFFRACTION8B243 - 341
9X-RAY DIFFRACTION9B342 - 376
10X-RAY DIFFRACTION10B377 - 557

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more