[English] 日本語
Yorodumi
- PDB-4pbh: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pbh
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM RUEGERIA POMEROYI DSS-3 (SPO1773, TARGET EFI-510260) WITH BOUND BENZOIC ACID
ComponentsTRAP dicarboxylate transporter, DctP subunit, putative
KeywordsSOLUTE-BINDING PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


C4-dicarboxylate transport / transmembrane transport / outer membrane-bounded periplasmic space / carbohydrate binding
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
BENZOIC ACID / Solute-binding protein SPO1773
Similarity search - Component
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093342 United States
CitationJournal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
History
DepositionApr 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Aug 26, 2015Group: Data collection
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRAP dicarboxylate transporter, DctP subunit, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6062
Polymers36,4841
Non-polymers1221
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.591, 62.929, 75.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit, putative


Mass: 36484.359 Da / Num. of mol.: 1 / Mutation: P37S, Y220C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi (bacteria) / Strain: DSS-3 / Gene: SPO1773 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LSJ5
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (67.94 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM BENZOIC ACID); Reservoir (0.1 M Bis-Tris Propane pH 7, 60 %(v/v) tacsimate); Cryoprotection (80% Reservoir + 20% glycerol)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 4, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.2→48.402 Å / Num. obs: 87202 / % possible obs: 92.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 6.78 Å2 / Rsym value: 0.087 / Net I/σ(I): 5.4 / Num. measured all: 953302

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.2→37.87 Å / FOM work R set: 0.9318 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1549 8406 5.04 %Random Selection
Rwork0.1415 158393 --
obs0.1422 166799 92.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.14 Å2 / Biso mean: 11.31 Å2 / Biso min: 3.05 Å2
Refinement stepCycle: final / Resolution: 1.2→37.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 14 470 2809
Biso mean--6.19 24.3 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122459
X-RAY DIFFRACTIONf_angle_d1.4323350
X-RAY DIFFRACTIONf_chiral_restr0.085375
X-RAY DIFFRACTIONf_plane_restr0.008443
X-RAY DIFFRACTIONf_dihedral_angle_d14.306896
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.21360.19581970.20063267346458
1.2136-1.22790.20881660.19723656382263
1.2279-1.24290.21932040.18263812401667
1.2429-1.25860.16682160.18484153436973
1.2586-1.27520.19522300.17614472470278
1.2752-1.29270.18762630.16544750501384
1.2927-1.31110.15482870.17095195548290
1.3111-1.33070.16163070.1555635594298
1.3307-1.35150.16122930.152256545947100
1.3515-1.37370.1653020.149957256027100
1.3737-1.39730.16993020.145357276029100
1.3973-1.42280.16232930.141957666059100
1.4228-1.45010.14632780.137657396017100
1.4501-1.47970.15462840.140457206004100
1.4797-1.51190.14822890.134757556044100
1.5119-1.54710.13822950.129357196014100
1.5471-1.58580.14352820.125157306012100
1.5858-1.62860.15462630.130257666029100
1.6286-1.67660.1473040.124357366040100
1.6766-1.73070.15483410.129556796020100
1.7307-1.79250.1433100.127257646074100
1.7925-1.86430.14713020.129456665968100
1.8643-1.94910.1433080.130257456053100
1.9491-2.05190.14693570.127456626019100
2.0519-2.18040.13492900.12757306020100
2.1804-2.34880.12953260.126656946020100
2.3488-2.58510.15833180.130257116029100
2.5851-2.9590.14592570.14115361561893
2.959-3.72760.16132950.14245156545190
3.7276-37.88890.17452470.1754248449575
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)
11.2165-0.4154-0.13762.44350.30750.8806-0.01380.0812-0.0776-0.0898-0.0039-0.04190.1508-0.00980.01030.05490.00290.00570.0438-0.00920.02858.985832.5968-1.3933
20.25890.23280.01380.4785-0.0890.4402-0.01540.004-0.0256-0.03650.012-0.01990.0306-0.0252-0.00070.03830.00440.00910.0403-0.00170.04025.559238.0279.578
32.31291.7575-0.761.5123-0.74050.40050.0353-0.1034-0.08920.0286-0.0686-0.08110.01010.05740.03010.05090.0053-0.00080.06150.00360.05216.964637.890617.0874
40.57230.1322-0.20671.845-0.15460.52490.04780.01250.10670.0023-0.0349-0.0237-0.10.0051-0.00970.04030.0002-0.00210.0475-0.00490.02759.50155.52238.9124
50.51730.32010.20480.51770.61452.1961-0.02460.03750.0283-0.02330.00650.0783-0.0537-0.07140.00580.04160.00560.00240.0507-0.0120.06962.457157.30688.5245
60.45270.3449-0.18821.0039-0.23310.4382-0.01570.0245-0.0123-0.0584-0.0087-0.05980.0216-0.00250.02650.03050.00550.0040.0509-0.00080.034412.924744.76993.68
70.15810.1098-0.34340.245-0.71222.42750.0187-0.01120.02540.0164-0.0704-0.0693-0.17120.17960.04910.0921-0.00340.0080.0748-0.00110.061716.183161.400112.3599
81.1347-0.1605-0.52290.35880.04831.53010.0752-0.31110.02350.0723-0.0293-0.0694-0.14870.3397-0.04270.105-0.0278-0.01790.10880.00850.083423.676646.736720.5545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 55 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 113 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 137 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 174 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 202 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 203 through 284 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 285 through 309 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 310 through 334 )A0

+
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