[English] 日本語
Yorodumi
- PDB-2qjv: Crystal structure of an iolb-like protein (stm4420) from salmonel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qjv
TitleCrystal structure of an iolb-like protein (stm4420) from salmonella typhimurium lt2 at 1.90 A resolution
ComponentsUncharacterized IolB-like protein
KeywordsISOMERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


glucuronate isomerase activity / inositol catabolic process
Similarity search - Function
5-deoxy-glucuronate isomerase, IolB / KduI/IolB isomerase / KduI/IolB family / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Putative inner membrane protein
Similarity search - Component
Biological speciesSalmonella typhimurium LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized IolB-like protein (16422983) from Salmonella typhimurium LT2 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Jan 25, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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. RESIDUES GLU 161 AND ASP 163 WERE MUTATED TO ALA IN THE EXPRESSED CONSTRUCT. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized IolB-like protein
B: Uncharacterized IolB-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,80319
Polymers61,7522
Non-polymers1,05117
Water12,989721
1
A: Uncharacterized IolB-like protein
B: Uncharacterized IolB-like protein
hetero molecules

A: Uncharacterized IolB-like protein
B: Uncharacterized IolB-like protein
hetero molecules

A: Uncharacterized IolB-like protein
B: Uncharacterized IolB-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,41057
Polymers185,2566
Non-polymers3,15451
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)200.140, 200.140, 200.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

21B-395-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ALA / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 2 - 264 / Label seq-ID: 3 - 265

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized IolB-like protein


Mass: 30876.041 Da / Num. of mol.: 2 / Mutation: E161A, D163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria)
Species: Salmonella typhimuriumSalmonella enterica subsp. enterica
Strain: LT2, SGSC1412 / Gene: 16422983, STM4420 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8ZK62

-
Non-polymers , 5 types, 738 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 721 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 0.01M Nickel (II) chloride, 1.0M Lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97913, 0.97883
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979131
30.978831
ReflectionResolution: 1.9→29.514 Å / Num. obs: 104039 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.76 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.27
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
1.9-1.970.6141.758613199
1.97-2.050.4752.2583481100
2.05-2.140.3742.855978199.9
2.14-2.250.3133.4569211100
2.25-2.390.2544.2580461100
2.39-2.580.2085.1605651100
2.58-2.840.1527587221100
2.84-3.250.08911.6590021100
3.25-4.080.04919.4583301100
4.08-29.5140.03625.159512199.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.514 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.495 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079
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. FOUR NI IONS, SEVEN CHLORIDE IONS, FOUR SULFATE IONS AND TWO GLYCEROL MOLECULES WERE MODELED. THE PRESENCE OF THE NI ATOMS ARE SUPPORTED BY X-RAY FLUORESCENCE MEASUREMENTS, ANOMALOUS DIFFERENCE FOURIERS AND GEOMETRY. 5. RESIDUES 1 AND 265 TO 269 IN EACH SUBUNIT ARE DISORDERED AND NOT MODELED IN THE STRUCTURE. 6. THE DISUFIDE BOND BETWEEN CYS 212 FROM EACH SUBUNIT IS PARTIALLY REDUCED.
RfactorNum. reflection% reflectionSelection details
Rfree0.181 5190 5 %RANDOM
Rwork0.16 ---
obs0.161 103941 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.283 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 43 721 4959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214464
X-RAY DIFFRACTIONr_bond_other_d0.0030.022950
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.9486108
X-RAY DIFFRACTIONr_angle_other_deg1.1443.0017149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4015552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.36123.426216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05815.101691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.1461533
X-RAY DIFFRACTIONr_chiral_restr0.0730.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025063
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02946
X-RAY DIFFRACTIONr_nbd_refined0.1830.3618
X-RAY DIFFRACTIONr_nbd_other0.2010.33032
X-RAY DIFFRACTIONr_nbtor_refined0.1720.51904
X-RAY DIFFRACTIONr_nbtor_other0.0860.52260
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.5820
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.546
X-RAY DIFFRACTIONr_mcbond_it1.93332843
X-RAY DIFFRACTIONr_mcbond_other0.53731086
X-RAY DIFFRACTIONr_mcangle_it2.71454391
X-RAY DIFFRACTIONr_scbond_it4.96881961
X-RAY DIFFRACTIONr_scangle_it6.436111717
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1526MEDIUM POSITIONAL0.110.5
1899LOOSE POSITIONAL0.455
1526MEDIUM THERMAL0.672
1899LOOSE THERMAL1.4110
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 383 -
Rwork0.267 7260 -
obs-7643 99.99 %
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)
11.4632-0.34310.22012.6027-0.16851.3277-0.10880.05740.1328-0.02020.0234-0.0228-0.1360.04140.0853-0.2-0.0206-0.0258-0.26950.0088-0.210558.0982.42550.787
22.072-0.55130.96361.1055-0.05661.2433-0.03340.203-0.0453-0.14730.0116-0.0584-0.05720.20480.0218-0.2125-0.02430.0077-0.220.0094-0.234559.62567.55439.627
31.61480.1928-0.53571.3743-0.21012.6992-0.08690.14430.013-0.16980.06150.0317-0.0048-0.04470.0254-0.1944-0.0194-0.0124-0.21710.0036-0.266541.8094514.901
42.27210.8827-0.49031.12120.05561.0951-0.0387-0.01190.2144-0.07380.02090.1833-0.143-0.05090.0178-0.21240.008-0.0212-0.23090.012-0.232840.09757.46528.867
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1583 - 159
2X-RAY DIFFRACTION2AA159 - 264160 - 265
3X-RAY DIFFRACTION3BB2 - 1583 - 159
4X-RAY DIFFRACTION4BB159 - 264160 - 265

+
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