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- PDB-8bm3: H207A mutant of E. coli PgpB, a PAP2 type phosphatidyl glycerol p... -

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Basic information

Entry
Database: PDB / ID: 8bm3
TitleH207A mutant of E. coli PgpB, a PAP2 type phosphatidyl glycerol phosphate and C55-PP phosphatase, in complex with farnesyl pyrophosphate
ComponentsPhosphatidylglycerophosphatase B
KeywordsHYDROLASE / C15-PP / PGP phosphatase / lipid metabolism
Function / homology
Function and homology information


diacylglycerol diphosphate phosphatase / diacylglycerol diphosphate phosphatase activity / phosphatidate phosphatase / phosphatidylglycerophosphatase / undecaprenyl-diphosphate phosphatase / phosphatidylglycerol biosynthetic process / phosphatidate phosphatase activity / undecaprenyl-diphosphatase activity / phosphatidylglycerophosphatase activity / glycerophospholipid biosynthetic process ...diacylglycerol diphosphate phosphatase / diacylglycerol diphosphate phosphatase activity / phosphatidate phosphatase / phosphatidylglycerophosphatase / undecaprenyl-diphosphate phosphatase / phosphatidylglycerol biosynthetic process / phosphatidate phosphatase activity / undecaprenyl-diphosphatase activity / phosphatidylglycerophosphatase activity / glycerophospholipid biosynthetic process / phospholipid catabolic process / peptidoglycan biosynthetic process / cell outer membrane / plasma membrane
Similarity search - Function
Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily
Similarity search - Domain/homology
FARNESYL DIPHOSPHATE / Phosphatidylglycerophosphatase B
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsDelbrassine, F. / El Ghachi, M. / Lambion, A. / Herman, R. / Kerff, F.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)MIS 6983808 Belgium
Fonds National de la Recherche Scientifique (FNRS)PDR-40008487 Belgium
CitationJournal: To Be Published
Title: H207A mutant of E. coli PgpB, a PAP2 type phosphatidyl glycerol phosphate and C55-PP phosphatase, in complex with farnesyl pyrophosphate
Authors: Delbrassine, F. / El Ghachi, M. / Lambion, A. / Herman, R. / Kerff, F.
History
DepositionNov 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylglycerophosphatase B
B: Phosphatidylglycerophosphatase B
C: Phosphatidylglycerophosphatase B
D: Phosphatidylglycerophosphatase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5838
Polymers121,0544
Non-polymers1,5294
Water00
1
A: Phosphatidylglycerophosphatase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6462
Polymers30,2641
Non-polymers3821
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylglycerophosphatase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6462
Polymers30,2641
Non-polymers3821
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphatidylglycerophosphatase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6462
Polymers30,2641
Non-polymers3821
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphatidylglycerophosphatase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6462
Polymers30,2641
Non-polymers3821
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.720, 61.620, 144.240
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Phosphatidylglycerophosphatase B / Diacylglycerol pyrophosphate phosphatase / DGPP phosphatase / Phosphatidate phosphatase / ...Diacylglycerol pyrophosphate phosphatase / DGPP phosphatase / Phosphatidate phosphatase / Undecaprenyl pyrophosphate phosphatase / Undecaprenyl-diphosphatase


Mass: 30263.545 Da / Num. of mol.: 4 / Mutation: H207A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: pgpB, b1278, JW1270 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A924, phosphatidylglycerophosphatase, EC: 3.1.3.81, phosphatidate phosphatase, undecaprenyl-diphosphate phosphatase
#2: Chemical
ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
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: 3.26 Å3/Da / Density % sol: 62.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl pH 7, ammonium sulfate 2,77 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.5→47.77 Å / Num. obs: 19616 / % possible obs: 97.6 % / Redundancy: 2.5 % / CC1/2: 0.99 / Net I/σ(I): 4.82
Reflection shellResolution: 3.5→3.71 Å / Redundancy: 2.51 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 3084 / CC1/2: 0.502 / % possible all: 95.8

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Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JWY

6jwy


Resolution: 3.5→47.77 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.863 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.585
RfactorNum. reflection% reflectionSelection details
Rfree0.273 981 5 %RANDOM
Rwork0.237 ---
obs0.239 19616 97.6 %-
Displacement parametersBiso mean: 113.47 Å2
Baniso -1Baniso -2Baniso -3
1-16.4724 Å20 Å23.4172 Å2
2---8.5897 Å20 Å2
3----7.8826 Å2
Refine analyzeLuzzati coordinate error obs: 0.59 Å
Refinement stepCycle: 1 / Resolution: 3.5→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7712 0 96 0 7808
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018056HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0911012HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2660SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1276HARMONIC5
X-RAY DIFFRACTIONt_it8056HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion21.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1016SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10204SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.69 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3136 142 4.99 %
Rwork0.2357 2703 -
all0.2396 2845 -
obs--97.27 %
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)
14.0169-0.83031.12032.55230.37212.65240.06170.49050.1261-0.2668-0.0839-0.1636-0.20770.03910.0222-0.0247-0.10850.15640.34870.0149-0.42930.304988.7194172.1282
23.14840.651-0.68162.7498-0.25983.94410.0484-0.557-0.08810.2009-0.0505-0.17330.1058-0.02880.0022-0.07960.0480.03760.3490.0285-0.367274.654691.1753188.4623
34.89920.7980.89781.48590.89954.380.0840.2048-0.5173-0.1991-0.0416-0.22970.62020.1609-0.0424-0.03560.08160.08680.3161-0.0411-0.424854.323666.5522171.1465
45.6949-0.3207-1.28881.47860.21213.2278-0.0234-0.58940.58270.27940.119-0.2026-0.58040.201-0.09560.0462-0.13830.01890.1662-0.073-0.39129.953113.367189.4243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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