[English] 日本語
Yorodumi
- PDB-5kkw: Crystal structure of SAR11_1068 bound to a sulfobetaine (3-(1-met... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kkw
TitleCrystal structure of SAR11_1068 bound to a sulfobetaine (3-(1-methylpiperidinium-1-yl)propane-1-sulfonate)
ComponentsCyclohexadienyl dehydratase
KeywordsLYASE / Solute-binding protein / periplasmic binding protein / transport protein
Function / homology
Function and homology information


Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(1-methylpiperidinium-1-yl)propane-1-sulfonate / Cyclohexadienyl dehydratase
Similarity search - Component
Biological speciesPelagibacter ubique (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsClifton, B.E. / Carr, P.D. / Jackson, C.J.
CitationJournal: To Be Published
Title: Crystal structure of SAR11_1068 bound to a sulfobetaine (3-(1-methylpiperidinium-1-yl)propane-1-sulfonate)
Authors: Clifton, B.E. / Kaczmarski, J.A. / Carr, P.D. / Jackson, C.J.
History
DepositionJun 22, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJul 5, 2017ID: 5HMT
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclohexadienyl dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2163
Polymers27,8991
Non-polymers3172
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.665, 77.665, 44.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsMonomer as determined by Size-exclusion chromatography

-
Components

#1: Protein Cyclohexadienyl dehydratase


Mass: 27898.885 Da / Num. of mol.: 1 / Fragment: residues 19-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelagibacter ubique (strain HTCC1062) (bacteria)
Strain: HTCC1062 / Gene: pheC, SAR11_1068 / Plasmid: pDOTS7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4FLR5
#2: Chemical ChemComp-KH2 / 3-(1-methylpiperidinium-1-yl)propane-1-sulfonate


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 uL protein (24 mg/mL protein in 10 mM TRIS pH 8.0, 50 mM NaCl, 10 mM 3-(1-methylpiperidinium-1-yl)propane-1-sulfonate) + 1 uL precipitant (0.1 M MES pH 6.5, 27% (w/v) PEG 3350, 0.1 M lithium sulfate)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.88→38.84 Å / Num. obs: 20952 / % possible obs: 95.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 22.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.2
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 3 / % possible all: 67.7

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSMay 1, 2016data reduction
Aimless0.1.29data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HMT

5hmt
PDB Unreleased entry


Resolution: 1.88→38.84 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.195 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 1064 5.1 %RANDOM
Rwork0.20504 ---
obs0.20672 19884 95.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.951 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-0 Å2
2---0.7 Å2-0 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.88→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 19 95 1951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021918
X-RAY DIFFRACTIONr_bond_other_d0.0010.021834
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.9782608
X-RAY DIFFRACTIONr_angle_other_deg0.87634252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3945244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69525.67674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82215341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.234154
X-RAY DIFFRACTIONr_chiral_restr0.1180.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02399
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_it1.8521.943955
X-RAY DIFFRACTIONr_mcbond_other1.8421.942954
X-RAY DIFFRACTIONr_mcangle_it2.6242.91194
X-RAY DIFFRACTIONr_mcangle_other2.6232.9021195
X-RAY DIFFRACTIONr_scbond_it2.4232.238963
X-RAY DIFFRACTIONr_scbond_other2.3412.219960
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4993.2161405
X-RAY DIFFRACTIONr_long_range_B_refined5.0816.0162192
X-RAY DIFFRACTIONr_long_range_B_other5.05915.9042171
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.881→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 53 -
Rwork0.254 1025 -
obs--66.91 %
Refinement TLS params.Method: refined / Origin x: 90.9363 Å / Origin y: -48.1394 Å / Origin z: -2.3818 Å
111213212223313233
T0.0648 Å2-0.0003 Å2-0.0224 Å2-0.0557 Å20.026 Å2--0.041 Å2
L0.3928 °20.0669 °2-0.1908 °2-2.0001 °2-0.8042 °2--0.4904 °2
S0.0954 Å °0.0499 Å °-0.0083 Å °-0.1048 Å °-0.1278 Å °-0.0839 Å °-0.0361 Å °0.0559 Å °0.0323 Å °

+
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