[English] 日本語
Yorodumi
- PDB-2heu: Atomic resolution structure of apo-form of RafE from Streptococcu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2heu
TitleAtomic resolution structure of apo-form of RafE from Streptococcus pneumoniae
ComponentsSugar ABC transporter, sugar-binding protein
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein
Function / homology
Function and homology information


transmembrane transport / plasma membrane
Similarity search - Function
: / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sugar ABC transporter, sugar-binding protein / Sugar ABC transporter, sugar-binding protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsPaterson, N.G. / Riboldi-Tunnicliffe, A. / Mitchell, T.J. / Isaacs, N.W.
CitationJournal: To be Published
Title: High resolution crystal structures of RafE from Streptococcus pneumoniae.
Authors: Paterson, N.G. / Riboldi-Tunnicliffe, A. / Mitchell, T.J. / Isaacs, N.W.
History
DepositionJun 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sugar ABC transporter, sugar-binding protein
B: Sugar ABC transporter, sugar-binding protein
C: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,6859
Polymers135,4113
Non-polymers2746
Water45,7762541
1
A: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1953
Polymers45,1371
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2083
Polymers45,1371
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2823
Polymers45,1371
Non-polymers1452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.219, 129.315, 119.420
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-3427-

HOH

21B-3815-

HOH

DetailsBiological subunit is monomeric

-
Components

#1: Protein Sugar ABC transporter, sugar-binding protein


Mass: 45136.852 Da / Num. of mol.: 3 / Fragment: Residues 33-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR 4 / Gene: rafE / Plasmid: pTBL2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q97NW2, UniProt: A0A0H2URJ7*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2541 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 0.1M Tris.HCl, 0.05M CaCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9393 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.04→19.82 Å / Num. all: 543433 / Num. obs: 543433 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.12 % / Biso Wilson estimate: 8.8 Å2 / Rmerge(I) obs: 0.062 / Χ2: 0.97 / Net I/σ(I): 9.8 / Scaling rejects: 16905
Reflection shellResolution: 1.04→1.08 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / Num. measured all: 162181 / Num. unique all: 52441 / Χ2: 1.05 / % possible all: 94.2

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å19.82 Å
Translation3 Å19.82 Å

-
Processing

Software
NameVersionClassificationNB
d*TREK9.5Ldata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ProDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.04→19.82 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.157 27325 5 %Extended from low resolution model
Rwork0.13 ---
all0.131 543423 --
obs0.131 516098 97.58 %-
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: 11.116 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.39 Å2
2--0.08 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.04→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10310 0 13 2552 12875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.02210647
X-RAY DIFFRACTIONr_bond_other_d00.027259
X-RAY DIFFRACTIONr_angle_refined_deg2.3231.95514555
X-RAY DIFFRACTIONr_angle_other_deg4.247317965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02451406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97126.081495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.037151955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.091526
X-RAY DIFFRACTIONr_chiral_restr0.140.21528
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212335
X-RAY DIFFRACTIONr_gen_planes_other0.0150.022059
X-RAY DIFFRACTIONr_nbd_refined0.2670.22683
X-RAY DIFFRACTIONr_nbd_other0.2490.27621
X-RAY DIFFRACTIONr_nbtor_refined0.1910.25519
X-RAY DIFFRACTIONr_nbtor_other0.1140.25085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.21772
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.257
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.2136
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.2220
X-RAY DIFFRACTIONr_mcbond_it2.2631.56526
X-RAY DIFFRACTIONr_mcbond_other4.0411.52617
X-RAY DIFFRACTIONr_mcangle_it3.057210680
X-RAY DIFFRACTIONr_scbond_it4.23934121
X-RAY DIFFRACTIONr_scangle_it5.7324.53857
X-RAY DIFFRACTIONr_rigid_bond_restr3.097317906
X-RAY DIFFRACTIONr_sphericity_free15.10332557
X-RAY DIFFRACTIONr_sphericity_bonded5.939317577
LS refinement shellResolution: 1.04→1.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 1889 -
Rwork0.226 36805 -
obs-38694 94.17 %

+
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