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- PDB-8hq9: Crystal structure of the MlaD domain of the MlaD protein from Esc... -

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Basic information

Entry
Database: PDB / ID: 8hq9
TitleCrystal structure of the MlaD domain of the MlaD protein from Escherichia coli (Form II)
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 / membrane / plasma membrane
Similarity search - Function
Probable phospholipid ABC transporter-binding protein MlaD / : / Mce/MlaD / MlaD protein
Similarity search - Domain/homology
CARBON DIOXIDE / Intermembrane phospholipid transport system binding protein MlaD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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

Downloads & links

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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
D: Intermembrane phospholipid transport system binding protein MlaD
E: Intermembrane phospholipid transport system binding protein MlaD
F: Intermembrane phospholipid transport system binding protein MlaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8428
Polymers104,7746
Non-polymers682
Water3,117173
1
A: Intermembrane phospholipid transport system binding protein MlaD
D: Intermembrane phospholipid transport system binding protein MlaD
F: Intermembrane phospholipid transport system binding protein MlaD
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)104,8428
Polymers104,7746
Non-polymers682
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6290 Å2
ΔGint-60 kcal/mol
Surface area32850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.420, 106.950, 117.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11F-215-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Intermembrane phospholipid transport system binding protein MlaD


Mass: 17462.348 Da / Num. of mol.: 6
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 BL21(DE3) (bacteria) / References: UniProt: P64604
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.81 Å3/Da / Density % sol: 31.89 % / Description: Orthorhombic
Crystal growTemperature: 293 K / Method: microbatch / pH: 5
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M sodium citrate tribasic dihyrate pH 5.0, 10% (w/v) PEG 20000

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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: Jan 7, 2020 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→79.1 Å / Num. obs: 21557 / % possible obs: 100 % / Redundancy: 8.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.052 / Rrim(I) all: 0.157 / Χ2: 1.01 / Net I/σ(I): 12.6 / Num. measured all: 190212
Reflection shellResolution: 2.7→2.83 Å / % possible obs: 100 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.612 / Num. measured all: 24884 / Num. unique obs: 2805 / CC1/2: 0.943 / Rpim(I) all: 0.216 / Rrim(I) all: 0.65 / Χ2: 0.93 / Net I/σ(I) obs: 3.9

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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: 2.7→78.98 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.872 / SU B: 25.664 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R: 2.063 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26108 1037 4.8 %RANDOM
Rwork0.20415 ---
obs0.20686 20487 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.567 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å20 Å2-0 Å2
2---2.06 Å20 Å2
3----1.82 Å2
Refinement stepCycle: 1 / Resolution: 2.7→78.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4824 0 4 173 5001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134937
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154733
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.6546733
X-RAY DIFFRACTIONr_angle_other_deg1.251.57910937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5845637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38622.851235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.15215822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0961530
X-RAY DIFFRACTIONr_chiral_restr0.0780.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025563
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021017
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_it1.9982.6052539
X-RAY DIFFRACTIONr_mcbond_other1.9992.6052538
X-RAY DIFFRACTIONr_mcangle_it3.4983.8913167
X-RAY DIFFRACTIONr_mcangle_other3.4983.8913168
X-RAY DIFFRACTIONr_scbond_it2.1742.862398
X-RAY DIFFRACTIONr_scbond_other2.1732.8592397
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7374.1663562
X-RAY DIFFRACTIONr_long_range_B_refined6.13529.1574864
X-RAY DIFFRACTIONr_long_range_B_other6.10629.0854840
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)
11A30060.08
12B30060.08
21A29610.09
22C29610.09
31A29800.09
32D29800.09
41A29440.08
42E29440.08
51A29700.09
52F29700.09
61B29950.09
62C29950.09
71B30140.09
72D30140.09
81B29710.08
82E29710.08
91B29930.08
92F29930.08
101C30800.06
102D30800.06
111C30880.07
112E30880.07
121C30060.06
122F30060.06
131D30100.07
132E30100.07
141D30070.08
142F30070.08
151E30590.06
152F30590.06
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 81 -
Rwork0.269 1480 -
obs--99.94 %
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)
11.60350.72450.70074.7856-0.81381.9001-0.10110.01520.0038-0.25020.04170.2299-0.1537-0.17760.05940.08540.0231-0.06110.0245-0.01760.052417.6669-36.2088-26.7669
21.86540.9036-0.15426.08710.94841.1889-0.10690.01130.078-0.16540.0324-0.19020.08650.12250.07450.09270.02050.05330.01680.02110.052439.7716-17.2757-28.1329
32.29030.5296-1.05763.8887-1.02972.36550.0183-0.00250.2070.05050.0562-0.0367-0.1325-0.0253-0.07450.0969-0.00330.02830.0083-0.0090.034339.2742-45.416-22.7234
41.6793-0.50810.62325.65560.66021.28490.02850.0837-0.1621-0.0017-0.01440.04680.0425-0.0008-0.01410.10.0159-0.06480.0249-0.00770.067618.3877-7.4642-21.8835
51.05810.87711.26733.1790.05366.5094-0.1622-0.11020.0686-0.23320.1077-0.31-0.27090.19510.05450.1176-0.0332-0.01130.0757-0.04520.070840.56211.4591-5.4303
61.64221.3455-0.74731.57740.69936.2798-0.1032-0.10840.0433-0.0990.07380.20230.1090.04970.02930.16610.0017-0.03130.18280.09290.172519.1439-55.5508-4.8124
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 140
2X-RAY DIFFRACTION2B37 - 140
3X-RAY DIFFRACTION3C37 - 144
4X-RAY DIFFRACTION4D37 - 141
5X-RAY DIFFRACTION5E37 - 144
6X-RAY DIFFRACTION6F37 - 140

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