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- PDB-6v8q: Structure of an inner membrane protein required for PhoPQ regulat... -

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Basic information

Entry
Database: PDB / ID: 6v8q
TitleStructure of an inner membrane protein required for PhoPQ regulated increases in outer membrane cardiolipin
ComponentsInner membrane protein YejM
KeywordsMEMBRANE PROTEIN / PbgA / CL transport / PhoPQ / outer membrane barrier
Function / homology
Function and homology information


Inner membrane protein YejM / Inner membrane protein YejM, N-terminal / : / Domain of unknown function (DUF3413) / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Chem-QSR / Inner membrane protein YejM
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69958498172 Å
AuthorsFan, J. / Miller, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1AI030479 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mbio / Year: 2020
Title: Structure of an Inner Membrane Protein Required for PhoPQ-Regulated Increases in Outer Membrane Cardiolipin.
Authors: Fan, J. / Petersen, E.M. / Hinds, T.R. / Zheng, N. / Miller, S.I.
History
DepositionDec 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inner membrane protein YejM
B: Inner membrane protein YejM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,19011
Polymers136,1072
Non-polymers7,0839
Water00
1
A: Inner membrane protein YejM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6156
Polymers68,0531
Non-polymers3,5625
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inner membrane protein YejM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5755
Polymers68,0531
Non-polymers3,5224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.831, 64.847, 146.364
Angle α, β, γ (deg.)90.0, 97.657, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Inner membrane protein YejM / PbgA


Mass: 68053.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Gene: yejM, STM2228 / Production host: Escherichia coli (E. coli) / References: UniProt: P40709
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-QSR / (9Z,21R,24R,30R,33R,44Z)-24,27,30-trihydroxy-18,24,30,36-tetraoxo-19,23,25,29,31,35-hexaoxa-24lambda~5~,30lambda~5~-dip hosphatripentaconta-9,44-diene-21,33-diyl (9Z,9'Z)di-octadec-9-enoate / tetraoleyl-cardiolipin


Mass: 1457.995 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H150O17P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
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: 4.7 Å3/Da / Density % sol: 73.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.4 M (NH4)2SO4, 0.1 M MES (pH 6.5), and 10% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 53782 / % possible obs: 97.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 53.9684885527 Å2 / Rpim(I) all: 0.086 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 763 / CC1/2: 0.31

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PbgA periplasmic domain

Resolution: 2.69958498172→48.342488687 Å / SU ML: 0.37638269452 / Cross valid method: FREE R-VALUE / σ(F): 1.35423336696 / Phase error: 36.5142096275
RfactorNum. reflection% reflection
Rfree0.291137215812 2716 5.05001673422 %
Rwork0.238587401325 51066 -
obs0.241307653313 53782 76.7185427157 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.3367581053 Å2
Refinement stepCycle: LAST / Resolution: 2.69958498172→48.342488687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8973 0 286 0 9259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00976382280199492
X-RAY DIFFRACTIONf_angle_d1.5728065493412911
X-RAY DIFFRACTIONf_chiral_restr0.06391194267451449
X-RAY DIFFRACTIONf_plane_restr0.009445058964381606
X-RAY DIFFRACTIONf_dihedral_angle_d17.65856260263328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6996-2.74870.381055325281130.289256518938201X-RAY DIFFRACTION5.93784683685
2.7487-2.80150.238087599173320.293247127124517X-RAY DIFFRACTION14.9225332971
2.8015-2.85870.339694009321540.281695315934796X-RAY DIFFRACTION23.4612199834
2.8587-2.92090.289987182152760.3134031779861306X-RAY DIFFRACTION37.7905386929
2.9209-2.98880.396381104577870.3193074329151846X-RAY DIFFRACTION52.7565502183
2.9888-3.06350.3334295488121180.3292413300742240X-RAY DIFFRACTION64.4967177243
3.0635-3.14630.354732878781300.3117325124142625X-RAY DIFFRACTION75.4174650972
3.1463-3.23890.389304598141530.3114992300393057X-RAY DIFFRACTION86.3599677159
3.2389-3.34340.334270610161450.2868940552883374X-RAY DIFFRACTION96.7821782178
3.3434-3.46290.3323556730951810.2561615923933476X-RAY DIFFRACTION99.5102040816
3.4629-3.60150.2894086309441860.2322146858713497X-RAY DIFFRACTION99.6213145794
3.6015-3.76540.2907086271351700.2290880463063482X-RAY DIFFRACTION99.4011976048
3.7654-3.96380.2863822093991990.2196110021133449X-RAY DIFFRACTION99.5361527967
3.9638-4.2120.2643544923481750.202522429763494X-RAY DIFFRACTION99.4848156182
4.212-4.5370.2177691334291970.1785619489923498X-RAY DIFFRACTION99.5152168058
4.537-4.99310.2327275678831970.1704568859073509X-RAY DIFFRACTION99.5968825585
4.9931-5.71470.2566801406871930.2140391786593506X-RAY DIFFRACTION99.7841920691
5.7147-7.19610.2559584437991920.2729107582883570X-RAY DIFFRACTION99.8937865109
7.1961-48.340.341904069892180.2605432851653623X-RAY DIFFRACTION99.3019648397
Refinement TLS params.Method: refined / Origin x: 140.315222582 Å / Origin y: -9.40515681879 Å / Origin z: 336.286619625 Å
111213212223313233
T0.333926257296 Å20.0289944236182 Å2-0.0482347584757 Å2-0.29098186035 Å2-0.0256325714667 Å2--0.245939888027 Å2
L0.446410536448 °20.0528740412141 °20.106468155748 °2-0.657123385316 °20.0774801419257 °2--0.27753866925 °2
S-0.00661260648592 Å °0.193960452083 Å °-0.0429849619068 Å °-0.280079624851 Å °0.0404610241692 Å °0.0902676606053 Å °-0.0313415142461 Å °-0.0418960110804 Å °-0.0374906768299 Å °
Refinement TLS groupSelection details: all

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