[English] 日本語
Yorodumi
- PDB-3otw: Structural and Functional Studies of Helicobacter pylori Wild-Typ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3otw
TitleStructural and Functional Studies of Helicobacter pylori Wild-Type and Mutated Proteins Phosphopantetheine adenylyltransferase
ComponentsPhosphopantetheine adenylyltransferase
KeywordsTRANSFERASE / protein-ligand complex / di-nucleotide binding fold / CoA synthase / CoA
Function / homology
Function and homology information


pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphopantetheine adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Phosphopantetheine adenylyltransferase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYin, H.S. / Cheng, C.S. / Chen, C.G. / Luo, Y.C. / Chen, W.T. / Cheng, S.Y.
CitationJournal: To be Published
Title: Structural and Functional Studies of Helicobacter pylori Wild-Type and Mutated Proteins Phosphopantetheine adenylyltransferase
Authors: Yin, H.S. / Cheng, C.S. / Chen, C.G. / Luo, Y.C. / Chen, W.T. / Cheng, S.Y.
History
DepositionSep 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphopantetheine adenylyltransferase
B: Phosphopantetheine adenylyltransferase
C: Phosphopantetheine adenylyltransferase
D: Phosphopantetheine adenylyltransferase
E: Phosphopantetheine adenylyltransferase
F: Phosphopantetheine adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,40019
Polymers111,1236
Non-polymers5,27813
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13630 Å2
ΔGint-141 kcal/mol
Surface area38070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.419, 119.846, 124.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Phosphopantetheine adenylyltransferase / Pantetheine-phosphate adenylyltransferase / PPAT / Dephospho-CoA pyrophosphorylase


Mass: 18520.461 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: coaD, kdtB, HP_1475 / Production host: Escherichia coli (E. coli)
References: UniProt: O26010, pantetheine-phosphate adenylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 2M (NH4)2SO4,0.2M Li2SO4, 0.1M Tris, pH 7, EVAPORATION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.796→26.03 Å / Num. all: 107342 / Num. obs: 101966 / % possible obs: 94.99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2
Reflection shellResolution: 1.79→1.85 Å / % possible all: 99.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H1T

1h1t


Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.821 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22198 5376 5 %RANDOM
Rwork0.18626 ---
all0.243 107342 --
obs0.18807 101966 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.759 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7427 0 323 605 8355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227911
X-RAY DIFFRACTIONr_angle_refined_deg1.7952.01410723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5395931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34924.151318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.355151398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2041530
X-RAY DIFFRACTIONr_chiral_restr0.1210.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215644
X-RAY DIFFRACTIONr_mcbond_it0.9371.54673
X-RAY DIFFRACTIONr_mcangle_it1.78427567
X-RAY DIFFRACTIONr_scbond_it2.97133238
X-RAY DIFFRACTIONr_scangle_it4.8424.53156
LS refinement shellResolution: 1.796→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 353 -
Rwork0.239 7111 -
obs--93.97 %
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)
10.9627-0.040.17340.85230.00131.4380.0005-0.08270.09350.1272-0.00350.0941-0.0362-0.04120.00310.1060.01880.02950.0731-0.02320.0283-22.206-2.181-13.376
21.4526-0.14310.36050.77860.17011.10780.04520.14580.1601-0.1057-0.0157-0.0811-0.0448-0.0192-0.02940.096-0.00890.01550.07560.04090.0347-12.535-3.45-40.681
31.0770.0757-0.0942.26550.25440.6806-0.02310.0019-0.1050.04370.0388-0.14830.02320.1034-0.01560.05490.0453-0.00190.0516-0.00570.07540.861-30.407-26.045
41.8145-0.3285-0.17051.4405-0.00050.882-0.0005-0.0403-0.28680.0068-0.03650.2852-0.0325-0.09420.03710.0109-0.02170.00060.07990.0040.1794-44.302-22.382-29.11
51.8627-0.94260.0082.3651-0.8991.68570.06210.335-0.3618-0.3022-0.06060.27490.18060.0324-0.00160.09740.001-0.06260.1388-0.10440.1361-25.122-33.763-47.196
62.29730.47880.23562.02990.52491.3159-0.0796-0.331-0.31310.37040.08980.18460.1064-0.0539-0.01010.15070.06310.07940.10560.10220.1049-20.838-35.314-8.373
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 157
2X-RAY DIFFRACTION2B1 - 156
3X-RAY DIFFRACTION3C1 - 156
4X-RAY DIFFRACTION4D1 - 156
5X-RAY DIFFRACTION5E1 - 156
6X-RAY DIFFRACTION6F1 - 156

+
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