[English] 日本語
Yorodumi
- PDB-7pdi: Crystal structure of the holo-acyl carrier protein (holo-AcpP) fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pdi
TitleCrystal structure of the holo-acyl carrier protein (holo-AcpP) from Pseudomonas putida KT2440. Produced as an apo/holo mixture.
ComponentsAcyl carrier protein
KeywordsLIPID BINDING PROTEIN / phosphopantetheine / acyl-binding / fatty acid transport / holo-AcpP
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / cytosol
Similarity search - Function
Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Acyl carrier protein
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsVenter, P. / Sewell, B.T. / Trindade, M. / Mandyoli, L. / van Zyl, L.
Funding support United Kingdom, South Africa, 3items
OrganizationGrant numberCountry
Global Challenges Research FundGCRF-START ST/R002754/1 United Kingdom
National Research Foundation in South Africa110428 South Africa
Council of Scientific & Industrial Research (CSIR)DSI-CSIR IBS South Africa
CitationJournal: To Be Published
Title: Crystal structure of the holo-acyl carrier protein (holo-AcpP) from Pseudomonas putida. Produced as an apo/holo mixture.
Authors: Venter, P.
History
DepositionAug 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.name / _chem_comp.pdbx_synonyms

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)9,3401
Polymers9,3401
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Native gel electrophoresis confirmed that the acyl carrier protein was a mixture of the apo-AcpP and holo-AcpP form.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.492, 56.973, 61.937
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-129-

HOH

21A-133-

HOH

-
Components

#1: Protein Acyl carrier protein / ACP


Mass: 9340.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: holo-acyl carrier protein (holo-AcpP). The protein was produced and crystallized as an apo/holo-AcpP mixture and therefore has lower occupancy of the posttranslationally attached ligand ...Details: holo-acyl carrier protein (holo-AcpP). The protein was produced and crystallized as an apo/holo-AcpP mixture and therefore has lower occupancy of the posttranslationally attached ligand (phosphopantetheine (4HH))
Source: (gene. exp.) Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440) (bacteria)
Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: acpP, PP_1915 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q88LL5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% (v/v) PEG 500 MME, 10% (w/v) PEG 20000, 0.1 M Tris Bicine buffer, pH 8.5, 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.69→30.988 Å / Num. obs: 9120 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.9994 / Rmerge(I) obs: 0.0705 / Net I/σ(I): 14.05
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 9.7 % / Num. unique obs: 459 / CC1/2: 0.397 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALS2.210-g6dafd9427data reduction
DIALS2.210-g6dafd9427data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T8K

1t8k


Resolution: 1.69→30.988 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.189 / SU B: 4.768 / SU ML: 0.136 / Average fsc free: 0.7495 / Average fsc work: 0.7582 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2448 874 9.583 %
Rwork0.2047 8246 -
all0.208 --
obs-9120 99.989 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.778 Å2
Baniso -1Baniso -2Baniso -3
1-0.027 Å20 Å2-0 Å2
2--0.061 Å20 Å2
3----0.088 Å2
Refinement stepCycle: LAST / Resolution: 1.69→30.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms651 0 0 37 688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.013656
X-RAY DIFFRACTIONr_bond_other_d0.0010.017625
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.655889
X-RAY DIFFRACTIONr_angle_other_deg1.3411.5811458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.029581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.66426.36433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76215119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.979151
X-RAY DIFFRACTIONr_chiral_restr0.0690.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02107
X-RAY DIFFRACTIONr_nbd_refined0.2020.2123
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.2544
X-RAY DIFFRACTIONr_nbtor_refined0.1540.2334
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2287
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.221
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.28
X-RAY DIFFRACTIONr_nbd_other0.2170.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2810.210
X-RAY DIFFRACTIONr_mcbond_it3.5254.197327
X-RAY DIFFRACTIONr_mcbond_other3.5134.18326
X-RAY DIFFRACTIONr_mcangle_it5.0316.271407
X-RAY DIFFRACTIONr_mcangle_other5.0296.293408
X-RAY DIFFRACTIONr_scbond_it6.2245.348329
X-RAY DIFFRACTIONr_scbond_other6.2165.362330
X-RAY DIFFRACTIONr_scangle_it9.3277.674482
X-RAY DIFFRACTIONr_scangle_other9.3177.69483
X-RAY DIFFRACTIONr_lrange_it10.96652.186677
X-RAY DIFFRACTIONr_lrange_other10.97452.296676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.7340.472590.496614X-RAY DIFFRACTION100
1.734-1.7810.494570.446572X-RAY DIFFRACTION100
1.781-1.8330.365510.405578X-RAY DIFFRACTION100
1.833-1.8890.447730.361539X-RAY DIFFRACTION100
1.889-1.9510.348530.29532X-RAY DIFFRACTION100
1.951-2.0190.309520.283530X-RAY DIFFRACTION100
2.019-2.0950.277490.237490X-RAY DIFFRACTION100
2.095-2.180.273620.211473X-RAY DIFFRACTION100
2.18-2.2770.223460.203479X-RAY DIFFRACTION100
2.277-2.3870.275620.179434X-RAY DIFFRACTION100
2.387-2.5160.207490.167410X-RAY DIFFRACTION100
2.516-2.6680.217430.19404X-RAY DIFFRACTION100
2.668-2.8510.263340.2392X-RAY DIFFRACTION100
2.851-3.0770.232300.202359X-RAY DIFFRACTION100
3.077-3.3680.295360.193330X-RAY DIFFRACTION100
3.368-3.7620.269300.174304X-RAY DIFFRACTION100
3.762-4.3350.135320.137263X-RAY DIFFRACTION100
4.335-5.290.209280.154236X-RAY DIFFRACTION100
5.29-7.3970.203190.26186X-RAY DIFFRACTION100
7.397-30.9880.36790.228121X-RAY DIFFRACTION99.2366

+
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