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

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Basic information

Entry
Database: PDB / ID: 8hpz
TitleCrystal structure of the MlaD domain of the MlaD protein from Escherichia coli (Form I)
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-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: 2.3 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4935
Polymers52,3873
Non-polymers1062
Water1,45981
1
A: Intermembrane phospholipid transport system binding protein MlaD
B: Intermembrane phospholipid transport system binding protein MlaD
hetero molecules

A: Intermembrane phospholipid transport system binding protein MlaD
B: Intermembrane phospholipid transport system binding protein MlaD
hetero molecules

C: Intermembrane phospholipid transport system binding protein MlaD

C: Intermembrane phospholipid transport system binding protein MlaD


Theoretical massNumber of molelcules
Total (without water)104,98610
Polymers104,7746
Non-polymers2124
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area5940 Å2
ΔGint-44 kcal/mol
Surface area33550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.280, 107.290, 117.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
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 BL21(DE3) (bacteria) / References: UniProt: P64604
#2: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.82 Å3/Da / Density % sol: 32.41 % / Description: Orthorhombic
Crystal growTemperature: 293 K / Method: microbatch / pH: 5
Details: 1.8 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 4, 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: 2.3→79.36 Å / Num. obs: 17387 / % possible obs: 99.9 % / Redundancy: 7.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.032 / Rrim(I) all: 0.088 / Χ2: 0.89 / Net I/σ(I): 13.6 / Num. measured all: 137255
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.595 / Num. measured all: 13294 / Num. unique obs: 1678 / CC1/2: 0.936 / Rpim(I) all: 0.223 / Rrim(I) all: 0.636 / Χ2: 0.84 / Net I/σ(I) obs: 3.3

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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: 2.3→79.36 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.888 / SU B: 17.579 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 859 4.9 %RANDOM
Rwork0.22505 ---
obs0.22746 16498 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.142 Å2
Baniso -1Baniso -2Baniso -3
1-5.78 Å20 Å2-0 Å2
2---2.94 Å20 Å2
3----2.84 Å2
Refinement stepCycle: 1 / Resolution: 2.3→79.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 7 81 2488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132444
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152348
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.6563324
X-RAY DIFFRACTIONr_angle_other_deg1.2891.5795423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7735312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.96522.632114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.62315408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4391515
X-RAY DIFFRACTIONr_chiral_restr0.0850.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02501
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_it2.6593.3331257
X-RAY DIFFRACTIONr_mcbond_other2.6413.3311256
X-RAY DIFFRACTIONr_mcangle_it4.3984.9791566
X-RAY DIFFRACTIONr_mcangle_other4.3984.9831567
X-RAY DIFFRACTIONr_scbond_it2.8263.6641187
X-RAY DIFFRACTIONr_scbond_other2.8253.6671188
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6165.3231759
X-RAY DIFFRACTIONr_long_range_B_refined7.23438.4082426
X-RAY DIFFRACTIONr_long_range_B_other7.23238.4212424
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)
11A28990.13
12B28990.13
21A29320.11
22C29320.11
31B28470.13
32C28470.13
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 69 -
Rwork0.276 1198 -
obs--99.92 %
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)
11.2721-0.73380.57923.01420.62156.5616-0.14690.20830.0910.19930.1550.419-0.1952-0.148-0.00810.03920.02050.010.14470.03360.154419.263528.7655.3037
21.4909-0.378-0.76634.9903-1.56172.63470.01110.0024-0.06660.62840.03090.52650.0442-0.0563-0.0420.1797-0.00920.13660.0021-0.00490.17818.98229.472727.382
30.7173-0.37970.99856.6301-1.15761.63310.02210.0333-0.16230.34170.01-0.0901-0.07840.0253-0.03210.0844-0.0002-0.0920.096-0.0250.213440.64419.428122.5317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 141
2X-RAY DIFFRACTION2B37 - 141
3X-RAY DIFFRACTION3C37 - 141

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