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- PDB-5i5h: Ecoli global domain 245-586 -

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Basic information

Entry
Database: PDB / ID: 5i5h
TitleEcoli global domain 245-586
ComponentsInner membrane protein YejM
KeywordsMEMBRANE PROTEIN / Ecoli 245-586
Function / homologyInner membrane protein YejM / Inner membrane protein YejM, N-terminal / Domain of unknown function (DUF3413) / sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / plasma membrane / Inner membrane protein YejM
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDong, C. / Dong, H.
CitationJournal: Sci Rep / Year: 2016
Title: Structural insights into cardiolipin transfer from the Inner membrane to the outer membrane by PbgA in Gram-negative bacteria.
Authors: Dong, H. / Zhang, Z. / Tang, X. / Huang, S. / Li, H. / Peng, B. / Dong, C.
History
DepositionFeb 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inner membrane protein YejM


Theoretical massNumber of molelcules
Total (without water)67,3651
Polymers67,3651
Non-polymers00
Water8,917495
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.860, 56.860, 191.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-820-

HOH

21A-974-

HOH

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Components

#1: Protein Inner membrane protein YejM


Mass: 67364.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: yejM, yejN, b2188, JW2176 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AD27
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / 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

Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: 0.2 M lithium sulphate, 0.1 M sodium acetate pH 4.3 and 48% PEG400
PH range: 4.0-4.6

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.65→47.83 Å / % possible obs: 99.6 % / Redundancy: 9.6 % / Net I/σ(I): 17.8
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 9.6 % / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I5D

5i5d


Resolution: 1.65→47.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.04 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.023 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23743 2208 5 %RANDOM
Rwork0.17528 ---
obs0.17829 41797 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.212 Å2
Baniso -1Baniso -2Baniso -3
1-25.61 Å20 Å20 Å2
2--25.61 Å20 Å2
3----51.21 Å2
Refinement stepCycle: LAST / Resolution: 1.65→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 0 495 3099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192690
X-RAY DIFFRACTIONr_bond_other_d0.0020.022478
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9373659
X-RAY DIFFRACTIONr_angle_other_deg1.05935670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9575329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6223.986138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56515434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5321521
X-RAY DIFFRACTIONr_chiral_restr0.0930.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213127
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02676
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_it2.2392.5641319
X-RAY DIFFRACTIONr_mcbond_other2.2162.5611318
X-RAY DIFFRACTIONr_mcangle_it2.353.8361647
X-RAY DIFFRACTIONr_mcangle_other2.3573.8391648
X-RAY DIFFRACTIONr_scbond_it2.5753.0031371
X-RAY DIFFRACTIONr_scbond_other2.5753.0031372
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.654.332013
X-RAY DIFFRACTIONr_long_range_B_refined5.124.3833585
X-RAY DIFFRACTIONr_long_range_B_other3.90322.5563292
X-RAY DIFFRACTIONr_rigid_bond_restr2.15935167
X-RAY DIFFRACTIONr_sphericity_free32.1325136
X-RAY DIFFRACTIONr_sphericity_bonded10.54655478
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 139 -
Rwork0.444 2781 -
obs--90.43 %
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)
10.126-0.05940.02860.49880.09950.27980.0133-0.0258-0.0056-0.0243-0.02320.0370.00810.02480.00990.031-0.0262-0.0090.03810.0120.220.852637.576414.0851
20.232-0.05020.03510.36250.08510.1292-0.0092-0.0415-0.0368-0.0447-0.0080.0203-0.0103-0.00250.01720.0467-0.0347-0.0030.04580.01470.22330.63837.12213.2541
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A246 - 575
2X-RAY DIFFRACTION2B576 - 1084

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