[English] 日本語
Yorodumi
- PDB-4mdy: Crystal structure of periplasmic solute binding protein from Myco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mdy
TitleCrystal structure of periplasmic solute binding protein from Mycobacterium smegmatis str. MC2 155
ComponentsPeriplasmic binding protein
KeywordsTRANSPORT PROTEIN / MCSG / STRUCTURAL GENOMICS / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / Protein Structure Initiative / ABC transporter system / solute binding protein
Function / homology
Function and homology information


: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Periplasmic binding protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsChang, C. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of periplasmic solute binding protein from Mycobacterium smegmatis str. MC2 155
Authors: Chang, C. / Wu, R. / Endres, M. / Joachimiak, A.
History
DepositionAug 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5992
Polymers31,4931
Non-polymers1061
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.606, 90.449, 33.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Periplasmic binding protein / Periplasmic iron-transport lipoprotein


Mass: 31493.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_0438, MSMEI_0427 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: A0QPL3
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M Sodium Citrate, 0.1 M Phosphate-citrate, 20 % PEG 8000, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 25588 / Num. obs: 24908 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 23.1
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 1.92 / Num. unique all: 1170 / % possible all: 97.3

-
Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-CollectCOLLECTdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.78→31.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.729 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.128
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 1113 5 %RANDOM
Rwork0.1463 ---
all0.149 22242 --
obs0.149 22242 87.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.07 Å2 / Biso mean: 25.3141 Å2 / Biso min: 11.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2---1.75 Å2-0 Å2
3---2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.78→31.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 7 199 2351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022249
X-RAY DIFFRACTIONr_bond_other_d0.0010.022157
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.9713082
X-RAY DIFFRACTIONr_angle_other_deg0.72134963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2225292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03324.73795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77215335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5771514
X-RAY DIFFRACTIONr_chiral_restr0.0560.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212586
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
X-RAY DIFFRACTIONr_rigid_bond_restr1.80734405
X-RAY DIFFRACTIONr_sphericity_free29.141569
X-RAY DIFFRACTIONr_sphericity_bonded8.52254486
LS refinement shellResolution: 1.779→1.825 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 59 -
Rwork0.162 946 -
all-1005 -
obs-1005 54.98 %

+
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