[English] 日本語
Yorodumi
- PDB-7jfn: Crystal Structure of Leucine-, isoleucine-, valine-, threonine-, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jfn
TitleCrystal Structure of Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein from Brucella ovis, closed conformation
ComponentsPutative branched chain amino acid ABC transporter, periplasmic amino acid-binding protein
KeywordsTRANSPORT PROTEIN / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyLeu/Ile/Val-binding protein / : / Leucine-binding protein domain / Periplasmic binding protein / amino acid transport / Periplasmic binding protein-like I / : / NITRATE ION / Putative branched chain amino acid ABC transporter, periplasmic amino acid-binding protein
Function and homology information
Biological speciesBrucella ovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein from Brucella ovis, closed conformation
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 1.2Nov 13, 2024Group: Structure summary / Category: 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: Putative branched chain amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3976
Polymers43,1101
Non-polymers2875
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.770, 69.390, 120.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Putative branched chain amino acid ABC transporter, periplasmic amino acid-binding protein


Mass: 43109.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512) (bacteria)
Strain: ATCC 25840 / 63/290 / NCTC 10512 / Gene: BOV_A0021 / Plasmid: BrovA.17370.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3ATZ3
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: RigakuReagents JCSG+ screen, condition A12: 20% PEG 3350, 200mM Potassium nitrate: BrovA.17370.a.B2.PS02137 at 25mg/ml: over night soak with 10mM Thr (did not show in electron density): tray: ...Details: RigakuReagents JCSG+ screen, condition A12: 20% PEG 3350, 200mM Potassium nitrate: BrovA.17370.a.B2.PS02137 at 25mg/ml: over night soak with 10mM Thr (did not show in electron density): tray: 257609a12, cryo: 20%EG+soak, puck tds8-10

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 20, 2020 / Details: Beryllium 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: 1.7→50 Å / Num. obs: 43048 / % possible obs: 97.7 % / Redundancy: 5.665 % / Biso Wilson estimate: 33.786 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.042 / Χ2: 0.971 / Net I/σ(I): 22.92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.743.9390.432.5726530.8420.48782.3
1.74-1.794.4620.3583.5127790.9020.40288.9
1.79-1.845.2590.2835.1429720.9540.31498
1.84-1.96.0040.2267.3229710.9750.247100
1.9-1.966.0780.1749.728710.9850.19100
1.96-2.036.0750.13312.8627990.990.146100
2.03-2.116.0460.10216.7626540.9940.11299.9
2.11-2.196.0270.08519.8926100.9960.09399.9
2.19-2.296.020.07123.2924780.9960.07899.9
2.29-2.45.9540.0626.7523960.9970.06599.9
2.4-2.535.9240.05330.5622750.9980.05999.8
2.53-2.695.890.04633.5921390.9980.05199.9
2.69-2.875.8740.0437.2220380.9980.04499.9
2.87-3.15.810.03640.9519050.9990.0499.9
3.1-3.45.8090.03344.1517500.9990.03699.9
3.4-3.85.8010.02947.2215910.9990.03199.9
3.8-4.395.7860.02748.714280.9990.0399.8
4.39-5.385.8120.02349.8612140.9990.025100
5.38-7.65.7010.02148.989740.9990.023100
7.6-504.9850.0246.255510.9990.02296.3

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: open form structure, PDB entry 4xfk

4xfk


Resolution: 1.7→34.82 Å / SU ML: 0.1953 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.8366
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 1944 4.52 %0
Rwork0.1555 41102 --
obs0.1571 43046 97.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.77 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 17 288 3223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833065
X-RAY DIFFRACTIONf_angle_d0.90864169
X-RAY DIFFRACTIONf_chiral_restr0.0607464
X-RAY DIFFRACTIONf_plane_restr0.006554
X-RAY DIFFRACTIONf_dihedral_angle_d15.83461119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.32411150.2582441X-RAY DIFFRACTION82.05
1.74-1.790.26361200.22532623X-RAY DIFFRACTION88.8
1.79-1.840.24611520.19192863X-RAY DIFFRACTION97.7
1.84-1.90.19611440.16962971X-RAY DIFFRACTION100
1.9-1.970.18641470.16452940X-RAY DIFFRACTION100
1.97-2.050.23421380.1593004X-RAY DIFFRACTION99.97
2.05-2.140.20831420.15742962X-RAY DIFFRACTION99.9
2.14-2.250.19451330.15222987X-RAY DIFFRACTION99.84
2.25-2.40.18741530.1552985X-RAY DIFFRACTION99.97
2.4-2.580.22151170.15723023X-RAY DIFFRACTION99.78
2.58-2.840.23011380.15852995X-RAY DIFFRACTION99.9
2.84-3.250.1821750.15493011X-RAY DIFFRACTION99.91
3.25-4.10.17091380.1423075X-RAY DIFFRACTION99.84
4.1-34.820.17211320.14823222X-RAY DIFFRACTION99.5
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)
11.257439207780.333350332879-0.02838022553981.68443489154-0.4547047013192.098387861-0.0337459621483-0.03704532105490.07543551566040.142354224403-0.0684075580807-0.0168608236401-0.05180524985380.09378761080560.1008457713340.145460924878-0.0096991084721-0.006496486845360.1536605800370.006367573037270.15911189325721.141821975113.599010133312.6447103541
22.17359459107-1.152350862910.7808767689523.63675387081-0.5320588492152.76184814857-0.022054500598-0.0109414353439-0.2631099187930.110263850538-0.02403477097240.1714835142860.1943501482070.1868189907090.04822682982610.1894204971150.0004877667327350.02817372177110.1577222167410.007484781306210.17352727727718.3772096085-15.80138329215.5670091731
32.759846102010.3179071429470.5189723434142.774883744991.068814870413.966301558650.01611225318240.249294335873-0.0231517386908-0.3725121821620.00437879050180.305919858952-0.12267683227-0.0370507151718-0.04262917323080.144387677034-0.00763496967223-0.05564960372870.1586040400680.04184529068960.18414631486710.58976252279.990911578463.2231056025
42.2141593031-1.31158567678-0.2697786715175.040142335251.216517274482.399660619470.07257758498890.14886956796-0.16193416070.0117999008087-0.1705240795310.5208793733620.0975461622831-0.08150609471430.1211792631020.134842167942-0.0142344241775-0.00780751584720.221351654882-0.00464077373920.2477891428047.88122257104-2.695254322269.85857216226
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 81 through 209 )81 - 2091 - 129
22chain 'A' and (resid 210 through 345 )210 - 345130 - 265
33chain 'A' and (resid 346 through 403 )346 - 403266 - 323
44chain 'A' and (resid 404 through 470 )404 - 470324 - 390

+
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