[English] 日本語
Yorodumi
- PDB-3e7j: HeparinaseII H202A/Y257A double mutant complexed with a heparan s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3e7j
TitleHeparinaseII H202A/Y257A double mutant complexed with a heparan sulfate tetrasaccharide substrate
ComponentsHeparinase II protein
KeywordsSUGAR BINDING PROTEIN / LYASE / alpha and beta lyase / alpha6/alpha6 incomplete toroid
Function / homology
Function and homology information


heparin lyase / heparin lyase activity / heparin-sulfate lyase / heparin-sulfate lyase activity / heparin catabolic process / heparin binding / periplasmic space / metal ion binding
Similarity search - Function
Immunoglobulin-like - #2750 / Heparinase II, C-terminal / Heparinase II C-terminal domain / Heparinase II, N-terminal / Domain of unknown function (DUF4962) / Beta-galactosidase; Chain A, domain 5 - #70 / Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase ...Immunoglobulin-like - #2750 / Heparinase II, C-terminal / Heparinase II C-terminal domain / Heparinase II, N-terminal / Domain of unknown function (DUF4962) / Beta-galactosidase; Chain A, domain 5 - #70 / Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Heparin and heparin-sulfate lyase / Heparin and heparin-sulfate lyase
Similarity search - Component
Biological speciesPedobacter heparinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsShaya, D. / Cygler, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Catalytic mechanism of heparinase II investigated by site-directed mutagenesis and the crystal structure with its substrate.
Authors: Shaya, D. / Zhao, W. / Garron, M.L. / Xiao, Z. / Cui, Q. / Zhang, Z. / Sulea, T. / Linhardt, R.J. / Cygler, M.
History
DepositionAug 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 29, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heparinase II protein
B: Heparinase II protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,57611
Polymers169,6332
Non-polymers1,9439
Water14,088782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.951, 162.210, 93.838
Angle α, β, γ (deg.)90.00, 105.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A B
12A B
13A B

NCS domain segments:

Dom-ID: 1 / Refine code: 2

Component-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEUAA30 - 3607 - 337
21ASPASPLEULEUBB30 - 3607 - 337
12GLYGLYASPASPAA361 - 675338 - 652
22GLYGLYASPASPBB361 - 675338 - 652
13ASNASNARGARGAA676 - 772653 - 749
23ASNASNARGARGBB676 - 772653 - 749

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Heparinase II protein


Mass: 84816.531 Da / Num. of mol.: 2 / Fragment: UNP residues 24-772 / Mutation: H202A, Y257A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pedobacter heparinus (bacteria) / Production host: Escherichia coli / Strain (production host): BL21(DE3) / References: UniProt: Q46080, UniProt: C6XZB6*PLUS
#2: Polysaccharide 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 758.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2122A-1a_1-5][a21eEA-1a_1-5]/1-2-1-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-L-4-deoxy-IdopA]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 782 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHOR'S NATIVE CLONE WAS SEQUENCED AND REVEALED ALA RATHER THAN PRO AT THIS POSITION. THE ...THE AUTHOR'S NATIVE CLONE WAS SEQUENCED AND REVEALED ALA RATHER THAN PRO AT THIS POSITION. THE AUTHORS BELIEVE THAT PRO IS A MISTAKE IN THE UNP DATABASE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.55 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 72010 / % possible obs: 82.9 % / Observed criterion σ(F): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 1.5 / % possible all: 36.1

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementStarting model: PDB ENTRY 2FUT

2fut


Resolution: 2.1→42.52 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.869 / SU ML: 0.191 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 3630 5 %RANDOM
Rwork0.19936 ---
obs0.20116 68316 82.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.966 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å22.48 Å2
2---4.69 Å20 Å2
3---5.66 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11876 0 126 782 12784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02212315
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9661.96716669
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95551484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98523.944568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.924152072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0641568
X-RAY DIFFRACTIONr_chiral_restr0.0660.21756
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219438
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_it0.0771.57405
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.132211912
X-RAY DIFFRACTIONr_scbond_it0.27534910
X-RAY DIFFRACTIONr_scangle_it0.3974.54757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11324tight positional0.020.05
21260tight positional0.020.05
3388tight positional0.090.05
11397medium positional0.10.5
21193medium positional0.070.5
3376medium positional0.380.5
11324tight thermal0.020.5
21260tight thermal0.020.5
3388tight thermal0.10.5
11397medium thermal0.022
21193medium thermal0.032
3376medium thermal0.172
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 104 -
Rwork0.321 2115 -
obs--34.6 %
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)
11.04660.431-0.07283.60840.7490.4532-0.0194-0.0131-0.0923-0.08920.03150.07930.167-0.0428-0.0122-0.15850.0087-0.0469-0.08360.0618-0.08849.654-20.531433.6705
21.26490.096-0.18341.74630.11310.9680.0285-0.06710.00350.08130.03030.02090.0135-0.0187-0.0589-0.2718-0.0004-0.0535-0.15810.0468-0.11069.701112.352747.2246
30.54320.5271-0.16482.1363-1.0442.99780.0063-0.03490.20520.0845-0.0211-0.1236-0.32960.22590.0149-0.1798-0.03490.0088-0.09980.0014-0.017625.338431.282435.8104
40.9967-1.00540.12084.08420.29651.04710.00270.12220.0313-0.6026-0.0942-0.0812-0.273-0.14930.09140.0655-0.02240.0141-0.02520.0136-0.084917.197856.72928.0382
51.0364-0.2553-0.10452.04620.83921.99420.0550.19020.095-0.5399-0.0509-0.0575-0.11-0.0813-0.00410.094-0.05230.0923-0.0880.0385-0.045523.800123.8068-3.7864
60.8760.417-0.83071.7499-0.9992.4563-0.071-0.0184-0.1596-0.45890.0386-0.22830.26850.30320.0324-0.0249-0.00920.0839-0.0575-0.00910.040731.19084.715913.9582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA30 - 3607 - 337
2X-RAY DIFFRACTION2AA361 - 675338 - 652
3X-RAY DIFFRACTION3AA676 - 772653 - 749
4X-RAY DIFFRACTION4BB30 - 3607 - 337
5X-RAY DIFFRACTION5BB361 - 675338 - 652
6X-RAY DIFFRACTION6BB676 - 772653 - 749

+
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