[English] 日本語
Yorodumi
- PDB-6mla: Crystal structure of the periplasmic Lysine-, Arginine-, Ornithin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mla
TitleCrystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D161A mutant from Salmonella typhimurium complexed with arginine
ComponentsLysine/arginine/ornithine-binding periplasmic protein
KeywordsPROTEIN BINDING / Periplasmic Binding Protein / LAO / Thermodynamics / Protein Ligand Complex
Function / homology
Function and homology information


amino acid binding / amino acid transport / outer membrane-bounded periplasmic space
Similarity search - Function
Specific amino acids and opine-binding periplasmic protein, ABC transporter / 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
ACETATE ION / ARGININE / PHOSPHATE ION / Lysine/arginine/ornithine-binding periplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.582 Å
AuthorsRomero-Romero, S. / Vergara, R. / Espinoza-Perez, G. / Rodriguez-Romero, A.
Funding support Mexico, 4items
OrganizationGrant numberCountry
Other governmentIN208418 Mexico
Other government221169 Mexico
Other government254514 Mexico
Other governmentIN220516 Mexico
CitationJournal: Febs J. / Year: 2020
Title: The interplay of protein-ligand and water-mediated interactions shape affinity and selectivity in the LAO binding protein.
Authors: Vergara, R. / Romero-Romero, S. / Velazquez-Lopez, I. / Espinoza-Perez, G. / Rodriguez-Hernandez, A. / Pulido, N.O. / Sosa-Peinado, A. / Rodriguez-Romero, A. / Fernandez-Velasco, D.A.
History
DepositionSep 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Lysine/arginine/ornithine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4365
Polymers26,0141
Non-polymers4214
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-8 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.330, 57.790, 101.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules E

#1: Protein Lysine/arginine/ornithine-binding periplasmic protein / LAO-binding protein


Mass: 26014.305 Da / Num. of mol.: 1 / Mutation: D161A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: argT, STM2355 / Plasmid: pET12b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: P02911

-
Non-polymers , 5 types, 303 molecules

#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Acetato de sodio trihidratado. 0.05 M Cacodilato de sodio trihidratado, pH: 6.5. 15% w/v Polietilenglicol 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 10, 2018 / Details: Osmic VariMax Cu-HF
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 60426 / % possible obs: 99.5 % / Redundancy: 10.4 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 46.5
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2962 / CC1/2: 0.648 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LAF

1laf


Resolution: 1.582→35.048 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 1998 6.56 %
Rwork0.1827 --
obs0.185 57404 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.582→35.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 27 299 2121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061855
X-RAY DIFFRACTIONf_angle_d0.9572506
X-RAY DIFFRACTIONf_dihedral_angle_d13.018667
X-RAY DIFFRACTIONf_chiral_restr0.036278
X-RAY DIFFRACTIONf_plane_restr0.005327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5817-1.60170.34051220.32351774X-RAY DIFFRACTION86
1.6017-1.62280.30271310.28411909X-RAY DIFFRACTION94
1.6228-1.6450.31981350.26151899X-RAY DIFFRACTION96
1.645-1.66850.33351380.24951952X-RAY DIFFRACTION97
1.6685-1.69340.2631390.2611995X-RAY DIFFRACTION98
1.6934-1.71980.31171370.24021955X-RAY DIFFRACTION98
1.7198-1.7480.23911390.24831988X-RAY DIFFRACTION99
1.748-1.77820.36751380.24212016X-RAY DIFFRACTION99
1.7782-1.81050.2931380.23841987X-RAY DIFFRACTION99
1.8105-1.84530.25871400.20421986X-RAY DIFFRACTION100
1.8453-1.8830.2321390.21142023X-RAY DIFFRACTION100
1.883-1.92390.22111390.20271985X-RAY DIFFRACTION100
1.9239-1.96870.25151460.20952052X-RAY DIFFRACTION100
1.9687-2.01790.25681320.21391976X-RAY DIFFRACTION100
2.0179-2.07250.25131430.20982030X-RAY DIFFRACTION100
2.0725-2.13350.26981350.2031999X-RAY DIFFRACTION100
2.1335-2.20230.25061470.19632027X-RAY DIFFRACTION100
2.2023-2.2810.23041380.19052004X-RAY DIFFRACTION100
2.281-2.37230.22941460.18522014X-RAY DIFFRACTION100
2.3723-2.48030.25191440.1862019X-RAY DIFFRACTION100
2.4803-2.6110.20821390.18971998X-RAY DIFFRACTION100
2.611-2.77450.23141360.1891998X-RAY DIFFRACTION100
2.7745-2.98860.22361400.17592014X-RAY DIFFRACTION100
2.9886-3.28920.19881450.15692024X-RAY DIFFRACTION100
3.2892-3.76460.16361430.13892015X-RAY DIFFRACTION100
3.7646-4.74120.13131490.12171998X-RAY DIFFRACTION100
4.7412-35.05610.16121450.14232004X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.6439 Å / Origin y: -0.3726 Å / Origin z: -12.9983 Å
111213212223313233
T0.0779 Å2-0.0053 Å20.0031 Å2-0.1297 Å20.0025 Å2--0.0832 Å2
L1.7556 °20.1861 °20.4116 °2-1.8814 °2-0.4112 °2--1.3992 °2
S-0.0238 Å °0.1225 Å °0.1062 Å °-0.0202 Å °0.0141 Å °0.0741 Å °-0.0622 Å °0.0592 Å °0.0062 Å °
Refinement TLS groupSelection details: all

+
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