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- PDB-6bui: Crystal structure of a membrane protein, crystal form III -

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Basic information

Entry
Database: PDB / ID: 6bui
TitleCrystal structure of a membrane protein, crystal form III
ComponentsIntegral membrane protein
KeywordsMEMBRANE PROTEIN
Function / homologyD-alanyl transfer protein DltB / Alginate O-acetyltransferase AlgI/D-alanyl transfer protein DltB / lipoteichoic acid biosynthetic process / Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / plasma membrane / Teichoic acid D-alanyltransferase
Function and homology information
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Integral membrane protein
A: Integral membrane protein
B: Integral membrane protein
D: Integral membrane protein


Theoretical massNumber of molelcules
Total (without water)200,7694
Polymers200,7694
Non-polymers00
Water00
1
C: Integral membrane protein


Theoretical massNumber of molelcules
Total (without water)50,1921
Polymers50,1921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Integral membrane protein


Theoretical massNumber of molelcules
Total (without water)50,1921
Polymers50,1921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Integral membrane protein


Theoretical massNumber of molelcules
Total (without water)50,1921
Polymers50,1921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Integral membrane protein


Theoretical massNumber of molelcules
Total (without water)50,1921
Polymers50,1921
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.182, 242.062, 96.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
12C
22B
13C
23D
14A
24B
15A
25D
16B
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1 - 414 / Label seq-ID: 1 - 414

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11CA
21AB
12CA
22BC
13CA
23DD
14AB
24BC
15AB
25DD
16BC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Integral membrane protein / 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

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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: 4.19 Å3/Da / Density % sol: 70.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES pH7.5, 200mM sodium citrate tribasic dihydrate, 3% (w/v) 1,5-diaminopentane dihydrochloride, 27% (w/v) PEG 400

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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: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.27→121.31 Å / Num. obs: 47040 / % possible obs: 97.5 % / Redundancy: 3.8 % / Rsym value: 0.115 / Net I/σ(I): 11.5
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4083 / CC1/2: 0.563 / Rsym value: 1.203 / % possible all: 98.1

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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: 3.27→121.31 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.903 / SU B: 81.579 / SU ML: 0.561 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.548
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3003 2434 4.9 %RANDOM
Rwork0.2802 ---
obs0.2812 47040 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 327.69 Å2 / Biso mean: 151.657 Å2 / Biso min: 79.77 Å2
Baniso -1Baniso -2Baniso -3
1-13.5 Å20 Å20 Å2
2--0.23 Å20 Å2
3----13.73 Å2
Refinement stepCycle: final / Resolution: 3.27→121.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13792 0 0 0 13792
Num. residues----1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214224
X-RAY DIFFRACTIONr_angle_refined_deg1.41.94819244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58851652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79122.436624
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.443152468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5041572
X-RAY DIFFRACTIONr_chiral_restr0.1020.22080
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110604
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C293420.04
12A293420.04
21C293660.04
22B293660.04
31C292120.04
32D292120.04
41A293340.03
42B293340.03
51A292060.04
52D292060.04
61B292300.04
62D292300.04
LS refinement shellResolution: 3.275→3.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 167 -
Rwork0.398 3060 -
all-3227 -
obs--86.58 %
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)
10.91070.25140.08560.9380.33490.72080.07180.1887-0.12120.17260.02280.0543-0.05530.1805-0.09460.15280.0292-0.08520.1827-0.04430.6407-41.837513.1026-17.7277
21.2589-0.8317-0.21481.57160.07690.1119-0.06320.15680.17350.05990.0597-0.08890.13530.00140.00350.26390.14860.02770.257-0.01550.5085-47.233-38.1532-27.8656
30.4925-0.28870.36550.59410.06571.36960.0651-0.0026-0.1468-0.2157-0.0071-0.0381-0.4120.1497-0.05810.51540.17780.15120.26590.02180.4356-29.7899-55.7189-67.7556
40.17720.28820.28550.6422-0.07012.77810.15240.144-0.09770.56290.47950.0364-0.6953-0.7374-0.63190.84740.61940.43910.59010.25410.477417.9175-25.8744-76.0978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 414
2X-RAY DIFFRACTION2A1 - 414
3X-RAY DIFFRACTION3B1 - 414
4X-RAY DIFFRACTION4D1 - 414

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