[English] 日本語
Yorodumi
- PDB-3lwc: Crystal structure of Structural Genomics, unknown function (YP_76... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lwc
TitleCrystal structure of Structural Genomics, unknown function (YP_766765.1) from Rhizobium leguminosarum BV. viciae 3841 at 1.40 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Cupin domain / ethanolamine utilization
Function / homologyAcetate kinase EutQ / Ethanolamine utilisation protein EutQ / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Ethanolamine utilization protein
Function and homology information
Biological speciesRhizobium leguminosarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Structural Genomics, unknown function (YP_766765.1) from Rhizobium leguminosarum BV. viciae 3841 at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3084
Polymers13,0541
Non-polymers2543
Water1,06359
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6168
Polymers26,1082
Non-polymers5086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area3770 Å2
ΔGint-65 kcal/mol
Surface area9450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.663, 90.663, 45.129
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Uncharacterized protein


Mass: 13053.868 Da / Num. of mol.: 1 / Fragment: sequence database residues 14-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium leguminosarum (bacteria) / Strain: bv. viciae str. 3841 / Gene: RL1159 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1MK54
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 14-131 OF THE FULL LENGTH PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.0000M ammonium sulfate, 0.1M sodium acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97944,0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979441
30.979321
ReflectionResolution: 1.4→29.676 Å / Num. obs: 21970 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.91 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.37
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.4-1.450.0112.4427453934195.9
1.45-1.510.0113.64699842391100
1.51-1.580.0114.84592041091100
1.58-1.660.0116.54463839491100
1.66-1.760.0119.1444573902199.9
1.76-1.90.01113.64863042501100
1.9-2.090.01120.84647240561100
2.09-2.390.01127.24693640881100
2.39-3.010.01132.5470814107199.9
3.01-29.6760.01142.4463834130199.7

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→29.676 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.876 / SU ML: 0.034 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.06
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.SULFATE IONS AND ETHYLENE GLYCOL FROM CRYSTALLIZATION/ CRYOPROTECTANT ARE MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1126 5.1 %RANDOM
Rwork0.181 ---
obs0.181 21944 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.83 Å2 / Biso mean: 14.381 Å2 / Biso min: 5.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.12 Å20 Å2
2---0.25 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 0 14 59 828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021989
X-RAY DIFFRACTIONr_bond_other_d0.0010.02644
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.9921361
X-RAY DIFFRACTIONr_angle_other_deg0.88231582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0895141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.98223.71435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8615156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.753157
X-RAY DIFFRACTIONr_chiral_restr0.10.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211173
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02190
X-RAY DIFFRACTIONr_mcbond_it1.1041.5659
X-RAY DIFFRACTIONr_mcbond_other0.2891.5268
X-RAY DIFFRACTIONr_mcangle_it2.02621073
X-RAY DIFFRACTIONr_scbond_it3.0563330
X-RAY DIFFRACTIONr_scangle_it4.8284.5288
LS refinement shellResolution: 1.402→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 89 -
Rwork0.23 1495 -
all-1584 -
obs--99 %
Refinement TLS params.Method: refined / Origin x: 19.7004 Å / Origin y: 52.9889 Å / Origin z: 16.5822 Å
111213212223313233
T0.0366 Å2-0.0044 Å20.0074 Å2-0.0222 Å2-0.0161 Å2--0.032 Å2
L0.825 °2-0.4665 °2-0.015 °2-0.6112 °2-0.1995 °2--0.5996 °2
S0.0244 Å °-0.0642 Å °0.0456 Å °-0.0107 Å °-0.0216 Å °-0.0388 Å °-0.0521 Å °0.0322 Å °-0.0028 Å °

+
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