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- PDB-7vr6: Crystal structure of MlaC from Escherichia coli in quasi-open state -

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Basic information

Entry
Database: PDB / ID: 7vr6
TitleCrystal structure of MlaC from Escherichia coli in quasi-open state
ComponentsIntermembrane phospholipid transport system binding protein MlaC
KeywordsTRANSPORT PROTEIN / ABC transporter / Periplasmic protein / Membrane lipid asymmetry / Segmented domain movement / Mla transport system
Function / homologyTgt2/MlaC superfamily / Toluene tolerance Ttg2/phospholipid-binding protein MlaC / MlaC protein / intermembrane phospholipid transfer / phospholipid transport / outer membrane-bounded periplasmic space / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Intermembrane phospholipid transport system binding protein MlaC
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsDutta, A. / Kanaujia, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)ECR/2018/000013 India
CitationJournal: J.Struct.Biol. / Year: 2022
Title: MlaC belongs to a unique class of non-canonical substrate-binding proteins and follows a novel phospholipid-binding mechanism.
Authors: Dutta, A. / Prasad Kanaujia, S.
History
DepositionOct 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intermembrane phospholipid transport system binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4723
Polymers22,7181
Non-polymers7542
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-16 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.940, 114.940, 46.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Intermembrane phospholipid transport system binding protein MlaC


Mass: 22717.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: mlaC / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ADV7
#2: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL / Phosphatidylethanolamine


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.7 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.7 M sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane pH 7.0

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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: Mar 28, 2018 / Details: VariMax HF
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→57.47 Å / Num. obs: 7857 / % possible obs: 100 % / Redundancy: 4.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.05 / Rrim(I) all: 0.108 / Net I/σ(I): 13.5 / Num. measured all: 35454 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.60.41139988980.8650.2210.4683.8100
9.01-57.470.0287381640.9990.0150.0323699

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.21 Å57.47 Å
Translation5.21 Å57.47 Å

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Processing

Software
NameVersionClassification
HKL-30003000data collection
Aimless0.7.4data scaling
MOSFLM7.3.0data reduction
PHASER2.8.3phasing
REFMAC5.8.0267refinement
Coot0.9.6model building
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UWA

5uwa


Resolution: 2.5→57.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.892 / SU ML: 0.186 / SU R Cruickshank DPI: 0.54 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 368 4.7 %RANDOM
Rwork0.1691 ---
obs0.1714 7487 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.04 Å2 / Biso mean: 31.629 Å2 / Biso min: 13.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.24 Å2-0 Å2
2--0.47 Å2-0 Å2
3----1.54 Å2
Refinement stepCycle: final / Resolution: 2.5→57.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 51 58 1602
Biso mean--57.4 31.78 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131591
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171558
X-RAY DIFFRACTIONr_angle_refined_deg1.9841.6732148
X-RAY DIFFRACTIONr_angle_other_deg1.3561.583590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8015188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15322.72788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.2515272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9921511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021774
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02372
LS refinement shellResolution: 2.501→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 31 -
Rwork0.237 542 -
all-573 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 6.431 Å / Origin y: 19.088 Å / Origin z: 4.362 Å
111213212223313233
T0.0223 Å2-0.0001 Å20.0128 Å2-0.0425 Å20.0238 Å2--0.039 Å2
L0.5346 °2-0.098 °20.0944 °2-1.4245 °20.3921 °2--1.4281 °2
S-0.0696 Å °-0.0698 Å °-0.0226 Å °0.0932 Å °0.079 Å °0.2185 Å °-0.0161 Å °-0.0667 Å °-0.0094 Å °

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