[English] 日本語
Yorodumi
- PDB-4n15: Crystal structure of a TRAP periplasmic solute binding protein fr... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 4n15
TitleCrystal structure of a TRAP periplasmic solute binding protein from Burkholderia ambifaria (BAM_6123), Target EFI-510059, with bound beta-D-glucuronate
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP periplasmic solute binding family / Enzyme Function Initiative / EFI / structural genomics
Function / homologyTRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP/TeaA / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / carbohydrate transport / transmembrane transport / outer membrane-bounded periplasmic space / Solute-binding protein Bamb_6123
Function and homology information
Specimen sourceBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 1.651 Å resolution
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Zhao, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
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. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 3, 2013 / Release: Oct 16, 2013
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 16, 2013Structure modelrepositoryInitial release
1.1Feb 25, 2015Structure modelDatabase references
1.2Nov 15, 2017Structure modelRefinement descriptionsoftware_software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
1.3Apr 4, 2018Structure modelData collectiondiffrn_source_diffrn_source.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,1253
Polyers36,9061
Non-polymers2182
Water5,441302
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)96.190, 101.781, 55.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC 2 2 21

-
Components

#1: Protein/peptide TRAP dicarboxylate transporter, DctP subunit / TRAP periplasmic solute binding protein


Mass: 36906.195 Da / Num. of mol.: 1 / Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: ATCC BAA-244 / AMMD / Gene: Bamb_6123 / Plasmid name: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0B2F6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 1 / Formula: C6H10O7 / Glucuronic acid
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.84 / Density percent sol: 33.19 %
Crystal growTemp: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 59.1 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-glucuronic acid, reservoir: 0.2 M magnesium acetate, 20% w/v PEG3350 (MCSG1 C5), cryoprotection: 4:1 50% w/v PEG3350:reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Details: mirrors / Detector: IMAGE PLATE / Collection date: Sep 21, 2013
RadiationMonochromator: graphite / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 14.59 Å2 / D resolution high: 1.65 Å / D resolution low: 1 Å / Number all: 32282 / Number obs: 32282 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.064 / Rsym value: 0.064 / Chi squared: 0.924 / NetI over sigmaI: 14.5 / Redundancy: 4.6 % / Percent possible obs: 97.6
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber unique allChi squaredRedundancyPercent possible all
0.3651.6501.68014730.6843.190.0
0.3341.6801.71016060.7863.998.3
0.2931.7101.74016190.8014.4100.0
0.2621.7401.78016430.8714.499.9
0.2411.7801.82016280.8784.5100.0
0.2061.8201.86016401.0104.399.9
0.1861.8601.90016301.0274.499.9
0.1611.9001.96016291.0694.5100.0
0.1381.9602.01016341.0424.6100.0
0.1252.0102.08016291.0834.6100.0
0.1132.0802.15016421.0994.699.7
0.1062.1502.24016311.2184.799.0
0.0982.2402.34016291.2684.798.6
0.0902.3402.46016221.1924.897.9
0.0852.4602.62015961.1744.997.2
0.0772.6202.82016221.1094.997.0
0.0662.8203.11015980.9034.996.6
0.0513.1103.55016100.6084.995.8
0.0383.5504.48016000.3764.994.5
0.0284.480100.00016010.1914.989.4

-
Processing

Software
NameVersionClassificationContact authorContact author emailLocationTypeLanguageDate
DENZOdata reductionZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/package
SCALEPACKdata scalingZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/package
PHENIX1.8.1_1168refinementPaul D. AdamsPDAdams[at]lbl.govhttp://www.phenix-online.org/packageC++
PDB_EXTRACT3.11data extractionPDBdeposit[at]deposit.rcsb.orghttp://sw-tools.pdb.org/apps/PDB_EXTRACT/packageC++April 22, 2011
StructureStudiodata collection
HKL-3000data reduction
AMoREphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LN5
Occupancy max: 1 / Occupancy min: 1 / Overall FOM work R set: 0.8784 / Overall SU ML: 0.15 / R Free selection details: RANDOM / Sigma F: 0 / Sigma I: 0 / Overall phase error: 19.23 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 78.71 Å2 / B iso mean: 22.7023 Å2 / B iso min: 6.02 Å2
Least-squares processR factor R free: 0.1955 / R factor R work: 0.1583 / R factor all: 0.1603 / R factor obs: 0.1603 / Highest resolution: 1.651 Å / Lowest resolution: 22.067 Å / Number reflection R free: 1572 / Number reflection all: 31126 / Number reflection obs: 31126 / Percent reflection R free: 5.05 / Percent reflection obs: 94.03
Refine hist #LASTHighest resolution: 1.651 Å / Lowest resolution: 22.067 Å
Number of atoms included #LASTProtein: 2327 / Nucleic acid: 0 / Ligand: 14 / Solvent: 302 / Total: 2643
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112397
X-RAY DIFFRACTIONf_angle_d1.2733250
X-RAY DIFFRACTIONf_chiral_restr0.074358
X-RAY DIFFRACTIONf_plane_restr0.007422
X-RAY DIFFRACTIONf_dihedral_angle_d13.004895
Refine LS shell

