[English] 日本語
Yorodumi
- PDB-5izz: Crystal structure of a marine metagenome TRAP solute binding prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5izz
TitleCrystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, locus tag GOS_1523157, Triple Surface Mutant K158A_K223A_K313A) in complex with metahydroxyphenylacetate, thermal exchange of ligand
ComponentsTRAP TRANSPORTER SOLUTE BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / ENZYME FUNCTION INITIATIVE / EFI
Function / homologyBacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / 3-HYDROXYPHENYLACETATE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Hogle, S.L. / Dupont, C.L. / Almo, S.C.
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, locus tag GOS_ ...Title: Crystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, locus tag GOS_1523157, Triple Surface Mutant K158A_K223A_K313A) in complex with metahydroxyphenylacetate, thermal exchange of ligand
Authors: Vetting, M.W. / Al Obaidi, N.F. / Hogle, S.L. / Dupont, C.L. / Almo, S.C.
History
DepositionMar 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 TRANSPORTER SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5097
Polymers36,8261
Non-polymers6836
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.784, 84.275, 45.910
Angle α, β, γ (deg.)90.000, 113.480, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein TRAP TRANSPORTER SOLUTE BINDING PROTEIN


Mass: 36826.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gene discovered by metagenome sequencing of ocean samples was synthesized by gibson synthesis. Surface mutants were prepared to potentially enhancing crystallization.
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-3HP / 3-HYDROXYPHENYLACETATE


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 1.92 Å3/Da / Density % sol: 35.83 % / Mosaicity: 1.162 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM 3-Hydroxyphenylacetic acid, soak 30 minutes at 60 C); Reservoir (MCSG1 (A2), 0.1 M CHES pH 9.5, 30 %(w/v) PEG 3000); Cryoprotection (20% ...Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM 3-Hydroxyphenylacetic acid, soak 30 minutes at 60 C); Reservoir (MCSG1 (A2), 0.1 M CHES pH 9.5, 30 %(w/v) PEG 3000); Cryoprotection (20% diethylene glycol, 80% reservoir)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 15, 2016 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 34550 / % possible obs: 94 % / Redundancy: 4.1 % / Biso Wilson estimate: 8.81 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.027 / Rrim(I) all: 0.059 / Χ2: 1.167 / Net I/av σ(I): 22.091 / Net I/σ(I): 12.3 / Num. measured all: 143046
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.632.80.26514700.8660.180.3220.90280.3
1.63-1.662.90.25215160.8970.1690.3050.92982.2
1.66-1.692.90.23315320.9130.1560.2820.93383.7
1.69-1.722.90.21515520.9320.1440.260.89585.7
1.72-1.762.90.19916140.9390.1320.240.96787.3
1.76-1.830.16816150.9560.1110.2020.90789.3
1.8-1.8530.16116860.9640.1060.1930.96291.5
1.85-1.930.13917330.9710.0910.1670.94893.5
1.9-1.953.10.11617040.9820.0760.1390.91194.8
1.95-2.023.10.10218000.9840.0660.1220.94296.8
2.02-2.093.30.08718040.9880.0550.1031.09298.3
2.09-2.173.60.08317960.9880.050.0971.20498.2
2.17-2.273.80.07218140.9930.0410.0831.21699
2.27-2.394.30.06418270.9950.0350.0731.23199.1
2.39-2.544.80.05918170.9960.0290.0661.18899.3
2.54-2.745.50.05418410.9960.0250.061.18299.7
2.74-3.016.60.04718380.9980.020.0511.20399.8
3.01-3.456.80.03718440.9990.0150.041.07799.9
3.45-4.346.70.03218560.9990.0130.0351.3100
4.34-1006.20.03518910.9990.0150.0391.77499.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.10.1_2155)refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I7I

5i7i


Resolution: 1.6→29.786 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.35
RfactorNum. reflection% reflection
Rfree0.1531 1724 5.01 %
Rwork0.1147 --
obs0.1166 34431 94.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.48 Å2 / Biso mean: 13.2012 Å2 / Biso min: 3.48 Å2
Refinement stepCycle: final / Resolution: 1.6→29.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 103 465 2966
Biso mean--14.66 26.29 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082525
X-RAY DIFFRACTIONf_angle_d0.993415
X-RAY DIFFRACTIONf_chiral_restr0.056379
X-RAY DIFFRACTIONf_plane_restr0.008438
X-RAY DIFFRACTIONf_dihedral_angle_d15.3951524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.64710.19211230.15072355247881
1.6471-1.70030.16931320.13812425255784
1.7003-1.7610.17131460.1312484263087
1.761-1.83150.16391540.12252601275590
1.8315-1.91490.15271450.12042679282493
1.9149-2.01580.16691410.11212778291996
2.0158-2.14210.16561580.10532845300398
2.1421-2.30740.14011500.10292870302099
2.3074-2.53950.12921380.10262883302199
2.5395-2.90670.13691490.111329093058100
2.9067-3.66110.15341430.111529223065100
3.6611-29.7910.15181450.118129563101100
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)
12.0162-0.01510.49850.56590.01941.01670.03280.0746-0.1569-0.0957-0.0621-0.16360.04240.06380.03030.05110.00410.01710.050.00820.074915.7254-10.49293.1363
21.2949-0.9102-0.22932.12560.4620.8924-0.02480.0085-0.09320.04830.00610.06120.0485-0.10180.01790.0472-0.00920.00020.0523-0.00340.05322.5568-13.33788.3009
30.6367-0.31740.06260.8877-0.19850.5743-0.0023-0.010.00990.02170.00290.0382-0.0005-0.0435-0.0050.0424-0.00790.00010.0466-0.00430.0405-2.75264.613410.2574
41.6913-0.86470.18921.8694-0.26180.66750.0027-0.124-0.09040.0836-0.0654-0.22690.03540.09910.04680.06720.0017-0.01860.06890.02620.095117.513-13.12315.5444
52.5418-1.39752.57051.4909-1.60643.8177-0.01440.16660.18410.0065-0.1282-0.1705-0.06380.16180.13830.04390.00210.00710.05820.00910.060610.6637.94654.5754
60.4123-0.47380.07770.7704-0.16350.9599-0.1079-0.11460.0240.24040.07110.0065-0.0029-0.11360.02770.1292-0.01470.00890.0855-0.01920.0728-2.547210.240821.646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 65 )A25 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 95 )A66 - 95
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 237 )A96 - 237
4X-RAY DIFFRACTION4chain 'A' and (resid 238 through 264 )A238 - 264
5X-RAY DIFFRACTION5chain 'A' and (resid 265 through 288 )A265 - 288
6X-RAY DIFFRACTION6chain 'A' and (resid 289 through 342 )A289 - 342

+
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