[English] 日本語
Yorodumi
- PDB-5nz8: Clostridium thermocellum cellodextrin phosphorylase with cellotet... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nz8
TitleClostridium thermocellum cellodextrin phosphorylase with cellotetraose and phosphate bound
ComponentsCellodextrin phosphorylase
KeywordsHYDROLASE / glycoside hydrolase family 94 / cellodextrin phosphorylase / cellulose synthesis
Function / homology
Function and homology information


transferase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
beta-cellotetraose / PHOSPHATE ION / Cellodextrin phosphorylase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsO'Neill, E.C. / Pergolizzi, G. / Stevenson, C.E.M. / Lawson, D.M. / Nepogodiev, S.A. / Field, R.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 (MET) United Kingdom
EPSRC and InnovateUKBB/M02903411 United Kingdom
John Innes Foundation United Kingdom
CitationJournal: Carbohydr. Res. / Year: 2017
Title: Cellodextrin phosphorylase from Ruminiclostridium thermocellum: X-ray crystal structure and substrate specificity analysis.
Authors: O'Neill, E.C. / Pergolizzi, G. / Stevenson, C.E.M. / Lawson, D.M. / Nepogodiev, S.A. / Field, R.A.
History
DepositionMay 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / 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.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellodextrin phosphorylase
B: Cellodextrin phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,5186
Polymers228,9952
Non-polymers1,5234
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-26 kcal/mol
Surface area63100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.810, 152.970, 92.220
Angle α, β, γ (deg.)90.000, 114.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 1 - 984 / Label seq-ID: 26 - 1009

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Cellodextrin phosphorylase /


Mass: 114497.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein was expressed with a 25 residue nickel affinity tag with sequence MGSSHHHHHHSSGLVPRGSHMLEDP appended to the N-terminus of the full-length amino acid sequence
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: cdp-ym4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star / References: UniProt: Q93HT8
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: NULL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→27.62 Å / Num. obs: 41938 / % possible obs: 98 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.041 / Rrim(I) all: 0.077 / Net I/σ(I): 12.8 / Num. measured all: 141679 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3-3.083.41.0860.4250.6921.29194.8
13.42-27.623.20.0210.9990.0140.02580

-
Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
REFMAC5refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMAC5phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5NZ7
Resolution: 3→27.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 58.237 / SU ML: 0.449 / SU R Cruickshank DPI: 0.4498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.487
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 2133 5.2 %RANDOM
Rwork0.2101 ---
obs0.2128 39167 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 213.65 Å2 / Biso mean: 106.195 Å2 / Biso min: 67.33 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å20 Å20.03 Å2
2---4.06 Å20 Å2
3---4.6 Å2
Refinement stepCycle: final / Resolution: 3→27.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14027 0 100 0 14127
Biso mean--133.71 --
Num. residues----1858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914451
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212578
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.93819676
X-RAY DIFFRACTIONr_angle_other_deg0.899328896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20951848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36724.094640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.367152060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3931564
X-RAY DIFFRACTIONr_chiral_restr0.0660.22244
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023140
Refine LS restraints NCS

Ens-ID: 1 / Number: 53420 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.001→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 134 -
Rwork0.35 2438 -
all-2572 -
obs--82.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.59670.40691.51341.5791-1.45515.8426-0.1771-0.39470.42190.3136-0.0074-0.3892-0.33390.51330.18450.12230.0316-0.09350.5916-0.22120.547623.0145-11.599842.0915
23.0382-1.5307-0.22351.68850.51761.8001-0.1448-0.4996-0.46980.33110.27550.45930.2687-0.0046-0.13070.1235-0.0031-0.01160.15290.20830.3985-11.252-34.514143.1541
31.70770.2273-1.16740.37340.67353.3635-0.16881.22610.1096-0.14830.23830.210.4073-0.6734-0.06950.696-0.127-0.49990.9020.15510.7667-1.9601-49.388515.7414
43.149-0.4872-0.86192.59210.21681.3575-0.00250.3674-0.1514-0.60640.1728-0.11380.28760.2881-0.17030.3460.119-0.12830.3148-0.04490.329517.2618-46.398418.0709
52.0725-0.9235-1.05713.44793.21794.3122-0.2325-0.879-0.08540.77660.09130.3198-0.0002-0.15350.14120.59380.1930.09620.66190.24110.5873-33.6529-15.08857.5614
63.3552-1.1960.13422.00680.14851.4715-0.0067-0.10370.71830.03650.1276-0.2791-0.18290.2584-0.12090.0398-0.049-0.0350.07560.01320.3818-6.66310.24931.1253
70.08770.00940.12570.60581.38334.05630.08090.2495-0.0677-0.30220.02750.03870.0915-0.0542-0.10840.8432-0.116-0.10250.9910.15210.9987-31.4851-4.87872.0707
83.54470.2641-0.36872.5235-0.91442.3084-0.06550.50480.1028-0.48660.25090.54170.0474-0.4307-0.18530.1053-0.0251-0.12060.24980.2080.5044-44.3880.032619.971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 118
2X-RAY DIFFRACTION2A119 - 481
3X-RAY DIFFRACTION3A482 - 694
4X-RAY DIFFRACTION4A695 - 984
5X-RAY DIFFRACTION5B1 - 104
6X-RAY DIFFRACTION6B105 - 479
7X-RAY DIFFRACTION7B480 - 704
8X-RAY DIFFRACTION8B705 - 984

+
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