Refine ID: X-RAY DIFFRACTION / Total number of bins used: 11

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
1.6510.28550.19891.70451002069216973.0
1.70450.28150.19241.76541252470259588.0
1.76540.21620.19021.83611432687283095.0
1.83610.20410.19061.91961682752292098.0
1.91960.21700.18042.020714528092954100.0
2.02070.22580.16672.147213528472982100.0
2.14720.19670.15522.31291592817297699.0
2.31290.21960.15402.54531482787293598.0
2.54530.23400.15832.91291352796293197.0
2.91290.14950.14903.66721662745291196.0
3.66720.15970.132422.06861482775292392.0
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
11.46920.25360.18060.7491-0.02350.9385-0.05940.09930.1937-0.04620.0140-0.0995-0.23200.18810.03520.0969-0.0251-0.01230.13460.03770.134335.426526.51191.4250
21.82120.0344-0.76440.9111-0.13821.3247-0.04080.2345-0.0702-0.02640.0332-0.07450.25320.1303-0.00810.10780.0129-0.00480.1306-0.01100.096234.802612.9043-0.4799
31.08190.2662-0.18631.11250.20170.41980.1667-0.1447-0.01480.1498-0.0948-0.01900.33510.0242-0.00870.2618-0.0009-0.03520.06950.00390.091629.99429.572017.8865
40.57230.1040-0.04010.54180.10920.59120.0355-0.0382-0.02750.2084-0.0422-0.00720.18070.05310.00470.12600.0076-0.00430.0837-0.00190.090433.442712.458311.7415
50.8018-0.0025-0.04040.6101-0.08570.61320.0152-0.0569-0.08410.5236-0.18830.45950.2914-0.17440.25560.1720-0.17610.22600.1053-0.03030.205813.91123.33737.7627
60.72410.24570.25340.7432-0.05300.6911-0.18170.26590.0105-0.08190.07480.19500.0909-0.33380.05930.0808-0.07050.00800.1929-0.03130.122613.926014.74612.0402
71.76240.0523-0.17490.66310.34940.6909-0.09490.23150.00530.1113-0.00470.05020.1525-0.03530.03150.0980-0.01330.00940.1217-0.00840.076726.957415.70987.0740
82.50960.0613-0.12030.48370.14270.7258-0.0137-0.02150.15970.0621-0.02150.0583-0.05300.02610.01590.07750.0028-0.01510.0841-0.01030.112030.123325.763912.5311
90.7907-0.55060.03561.33400.24430.1359-0.1862-0.1328-0.05930.7452-0.02450.26260.4647-0.1444-0.11940.5414-0.03320.08800.1849-0.00800.169615.18964.953618.5801
102.3480-1.0830-0.89623.88731.84093.50100.24890.1244-0.1240-0.2899-0.1675-0.0239-0.02310.1512-0.03310.3000-0.0303-0.07860.15740.05440.163235.67491.589121.4692
Refine TLS group

Beg auth asym ID: A / Beg auth seq ID: 0 / End auth asym ID: A / End auth seq ID: 0 / Refine ID: X-RAY DIFFRACTION

IDRefine TLS IDSelection details
11chain 'A' and (resid 27 through 72 )
22chain 'A' and (resid 73 through 95 )
33chain 'A' and (resid 96 through 123 )
44chain 'A' and (resid 124 through 153 )
55chain 'A' and (resid 154 through 191 )
66chain 'A' and (resid 192 through 216 )
77chain 'A' and (resid 217 through 249 )
88chain 'A' and (resid 250 through 284 )
99chain 'A' and (resid 285 through 311 )
1010chain 'A' and (resid 312 through 327 )

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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