[English] 日本語
Yorodumi
- PDB-6bug: Crystal structure of a membrane protein, crystal form I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bug
TitleCrystal structure of a membrane protein, crystal form I
Components
  • D-alanyl carrier protein
  • D-alanyl transfer protein DltB
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


D-alanyl carrier activity / lipoteichoic acid biosynthetic process / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cell wall organization / plasma membrane / cytoplasm
Similarity search - Function
D-alanyl transfer protein DltB / Alginate O-acetyltransferase AlgI/D-alanyl transfer protein DltB / D-alanyl carrier protein / Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. ...D-alanyl transfer protein DltB / Alginate O-acetyltransferase AlgI/D-alanyl transfer protein DltB / D-alanyl carrier protein / Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
D-alanyl carrier protein / D-alanyl carrier protein / Teichoic acid D-alanyltransferase
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.27 Å
AuthorsMa, D. / Wang, Z. / Xu, W.
CitationJournal: Nature / Year: 2018
Title: Crystal structure of a membrane-bound O-acyltransferase.
Authors: Ma, D. / Wang, Z. / Merrikh, C.N. / Lang, K.S. / Lu, P. / Li, X. / Merrikh, H. / Rao, Z. / Xu, W.
History
DepositionDec 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-alanyl carrier protein
C: D-alanyl transfer protein DltB
B: D-alanyl carrier protein
D: D-alanyl transfer protein DltB
E: D-alanyl carrier protein
F: D-alanyl transfer protein DltB
G: D-alanyl transfer protein DltB


Theoretical massNumber of molelcules
Total (without water)228,7817
Polymers228,7817
Non-polymers00
Water00
1
A: D-alanyl carrier protein
C: D-alanyl transfer protein DltB


Theoretical massNumber of molelcules
Total (without water)59,5302
Polymers59,5302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-8 kcal/mol
Surface area25530 Å2
MethodPISA
2
B: D-alanyl carrier protein
D: D-alanyl transfer protein DltB


Theoretical massNumber of molelcules
Total (without water)59,5302
Polymers59,5302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-8 kcal/mol
Surface area25260 Å2
MethodPISA
3
E: D-alanyl carrier protein
F: D-alanyl transfer protein DltB


Theoretical massNumber of molelcules
Total (without water)59,5302
Polymers59,5302
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-8 kcal/mol
Surface area25420 Å2
MethodPISA
4
G: D-alanyl transfer protein DltB


Theoretical massNumber of molelcules
Total (without water)50,1921
Polymers50,1921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.713, 121.119, 126.529
Angle α, β, γ (deg.)90.000, 101.580, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13C
23D
14C
24F
15C
25G
16B
26E
17D
27F
18D
28G
19F
29G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 79
2010B1 - 79
1020A1 - 79
2020E1 - 79
1030C1 - 414
2030D1 - 414
1040C1 - 414
2040F1 - 414
1050C1 - 414
2050G1 - 414
1060B1 - 79
2060E1 - 79
1070D1 - 414
2070F1 - 414
1080D1 - 414
2080G1 - 414
1090F1 - 414
2090G1 - 414

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

-
Components

#1: Protein D-alanyl carrier protein / DCP / D-alanine--poly(phosphoribitol) ligase subunit 2


Mass: 9337.271 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: dltC / Production host: Escherichia coli (E. coli) / References: UniProt: Q5M0A6, UniProt: Q5M4V3*PLUS
#2: Protein
D-alanyl transfer protein DltB / D-alanyl-lipoteichoic acid biosynthesis protein DltB


Mass: 50192.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: dltB / Production host: Escherichia coli (E. coli) / References: UniProt: Q5M4V4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100mM Tris-HCl pH7.5, 100mM NaCl, 100mM MgCl2, 21% (w/v) PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.27→123.95 Å / Num. obs: 46614 / % possible obs: 99.5 % / Redundancy: 6.4 % / Rsym value: 0.17 / Net I/σ(I): 13.1
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4072 / CC1/2: 0.732 / Rsym value: 1.661 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.27→123.95 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.896 / SU B: 87.263 / SU ML: 0.611 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.602 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3109 2428 5 %RANDOM
Rwork0.2886 ---
obs0.2897 46614 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 335.72 Å2 / Biso mean: 141.976 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--6.03 Å20 Å23.77 Å2
2--0.56 Å20 Å2
3---3.62 Å2
Refinement stepCycle: final / Resolution: 3.27→123.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15679 0 0 0 15679
Num. residues----1893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216096
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.95121767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79751880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73722.961726
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.708152816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4831584
X-RAY DIFFRACTIONr_chiral_restr0.1020.22377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112002
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A43520.04
12B43520.04
21A43580.04
22E43580.04
31C300300.04
32D300300.04
41C299560.04
42F299560.04
51C298640.05
52G298640.05
61B43440.05
62E43440.05
71D299220.04
72F299220.04
81D298380.04
82G298380.04
91F299500.04
92G299500.04
LS refinement shellResolution: 3.267→3.352 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 169 -
Rwork0.405 2835 -
all-3004 -
obs--82.23 %
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)
10.0386-0.06190.08490.145-0.16490.6491-0.0750.01730.05090.0712-0.0224-0.2011-0.1873-0.52180.09740.21010.00390.07330.7810.01080.552711.671716.507222.1528
21.8004-0.1078-0.03640.34230.13380.0589-0.0595-0.47710.101-0.14260.08120.0641-0.05370.0079-0.02170.0680.0043-0.06270.4736-0.00750.43416.1537-8.076941.6181
33.12943.23972.56683.44762.66952.1141-0.60650.14590.2759-0.61360.3420.1859-0.48860.15020.26460.33110.09160.11960.4317-0.09380.578144.5827.461217.379
41.8163-0.0656-0.2080.1298-0.16070.3109-0.19140.0173-0.66050.07730.0102-0.0005-0.1273-0.09090.18120.1238-0.0044-0.04090.35070.03850.541249.08813.9217-10.6793
52.4486-2.1432-1.21387.5895-3.69734.56910.0543-0.12120.13720.20760.27070.1805-0.2331-0.1131-0.3250.0777-0.139-0.03850.4574-0.01920.236166.6418-21.43183.2869
61.44980.1146-0.32940.4852-0.32960.7077-0.072-0.28070.0381-0.051-0.1085-0.06970.0850.00990.18060.03940.0137-0.07230.4698-0.14750.384670.4916-12.352153.3324
71.64390.37430.03090.16020.18770.6117-0.17120.1881-0.5397-0.05980.1237-0.09-0.09890.03940.04750.03550.00010.03720.2622-0.04410.7103-5.27563.3941-16.9997
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 79
2X-RAY DIFFRACTION2C1 - 414
3X-RAY DIFFRACTION3B1 - 79
4X-RAY DIFFRACTION4D1 - 414
5X-RAY DIFFRACTION5E1 - 79
6X-RAY DIFFRACTION6F1 - 414
7X-RAY DIFFRACTION7G1 - 414

+
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