[English] 日本語
Yorodumi
- PDB-3ne9: Chronobacterium ammoiniagenes apo-ACPS structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ne9
TitleChronobacterium ammoiniagenes apo-ACPS structure
ComponentsPhosphopantetheine protein transferase, Ppt1p
KeywordsTRANSFERASE / acyl carrier protein synthase / acyl carrier protein / fatty acid synthase / ACPS / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / Structural Genomics
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
4'-phosphopantetheinyl transferase domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesCorynebacterium ammoniagenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsGokulan, K. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations.
Authors: Gokulan, K. / Aggarwal, A. / Shipman, L. / Besra, G.S. / Sacchettini, J.C.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 25, 2012Group: Database references / Structure summary
Revision 1.3Sep 9, 2020Group: Derived calculations / Structure summary / Category: struct / struct_conn / struct_site
Item: _struct.title / _struct_conn.pdbx_leaving_atom_flag ..._struct.title / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphopantetheine protein transferase, Ppt1p
B: Phosphopantetheine protein transferase, Ppt1p
C: Phosphopantetheine protein transferase, Ppt1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2557
Polymers50,8703
Non-polymers3844
Water1,31573
1
A: Phosphopantetheine protein transferase, Ppt1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1493
Polymers16,9571
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphopantetheine protein transferase, Ppt1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1493
Polymers16,9571
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphopantetheine protein transferase, Ppt1p


Theoretical massNumber of molelcules
Total (without water)16,9571
Polymers16,9571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.399, 59.002, 153.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Phosphopantetheine protein transferase, Ppt1p


Mass: 16956.828 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium ammoniagenes (bacteria)
Gene: ACPS, PPT1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O31302
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsACCORDING TO THE AUTHORS THE DISCREPANCIES MAY BE DUE TO ERRORS AT THE GENOMIC SEQUENCING

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growMethod: evaporation / pH: 6.5
Details: 100 mM MES buffer pH 6.5, 0.2 M ammonium sulfate, 30% PEG MME 5K, EVAPORATION

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9792, 0.97906, 0.96380
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.979061
30.96381
ReflectionResolution: 2.48→30 Å / Num. all: 16681 / Num. obs: 16681 / % possible obs: 94.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.35
Reflection shellResolution: 2.48→2.5 Å / Redundancy: 0.76 % / Mean I/σ(I) obs: 4.6 / % possible all: 75.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.866 / SU B: 10.148 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.607 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 842 5.1 %RANDOM
Rwork0.20483 ---
obs0.20811 15717 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.139 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2--1.12 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 20 73 3318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0213304
X-RAY DIFFRACTIONr_bond_other_d0.0040.023055
X-RAY DIFFRACTIONr_angle_refined_deg2.571.9494472
X-RAY DIFFRACTIONr_angle_other_deg1.27437063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3495405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2310.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023689
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02700
X-RAY DIFFRACTIONr_nbd_refined0.2210.2692
X-RAY DIFFRACTIONr_nbd_other0.2610.23664
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1080.22153
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4491.52043
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.64123263
X-RAY DIFFRACTIONr_scbond_it3.64731261
X-RAY DIFFRACTIONr_scangle_it6.0744.51209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 57
Rwork0.214 1118

+
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