[English] 日本語
Yorodumi
- PDB-3op1: Crystal Structure of Macrolide-efflux Protein SP_1110 from Strept... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3op1
TitleCrystal Structure of Macrolide-efflux Protein SP_1110 from Streptococcus pneumoniae
ComponentsMacrolide-efflux protein
KeywordsTRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / alpha-beta-alpha sandwich / beta barrel / kinase / cytosol
Function / homology
Function and homology information


riboflavin kinase / FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / ATP binding
Similarity search - Function
Riboflavin kinase, bacterial / FAD synthetase / FAD synthetase / Riboflavin kinase domain, bacterial/eukaryotic / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase-like / Riboflavin kinase domain superfamily / HUPs ...Riboflavin kinase, bacterial / FAD synthetase / FAD synthetase / Riboflavin kinase domain, bacterial/eukaryotic / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase-like / Riboflavin kinase domain superfamily / HUPs / Elongation Factor Tu (Ef-tu); domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / DI(HYDROXYETHYL)ETHER / Riboflavin biosynthesis protein / Riboflavin biosynthesis protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.488 Å
AuthorsKim, Y. / Li, H. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Macrolide-efflux Protein SP_1110 from Streptococcus pneumoniae
Authors: Kim, Y. / Li, H. / Cobb, G. / Joachimiak, A.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Macrolide-efflux protein
B: Macrolide-efflux protein
C: Macrolide-efflux protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,64525
Polymers105,6353
Non-polymers2,00922
Water4,234235
1
A: Macrolide-efflux protein
B: Macrolide-efflux protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,87618
Polymers70,4242
Non-polymers1,45316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-33 kcal/mol
Surface area28530 Å2
MethodPISA
2
C: Macrolide-efflux protein
hetero molecules

C: Macrolide-efflux protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,53714
Polymers70,4242
Non-polymers1,11312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7030 Å2
ΔGint-82 kcal/mol
Surface area24440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.153, 73.247, 87.518
Angle α, β, γ (deg.)90.00, 112.48, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Macrolide-efflux protein


Mass: 35211.816 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1110 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q97QT9, UniProt: A0A0H2UPY5*PLUS

-
Non-polymers , 6 types, 257 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M TRIS pH 8.5 40 %v/v PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97945 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jul 26, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 36456 / Num. obs: 36456 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 55.22 Å2 / Rsym value: 0.094 / Net I/σ(I): 7.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1785 / Rsym value: 0.497 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: 1.6.2_432)refinement
REFMAC5.5refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.488→35.761 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.93 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1816 4.99 %random
Rwork0.198 ---
all0.202 36417 --
obs0.202 36417 97.91 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.793 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso mean: 59.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.51 Å20 Å2-6.0295 Å2
2--12.1617 Å20 Å2
3----3.6517 Å2
Refinement stepCycle: LAST / Resolution: 2.488→35.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6868 0 125 235 7228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137129
X-RAY DIFFRACTIONf_angle_d1.469605
X-RAY DIFFRACTIONf_dihedral_angle_d18.7292672
X-RAY DIFFRACTIONf_chiral_restr0.0941058
X-RAY DIFFRACTIONf_plane_restr0.0081230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4881-2.5770.35121620.27432967312984
2.577-2.68010.34691760.27463426360298
2.6801-2.8020.34141630.25893490365399
2.802-2.94970.33211970.24893486368399
2.9497-3.13440.30641880.226735183706100
3.1344-3.37630.32631880.212335123700100
3.3763-3.71570.24651610.197435393700100
3.7157-4.25260.25441980.171935173715100
4.2526-5.3550.20431950.149835433738100
5.355-35.76420.23291880.19443603379199
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)
10.5707-0.0451-0.48261.15350.10660.72110.10490.0609-0.071-0.1407-0.28970.0055-0.1129-0.1580.14110.22560.1075-0.0210.1905-0.03770.164341.00620.2121-13.7653
20.4120.549-0.97811.3904-1.22481.59730.13-0.4751-0.28970.1769-0.573-0.3479-0.07810.66880.42080.1377-0.1066-0.08110.45310.2190.2458.58712.097525.2627
33.4047-0.62592.606-0.1911-0.39422.5783-0.2966-0.0553-0.03840.04320.1899-0.0568-0.3329-0.13110.07420.2663-0.08720.01390.278-0.00410.180111.092210.01749.398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

+
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://pdbjlvh1.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