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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6buh
TitleCrystal structure of a membrane protein, crystal form II
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 / MOLECULAR REPLACEMENT / Resolution: 3.15 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
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
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 carrier protein
H: D-alanyl transfer protein DltB


Theoretical massNumber of molelcules
Total (without water)238,1198
Polymers238,1198
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 area1490 Å2
ΔGint-9 kcal/mol
Surface area25590 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 area1500 Å2
ΔGint-9 kcal/mol
Surface area25310 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 area1510 Å2
ΔGint-10 kcal/mol
Surface area25450 Å2
MethodPISA
4
G: D-alanyl carrier protein
H: 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 area1530 Å2
ΔGint-8 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.677, 124.581, 126.712
Angle α, β, γ (deg.)90.000, 96.990, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13A
23G
14C
24D
15C
25F
16C
26H
17B
27E
18B
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA1 - 794 - 82
21ALAALABC1 - 794 - 82
12ALAALAAA1 - 794 - 82
22ALAALAEE1 - 794 - 82
13ALAALAAA1 - 794 - 82
23ALAALAGG1 - 794 - 82
14LYSLYSCB1 - 4141 - 414
24LYSLYSDD1 - 4141 - 414
15LYSLYSCB1 - 4141 - 414
25LYSLYSFF1 - 4141 - 414
16LYSLYSCB1 - 4141 - 414
26LYSLYSHH1 - 4141 - 414
17ALAALABC1 - 794 - 82
27ALAALAEE1 - 794 - 82
18ALAALABC1 - 794 - 82
28ALAALAGG1 - 794 - 82
19LYSLYSDD1 - 4141 - 414
29LYSLYSFF1 - 4141 - 414
110LYSLYSDD1 - 4141 - 414
210LYSLYSHH1 - 4141 - 414
111ALAALAEE1 - 794 - 82
211ALAALAGG1 - 794 - 82
112LYSLYSFF1 - 4141 - 414
212LYSLYSHH1 - 4141 - 414

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

-
Components

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


Mass: 9337.271 Da / Num. of mol.: 4
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, stu0762 / 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: 66.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100mM sodium citrate pH5.6, 200mM NH4H2PO4, and 100mM (NH4)2SO4, 27% (w/v) PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→125.77 Å / Num. obs: 54118 / % possible obs: 98.5 % / Redundancy: 3.6 % / Rsym value: 0.165 / Net I/σ(I): 8.6
Reflection shellResolution: 3.15→3.24 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4222 / CC1/2: 0.582 / Rsym value: 0.929 / % possible all: 87.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BUG

6bug


Resolution: 3.15→125.77 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.868 / SU B: 78.724 / SU ML: 0.565 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.53 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2992 2832 5 %RANDOM
Rwork0.2756 ---
obs0.2768 54118 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 222 Å2 / Biso mean: 96.365 Å2 / Biso min: 51.59 Å2
Baniso -1Baniso -2Baniso -3
1--3.94 Å20 Å2-1.84 Å2
2--6.22 Å20 Å2
3----1.78 Å2
Refinement stepCycle: final / Resolution: 3.15→125.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16308 0 0 0 16308
Num. residues----1972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216764
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.95322680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.41251964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41223.105760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.464152932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6641588
X-RAY DIFFRACTIONr_chiral_restr0.0960.22480
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112500
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A43500.05
12B43500.05
21A43440.07
22E43440.07
31A43200.06
32G43200.06
41C292220.03
42D292220.03
51C291340.03
52F291340.03
61C291660.03
62H291660.03
71B44320.05
72E44320.05
81B43720.06
82G43720.06
91D291700.03
92F291700.03
101D291640.03
102H291640.03
111E43720.06
112G43720.06
121F292560.03
122H292560.03
LS refinement shellResolution: 3.153→3.235 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 176 -
Rwork0.377 3454 -
all-3630 -
obs--84.69 %
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)
10.7489-1.43750.76122.7744-1.47710.7911-0.35-0.08720.28330.73720.1081-0.4952-0.4194-0.00770.24190.507-0.02530.11520.97730.03070.4011-1.69668.3115-14.256
21.07370.0663-0.17460.1542-0.15360.1906-0.01960.01570.0918-0.01530.0487-0.0565-0.0114-0.1533-0.02910.05540.04150.14040.56260.10050.37682.42616.288315.2002
33.196-0.75331.32776.3319-0.29290.5546-0.50160.3835-0.2274-0.42890.5601-0.7351-0.23270.1485-0.05850.30130.09710.0120.53720.04040.6458-50.452115.7026-13.1473
41.52550.0097-0.23870.20290.06180.0572-0.12330.2723-0.11120.04740.09960.02180.0341-0.01320.02360.0598-0.04420.13580.5002-0.04930.4254-45.982634.7405-37.1548
51.5723-0.28791.61694.9437-1.5151.9795-0.2616-0.58430.25130.635-0.06120.0529-0.44-0.5490.32280.26370.0015-0.0140.6863-0.13070.40214.439136.3035-80.4988
61.3718-0.13040.3820.31150.05740.5131-0.03140.3530.09590.0408-0.0274-0.0496-0.00780.0350.05880.0547-0.02020.12020.5211-0.02070.35658.205235.5529-49.7823
70.07920.0367-0.10980.0657-0.08030.1706-0.13790.0681-0.1033-0.13390.09230.10480.2474-0.11730.04550.8210.1336-0.03020.4637-0.02620.8174-55.105848.887642.9523
81.9556-0.4639-0.02930.44770.07630.1556-0.2124-0.29620.44850.04020.1879-0.08950.04240.03080.02450.05470.0790.04350.4884-0.00840.5374-51.925525.532223.1662
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 - 79
8X-RAY DIFFRACTION8H1 - 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