[English] 日本語
Yorodumi
- PDB-2x32: Structure of a polyisoprenoid binding domain from Saccharophagus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x32
TitleStructure of a polyisoprenoid binding domain from Saccharophagus degradans implicated in plant cell wall breakdown
ComponentsCELLULOSE-BINDING PROTEIN
KeywordsCARBOHYDRATE-BINDING PROTEIN / OXIDOREDUCTION / MARINE BACTERIA / POLYISOPRENOID TRANSPORT
Function / homology
Function and homology information


polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / membrane
Similarity search - Function
: / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II ...: / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / Chem-OTP / Cellulose-binding protein
Similarity search - Component
Biological speciesSACCHAROPHAGUS DEGRADANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsVincent, F. / Dal Molin, D. / Weiner, R.M. / Bourne, Y. / Henrissat, B.
CitationJournal: FEBS Lett. / Year: 2010
Title: Structure of a Polyisoprenoid Binding Domain from Saccharophagus Degradans Implicated in Plant Cell Wall Breakdown
Authors: Vincent, F. / Dalmolin, D. / Weiner, R.M. / Bourne, Y. / Henrissat, B.
History
DepositionJan 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CELLULOSE-BINDING PROTEIN
B: CELLULOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3077
Polymers38,6542
Non-polymers1,6535
Water9,746541
1
A: CELLULOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1193
Polymers19,3271
Non-polymers7922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELLULOSE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1884
Polymers19,3271
Non-polymers8613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.378, 64.360, 84.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.96196, -0.08183, 0.26066), (-0.085, -0.99638, 0.00087), (0.25964, -0.023, -0.96543)
Vector: -3.13641, 37.54768, 34.33506)

-
Components

#1: Protein CELLULOSE-BINDING PROTEIN / X158


Mass: 19326.820 Da / Num. of mol.: 2 / Fragment: YCEI-LIKE DOMAIN, RESIDUES 199-371
Source method: isolated from a genetically manipulated source
Details: OCTAPRENYL PYROPHOSPHATE BOUND TO THE PROTEIN / Source: (gene. exp.) SACCHAROPHAGUS DEGRADANS (bacteria) / Strain: 2-40 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS / References: UniProt: Q21LI5
#2: Chemical ChemComp-OTP / (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE / OCTAPRENYL PYROPHOSPHATE


Mass: 722.911 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H68O7P2
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL HISTIDINE TAG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.9 % / Description: NONE
Crystal growpH: 5.5 / Details: pH 5.5

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.55→35 Å / Num. obs: 51047 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 5.9 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.1
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X34

2x34


Resolution: 1.55→51.23 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.841 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.19418 2584 5.1 %RANDOM
Rwork0.1585 ---
obs0.16028 48401 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.379 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--0.16 Å2-0 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.55→51.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 113 541 3284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222980
X-RAY DIFFRACTIONr_bond_other_d0.0010.021867
X-RAY DIFFRACTIONr_angle_refined_deg1.8722.0014105
X-RAY DIFFRACTIONr_angle_other_deg1.0134631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.035409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.32224.919124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98415476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9171516
X-RAY DIFFRACTIONr_chiral_restr0.1090.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02583
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_it1.0621.51839
X-RAY DIFFRACTIONr_mcbond_other0.3311.5741
X-RAY DIFFRACTIONr_mcangle_it1.78623020
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.61231141
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.774.51055
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: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 172 -
Rwork0.248 3559 -
obs--99.92 %
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)
12.03091.01510.37031.3965-0.75591.6697-0.02750.18950.11160.0208-0.05920.022-0.08460.24730.08670.0325-0.00080.00730.060.00840.048325.215313.282326.3458
21.7977-0.05570.59230.806-0.20180.3004-0.03440.01090.0147-0.0359-0.0103-0.03570.03660.01020.04470.05670.00380.00480.0558-0.00790.038724.63116.832631.3302
31.0550.08530.52080.5257-0.27371.0091-0.0573-0.00590.07280.0270.05860.0159-0.05180.003-0.00130.04190.00510.00490.0258-0.00780.036119.751514.12131.8565
42.3083-0.5098-0.42161.3017-0.41081.7873-0.0006-0.1050.0247-0.08150.00220.04790.08770.1599-0.00160.03190.006-0.00670.0278-0.00610.037424.637225.914111.9509
51.5482-0.0645-0.45010.70360.12190.8488-0.07380.0247-0.0705-0.04380.05920.01660.0320.0060.01450.04730.0043-0.00710.0184-0.00310.020422.004124.54469.1185
63.5943-1.9893-2.23382.01921.32272.0558-0.2411-0.1872-0.15680.03770.19730.01160.22960.22040.04380.06310.02170.00570.0418-0.02230.046731.284916.78718.2066
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 26
2X-RAY DIFFRACTION2A27 - 59
3X-RAY DIFFRACTION3A60 - 173
4X-RAY DIFFRACTION4B-2 - 44
5X-RAY DIFFRACTION5B45 - 132
6X-RAY DIFFRACTION6B133 - 173

+
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