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- PDB-6bug: Crystal structure of a membrane protein, crystal form I -

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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 ...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
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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:

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
13LYSLYSCB1 - 4141 - 414
23LYSLYSDD1 - 4141 - 414
14LYSLYSCB1 - 4141 - 414
24LYSLYSFF1 - 4141 - 414
15LYSLYSCB1 - 4141 - 414
25LYSLYSGG1 - 4141 - 414
16ALAALABC1 - 794 - 82
26ALAALAEE1 - 794 - 82
17LYSLYSDD1 - 4141 - 414
27LYSLYSFF1 - 4141 - 414
18LYSLYSDD1 - 4141 - 414
28LYSLYSGG1 - 4141 - 414
19LYSLYSFF1 - 4141 - 414
29LYSLYSGG1 - 4141 - 414

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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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