[English] 日本語
Yorodumi
- PDB-6wgm: Crystal structure of a marine metagenome TRAP solute binding prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wgm
TitleCrystal structure of a marine metagenome TRAP solute binding protein specific for pyroglutamate (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, scf7180008839099) in complex with co-purified pyroglutamate
ComponentsTRAP-type C4-dicarboxylate transport system, periplasmic component
KeywordsSUGAR BINDING PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


transmembrane transport
Similarity search - Function
Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / PYROGLUTAMIC ACID / TRAP-type C4-dicarboxylate transport system, periplasmic component
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsFedorov, E. / Vetting, M.W. / Hogle, S.L. / Dupont, C.L. / Almo, S.C. / Ghosh, A.
CitationJournal: To Be Published
Title: Crystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, GOS_140), in ...Title: Crystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, GOS_140), in complex with co-purified pyroglutamate
Authors: Vetting, M.W. / Fedorov, E. / Hogle, S.L. / Dupont, C.L. / Almo, S.C. / Ghosh, A.
History
DepositionApr 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRAP-type C4-dicarboxylate transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,37319
Polymers35,3761
Non-polymers99718
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Superdex S200
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.251, 56.251, 193.919
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein TRAP-type C4-dicarboxylate transport system, periplasmic component


Mass: 35375.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Pyroglutamate
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: HIMB100_00003270 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PRIL / References: UniProt: G5ZWD6

-
Non-polymers , 5 types, 314 molecules

#2: Chemical ChemComp-PCA / PYROGLUTAMIC ACID


Type: L-peptide linking / Mass: 129.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.1 % / Description: Hexagonal
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.1M Malonic Acid, 0.15 M Ammonium Citrate tribasic, 0.072 M Succinic Acid, 0.18 M DL-Malic Acid, 0.24 M Sodium Acetate, 0.3 M Sodium Formate, 0.096 M Ammonium Tartrate Dibasic

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 8, 2017 / Details: KB MIRRORS
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→38.9 Å / Num. obs: 68041 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 14.5 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.034 / Rrim(I) all: 0.115 / Net I/av σ(I): 12.8 / Net I/σ(I): 12.7
Reflection shell

CC star: 0.94 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.4-1.4211.21.78912.833430.7850.5620.1699.9
7.67-38.99.40.0521.64160.9950.0180.05595.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.4 Å38.9 Å
Translation5.4 Å38.9 Å

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASER2.7.17phasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
DENZO720data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PFZ

2pfz


Resolution: 1.4→24.36 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.67 / Details: Individual B-Factors, TLS, Occupancies
RfactorNum. reflection% reflection
Rfree0.1679 3476 5.12 %
Rwork0.1507 --
obs0.1516 67843 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.29 Å2 / Biso mean: 22.0333 Å2 / Biso min: 10.79 Å2
Refinement stepCycle: final / Resolution: 1.4→24.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 64 298 2701
Biso mean--37.13 31.88 -
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052505
X-RAY DIFFRACTIONf_angle_d0.7543385
X-RAY DIFFRACTIONf_dihedral_angle_d6.477357
X-RAY DIFFRACTIONf_chiral_restr0.073360
X-RAY DIFFRACTIONf_plane_restr0.006436
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.420.35651400.29452555100
1.42-1.440.28961190.2766261299
1.44-1.460.29821220.2482549100
1.46-1.480.23851150.2352610100
1.48-1.510.25971280.22332565100
1.51-1.530.20741500.20452561100
1.53-1.560.23941540.19662612100
1.56-1.590.18651310.17792518100
1.59-1.620.21441240.16972577100
1.62-1.660.18981250.16432627100
1.66-1.70.16611310.15712589100
1.7-1.740.18941760.16442497100
1.74-1.790.17811220.15192592100
1.79-1.840.16721450.15212579100
1.84-1.90.15651550.1452562100
1.9-1.970.15511370.14772583100
1.97-2.050.1651330.14262577100
2.05-2.140.17611610.14252548100
2.14-2.250.15651710.13662579100
2.25-2.390.15221710.14532517100
2.39-2.580.14621470.14132599100
2.58-2.840.16211360.14962577100
2.84-3.250.17831370.14712586100
3.25-4.090.13941270.12692608100
4.09-24.360.14441190.1253258899
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)
10.93130.03840.40611.35860.31081.7285-0.0322-0.1051-0.04930.17610.04230.04570.1886-0.1758-0.01510.1472-0.00140.0070.11820.01180.126921.932-14.02413.249
21.0515-0.1674-0.21481.69440.06751.1393-0.08570.02390.0199-0.05940.1123-0.0346-0.0670.0858-0.02630.1654-0.0353-0.00330.14740.00980.159832.113-1.672-2.232
30.6580.10420.35390.72860.10441.2024-0.04860.1271-0.0328-0.07970.1035-0.04170.05570.0784-0.04780.1269-0.01560.00610.13370.00430.123627.876-12.115-7.026
40.51890.03830.29090.68270.30881.3065-0.0260.0828-0.0688-0.06250.05950.02070.11190.0716-0.03230.1506-0.01420.00070.1157-0.00210.144625.411-16.159-4.986
50.17280.19920.35151.00690.25451.0535-0.09290.1067-0.0682-0.0510.175-0.19760.13160.4311-0.06670.18560.01480.00420.2414-0.03310.202136.678-15.744-1.855
60.1787-0.0001-0.13991.6517-0.63430.6254-0.08690.09610.0736-0.17110.075-0.044-0.08970.0960.00780.1891-0.073-0.01610.18530.02310.178631.8354.083-8.162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 20:91 )A20 - 91
2X-RAY DIFFRACTION2( CHAIN A AND RESID 92:124 )A92 - 124
3X-RAY DIFFRACTION3( CHAIN A AND RESID 125:162 )A125 - 162
4X-RAY DIFFRACTION4( CHAIN A AND RESID 163:244 )A163 - 244
5X-RAY DIFFRACTION5( CHAIN A AND RESID 245:299 )A245 - 299
6X-RAY DIFFRACTION6( CHAIN A AND ( RESID 300:323 OR RESID 401:401 ) )A300 - 323
7X-RAY DIFFRACTION6( CHAIN A AND ( RESID 300:323 OR RESID 401:401 ) )A401

+
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