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- PDB-8hqa: Crystal structure of the ectodomain of the MlaD protein from Esch... -

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Basic information

Entry
Database: PDB / ID: 8hqa
TitleCrystal structure of the ectodomain of the MlaD protein from Escherichia coli in the resting state
ComponentsIntermembrane phospholipid transport system binding protein MlaD
KeywordsTRANSPORT PROTEIN / ABC transporter / Asymmetric protomer movement / Central channel / Gram-negative bacteria / Mla system / Transport
Function / homology
Function and homology information


phospholipid transfer activity / intermembrane phospholipid transfer / phospholipid transporter activity / phospholipid-translocating ATPase complex / phospholipid transport / phospholipid binding / extracellular region / membrane / plasma membrane
Similarity search - Function
Probable phospholipid ABC transporter-binding protein MlaD / Mce/MlaD / MlaD protein
Similarity search - Domain/homology
Intermembrane phospholipid transport system binding protein MlaD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDutta, A. / Kanaujia, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)ECR/2018/000013 India
CitationJournal: Protein J. / Year: 2024
Title: The Structural Features of MlaD Illuminate its Unique Ligand-Transporting Mechanism and Ancestry.
Authors: Dutta, A. / Kanaujia, S.P.
History
DepositionDec 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intermembrane phospholipid transport system binding protein MlaD
B: Intermembrane phospholipid transport system binding protein MlaD
C: Intermembrane phospholipid transport system binding protein MlaD


Theoretical massNumber of molelcules
Total (without water)52,3873
Polymers52,3873
Non-polymers00
Water39622
1
B: Intermembrane phospholipid transport system binding protein MlaD
C: Intermembrane phospholipid transport system binding protein MlaD

B: Intermembrane phospholipid transport system binding protein MlaD
C: Intermembrane phospholipid transport system binding protein MlaD

A: Intermembrane phospholipid transport system binding protein MlaD

A: Intermembrane phospholipid transport system binding protein MlaD


Theoretical massNumber of molelcules
Total (without water)104,7746
Polymers104,7746
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
crystal symmetry operation5_455-x-1/2,y+1/2,-z+1/41
Buried area9960 Å2
ΔGint-93 kcal/mol
Surface area35170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.280, 64.280, 231.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein Intermembrane phospholipid transport system binding protein MlaD


Mass: 17462.348 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mlaD, yrbD, b3193, JW3160 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (D3) / References: UniProt: P64604
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.64 % / Description: Tetragonal
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 0.01 M nickel(II) chloride hexahydrate, 0.1 M tris pH 8.5, 20% (w/v) PEG monoethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 12, 2019 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→77.02 Å / Num. obs: 8680 / % possible obs: 99.8 % / Redundancy: 10 % / CC1/2: 0.994 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.053 / Rrim(I) all: 0.175 / Χ2: 0.92 / Net I/σ(I): 9.6 / Num. measured all: 86434
Reflection shellResolution: 3.2→3.42 Å / % possible obs: 100 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.552 / Num. measured all: 15458 / Num. unique obs: 1516 / CC1/2: 0.934 / Rpim(I) all: 0.177 / Rrim(I) all: 0.582 / Χ2: 0.72 / Net I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.4.0data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
REFMAC5.8.0352refinement
Coot0.9.8.5model building
PDB_EXTRACT4data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→61.93 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.9 / SU B: 48.063 / SU ML: 0.381 / Cross valid method: THROUGHOUT / ESU R Free: 0.513 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27543 442 5.1 %RANDOM
Rwork0.20644 ---
obs0.21008 8175 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.249 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å2-0 Å2-0 Å2
2--1.99 Å2-0 Å2
3----3.98 Å2
Refinement stepCycle: 1 / Resolution: 3.2→61.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 0 22 2667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132694
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152599
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.653666
X-RAY DIFFRACTIONr_angle_other_deg1.2171.5785991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0275340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30122.769130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.20815454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0921516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023011
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02569
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6094.361369
X-RAY DIFFRACTIONr_mcbond_other2.6094.361368
X-RAY DIFFRACTIONr_mcangle_it4.3876.5241703
X-RAY DIFFRACTIONr_mcangle_other4.3866.5241704
X-RAY DIFFRACTIONr_scbond_it2.7724.7481325
X-RAY DIFFRACTIONr_scbond_other2.7714.7471326
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6616.9861963
X-RAY DIFFRACTIONr_long_range_B_refined7.32549.4762680
X-RAY DIFFRACTIONr_long_range_B_other7.349.4812680
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A32510.1
12B32510.1
21A32860.09
22C32860.09
31B32800.09
32C32800.09
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 38 -
Rwork0.259 565 -
obs--100 %
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)
11.79680.4611-0.54344.0963-1.10374.96460.19430.0199-0.3106-0.1044-0.1263-0.29290.04910.4778-0.06810.0934-0.0577-0.05570.17320.02980.09323.387712.856233.8644
23.0364-0.71280.7392.4342-0.14836.802-0.0529-0.1653-0.16790.1142-0.12060.0242-0.058-0.23370.17350.20490.0108-0.06650.0350.02880.1426-17.031826.443922.7452
33.0725-1.06770.38383.6719-0.61016.3631-0.06510.1303-0.3114-0.01870.1546-0.22850.5730.3209-0.08950.23740.11350.06760.08270.00620.1276-8.483418.1761-1.8674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 152
2X-RAY DIFFRACTION2B35 - 152
3X-RAY DIFFRACTION3C37 - 152

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