[English] 日本語
Yorodumi
- PDB-8bm3: H207A mutant of E. coli PgpB, a PAP2 type phosphatidyl glycerol p... -

+
Open data


ID or keywords:

Loading...

-
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 / phosphatidate phosphatase activity / phosphatidylglycerophosphatase / undecaprenyl-diphosphate phosphatase / undecaprenyl-diphosphatase activity / phosphatidylglycerol biosynthetic process / phosphatidylglycerophosphatase activity / glycerophospholipid biosynthetic process ...diacylglycerol diphosphate phosphatase / diacylglycerol diphosphate phosphatase activity / phosphatidate phosphatase / phosphatidate phosphatase activity / phosphatidylglycerophosphatase / undecaprenyl-diphosphate phosphatase / undecaprenyl-diphosphatase activity / phosphatidylglycerol biosynthetic process / phosphatidylglycerophosphatase activity / glycerophospholipid biosynthetic process / phospholipid catabolic process / plasma membrane => GO:0005886 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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, diacylglycerol diphosphate phosphatase, phosphatidate phosphatase, undecaprenyl-diphosphate phosphatase
#2: Chemical
ChemComp-FPP / FARNESYL DIPHOSPHATE / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more