[English] 日本語
Yorodumi
- PDB-4r1i: Structure and Function of Neisseria gonorrhoeae MtrF Illuminates ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r1i
TitleStructure and Function of Neisseria gonorrhoeae MtrF Illuminates a Class of Antimetabolite Efflux Pumps
ComponentsAminobenzoyl-glutamate transporter
KeywordsMEMBRANE PROTEIN / transmembrane protein
Function / homologyAbgT, Proteobacteria / secondary active p-aminobenzoyl-glutamate transmembrane transporter activity / p-aminobenzoyl-glutamate transmembrane transport / p-Aminobenzoyl-glutamate transport protein AbgT / AbgT putative transporter family / membrane => GO:0016020 / : / Aminobenzoyl-glutamate transporter
Function and homology information
Biological speciesNeisseria gonorrhoeae FA19 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.959 Å
AuthorsSu, C.-C. / Bolla, J.R. / Yu, E.W.
CitationJournal: Cell Rep / Year: 2015
Title: Structure and Function of Neisseria gonorrhoeae MtrF Illuminates a Class of Antimetabolite Efflux Pumps.
Authors: Su, C.C. / Bolla, J.R. / Kumar, N. / Radhakrishnan, A. / Long, F. / Delmar, J.A. / Chou, T.H. / Rajashankar, K.R. / Shafer, W.M. / Yu, E.W.
History
DepositionAug 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminobenzoyl-glutamate transporter
B: Aminobenzoyl-glutamate transporter


Theoretical massNumber of molelcules
Total (without water)112,3402
Polymers112,3402
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-41 kcal/mol
Surface area43810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.766, 120.766, 233.897
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Aminobenzoyl-glutamate transporter


Mass: 56170.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae FA19 (bacteria) / Strain: FA19 / Gene: NGEG_01484 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: D1DA20, UniProt: Q9RNX2*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.38 Å3/Da / Density % sol: 71.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 30% PEG400, 0.05M Mg(Ac)2, 0.1M NaAc(5.0), and 3% glycerol, pH 7.5, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2013
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.95→50 Å / Num. obs: 16468 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 202.86 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.95-4.112.20.921184.5
4.11-4.292.30.519191.3
4.29-4.522.30.356193.8
4.52-4.82.60.283197.6
4.8-5.172.70.278199.8
5.17-5.72.70.187199.3
5.7-6.522.50.138198.4
6.52-8.212.50.074196.3
8.21-502.30.05195.2

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 3.959→47.74 Å / SU ML: 0.94 / σ(F): 1.34 / Phase error: 53.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3383 869 5.3 %
Rwork0.3108 --
obs0.3124 16382 97.36 %
all-16382 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 232.14 Å2
Refinement stepCycle: LAST / Resolution: 3.959→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7684 0 0 0 7684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057883
X-RAY DIFFRACTIONf_angle_d110755
X-RAY DIFFRACTIONf_dihedral_angle_d17.6492721
X-RAY DIFFRACTIONf_chiral_restr0.0631290
X-RAY DIFFRACTIONf_plane_restr0.0051321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9592-4.20710.5491520.40172388X-RAY DIFFRACTION91
4.2071-4.53170.41911370.32452625X-RAY DIFFRACTION98
4.5317-4.98730.34361420.28032638X-RAY DIFFRACTION100
4.9873-5.70790.42611570.30592641X-RAY DIFFRACTION99
5.7079-7.18740.45311300.39472625X-RAY DIFFRACTION99
7.1874-47.74310.28271510.2872596X-RAY DIFFRACTION97
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)
10.4997-0.5435-0.23820.80340.29350.0733-0.161-0.6738-1.2452-0.10420.26391.05550.9562-0.09370.10990.58952.18660.15680.9769-0.17440.71713.775449.428128.7986
21.19810.9803-0.22521.7281-0.8960.85070.6809-0.22850.97280.99631.29250.8864-0.28090.11182.37080.69681.78060.30221.118-1.94260.630841.465661.036634.5016
30.58370.6347-0.50290.4706-0.2621.280.42210.3865-0.47080.09210.5291-0.24130.44680.20091.20532.11741.10240.59151.9594-0.57820.447142.327568.662632.4123
40.9123-0.86241.01452.25270.51712.21140.8018-0.34090.2173-0.53320.6852-1.64830.4165-0.80932.52020.05970.8716-0.1610.8338-0.21570.37525.036556.846829.051
50.1415-0.0879-0.01480.4062-0.06540.0398-0.6731-0.05210.40230.34590.3192-0.2326-1.0178-0.3786-0.06212.72751.8464-0.3391.21130.26390.674834.366255.117442.5499
61.46780.82940.17440.46540.09410.04760.03710.5031-0.75960.0283-0.2163-0.7729-0.24710.7928-0.23150.65291.53570.35981.58730.16460.680136.819966.8371-5.1668
70.09730.2182-0.14480.6946-0.3870.21480.3298-1.1291-0.14991.01120.0976-0.364-0.5541.1148-0.08091.3810.1328-0.0773.0809-0.99822.390413.750979.507-0.7141
80.02810.0093-0.15670.0533-0.25191.1627-0.574-0.16140.6186-0.1086-0.3304-0.13730.87040.5116-0.9223-0.69280.9914-1.01250.10130.35340.516922.328452.903110.6917
90.13-0.0353-0.12320.2232-0.17070.26080.23840.5885-0.10610.33390.4874-0.45640.11240.52210.38851.3240.7664-0.38740.8206-1.71312.211733.329730.4639-6.9941
101.28721.0532-0.62080.891-0.08543.84451.24140.35790.49210.20641.18831.82490.4518-0.69733.42050.22890.2953-1.07590.43710.5691.579217.980549.4162-4.6799
110.5234-0.00870.55440.272-0.07640.50130.0788-0.81980.24350.45270.5126-0.9838-0.0593-1.17880.27391.2481.5316-1.1023.3807-0.1879-1.160830.834427.6771-4.2299
124.47370.03991.02910.85051.43322.74212.50020.2218-1.2941-0.7045-0.0583-0.5605-0.8260.09173.76610.04911.514-0.13991.0241-0.12190.4920.07653.4388-0.6332
130.3672-0.17060.12450.18150.1324-0.1465-0.34880.431-0.12380.71870.3578-0.83861.59180.2498-0.8218-0.3189-0.291-1.37722.5284-1.77050.893732.774645.0414-14.2051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 111 )
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 214 )
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 314 )
4X-RAY DIFFRACTION4chain 'A' and (resid 315 through 432 )
5X-RAY DIFFRACTION5chain 'A' and (resid 433 through 516 )
6X-RAY DIFFRACTION6chain 'B' and (resid 11 through 44 )
7X-RAY DIFFRACTION7chain 'B' and (resid 45 through 84 )
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 111 )
9X-RAY DIFFRACTION9chain 'B' and (resid 112 through 179 )
10X-RAY DIFFRACTION10chain 'B' and (resid 180 through 231 )
11X-RAY DIFFRACTION11chain 'B' and (resid 232 through 292 )
12X-RAY DIFFRACTION12chain 'B' and (resid 293 through 453 )
13X-RAY DIFFRACTION13chain 'B' and (resid 454 through 516 )

+
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