[English] 日本語
Yorodumi
- PDB-4nlm: 1.18 Angstrom resolution crystal structure of uncharacterized pro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nlm
Title1.18 Angstrom resolution crystal structure of uncharacterized protein lmo1340 from Listeria monocytogenes EGD-e
ComponentsLmo1340 protein
KeywordsStructural genomics / Unknown function / Surface proteins / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology: / YqgU-like 6-bladed beta propeller domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lmo1340 protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.18 Å
AuthorsHalavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.18 Angstrom resolution crystal structure of uncharacterized protein lmo1340 from Listeria monocytogenes EGD-e
Authors: Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lmo1340 protein


Theoretical massNumber of molelcules
Total (without water)42,2231
Polymers42,2231
Non-polymers00
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.224, 69.990, 52.905
Angle α, β, γ (deg.)90.00, 95.61, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Lmo1340 protein


Mass: 42223.316 Da / Num. of mol.: 1 / Fragment: UNP residues 25-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo1340 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q8Y7E3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: protein - 7.5 mg/mL in 10 mM Tris-HCl, pH 8.3, 0.5 M NaCl 5 mM BME, Crystallization - The PACT Suite (#D2: 0.1 M MMT buffer pH 5, 25 % (w/v) PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2012 / Details: Be lenses
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.18→30 Å / Num. all: 112400 / Num. obs: 112400 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 31.7
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.33 / Num. unique all: 5714 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
MLPHAREphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.18→24.21 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.535 / SU ML: 0.031 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18116 5628 5 %RANDOM
Rwork0.14503 ---
obs0.14678 106618 95.86 %-
all-106618 --
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 19.499 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å2-0.02 Å2
2--2.4 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 1.18→24.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 0 499 3169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023003
X-RAY DIFFRACTIONr_bond_other_d0.0010.022828
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9664107
X-RAY DIFFRACTIONr_angle_other_deg0.71836561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8865381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28525.625144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.11715531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.941159
X-RAY DIFFRACTIONr_chiral_restr0.0960.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023516
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02695
X-RAY DIFFRACTIONr_rigid_bond_restr12.87235831
X-RAY DIFFRACTIONr_sphericity_free37.1787104
X-RAY DIFFRACTIONr_sphericity_bonded15.3676156
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 427 -
Rwork0.227 8018 -
obs-8018 97.94 %

+
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