[English] 日本語
Yorodumi
- PDB-3o6p: Crystal structure of peptide ABC transporter, peptide-binding protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o6p
TitleCrystal structure of peptide ABC transporter, peptide-binding protein
ComponentsPeptide ABC transporter, peptide-binding protein
KeywordsPROTEIN BINDING / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ABC transporter
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport
Similarity search - Function
Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Roll / Alpha Beta
Similarity search - Domain/homology
Peptide ABC transporter, peptide-binding protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsChang, C. / Bigelow, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of peptide ABC transporter, peptide-binding protein
Authors: Chang, C. / Bigelow, L. / Bearden, J. / Joachimiak, A.
History
DepositionJul 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptide ABC transporter, peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4312
Polymers25,4081
Non-polymers231
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.733, 53.653, 79.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Peptide ABC transporter, peptide-binding protein


Mass: 25408.211 Da / Num. of mol.: 1 / Fragment: residues 306-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_0907 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q837D6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M Zinc acetate, 0.1M imidazole, 35% 2-propanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 26921 / Num. obs: 26442 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 40.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 3.88 / Num. unique all: 1134 / % possible all: 85.6

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
RESOLVEphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.65→44.47 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.889 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.101
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 1333 5.1 %RANDOM
Rwork0.1491 ---
all0.1516 ---
obs0.1516 26442 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 105.67 Å2 / Biso mean: 22.3347 Å2 / Biso min: 8.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--1.51 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 1 305 2056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222018
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9612752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4265274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00425.30698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32915362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2051513
X-RAY DIFFRACTIONr_chiral_restr0.0990.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211617
X-RAY DIFFRACTIONr_mcbond_it1.3291.51281
X-RAY DIFFRACTIONr_mcangle_it2.2822080
X-RAY DIFFRACTIONr_scbond_it3.3253737
X-RAY DIFFRACTIONr_scangle_it5.1494.5672
X-RAY DIFFRACTIONr_rigid_bond_restr1.50632018
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 79 -
Rwork0.174 1606 -
all-1685 -
obs-1685 86.45 %
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)
10.0225-0.0101-0.0040.04140.00710.066-0.00190.0008-0.00040.00170.00230.00050.00150.0011-0.00050.040.0002-0.00090.0102-0.00010.030743.05918.215712.3793
20.11750.42020.2862.40780.25821.3526-0.0128-0.02620.03390.0431-0.00070.2064-0.0825-0.14710.01350.03690.00930.00670.02220.00160.040227.507426.163413.2511
30.02870.0190.00980.09230.04540.0490.0008-0.0007-0.00150.00160.0009-0.00660.00120.0029-0.00170.0397-0.0001-0.00020.00980.00050.030750.352415.720611.9304
40.8715-0.124-0.05540.3947-0.27020.20880.0026-0.00070.08190.0410.0078-0.0038-0.0275-0.0051-0.01040.0434-0.0004-0.00060.0052-0.00230.032135.256232.87013.5447
50.04650.0608-0.12460.1146-0.03880.79750.0085-0.0038-0.00180.0065-0.0080.0013-0.03090.0086-0.00050.03890.0017-0.00010.00830.00070.031739.765422.873816.2313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A301 - 347
2X-RAY DIFFRACTION2A348 - 374
3X-RAY DIFFRACTION3A375 - 456
4X-RAY DIFFRACTION4A457 - 516
5X-RAY DIFFRACTION5A517 - 526

+
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