[English] 日本語
Yorodumi
- PDB-6d8j: Mycobacterium tuberculosis polyketide synthase 13 N-terminal acyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d8j
TitleMycobacterium tuberculosis polyketide synthase 13 N-terminal acyl carrier protein domain
ComponentsPolyketide synthase
KeywordsBIOSYNTHETIC PROTEIN / PKS13 / N-terminal ACP
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Azurin / : / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxin / Phosphopantetheine attachment site
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsTang, S. / Sacchettini, J.
CitationJournal: To be Published
Title: Mycobacterium tuberculosis polyketide synthase 13 N-terminal acyl carrier protein domain
Authors: Tang, S. / Sacchettini, J.
History
DepositionApr 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8078
Polymers9,3511
Non-polymers4577
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-17 kcal/mol
Surface area5010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.972, 51.972, 74.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-104-

CA

-
Components

#1: Protein Polyketide synthase


Mass: 9350.620 Da / Num. of mol.: 1
Fragment: N-terminal acyl carrier protein domain (UNP residues 10-93)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: LH57_20715 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A089QYU6, UniProt: I6X8D2*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium acetate, 0.1 M sodium cacodylate, pH 6.5, 18-24% PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2013
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 12933 / % possible obs: 96.7 % / Redundancy: 9.5 % / Biso Wilson estimate: 19.27 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.026 / Rrim(I) all: 0.083 / Χ2: 1.109 / Net I/σ(I): 7.2 / Num. measured all: 122439
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.63-1.669.50.5466300.9040.1830.5780.598.4
1.66-1.699.30.4736540.9120.1610.5010.50499.2
1.69-1.729.60.3876320.9440.130.4090.5698.9
1.72-1.769.40.3716420.9440.1250.3920.54598.6
1.76-1.799.50.3196500.9630.1070.3380.698.6
1.79-1.849.50.2796360.970.0940.2960.63598.5
1.84-1.889.50.2266440.9660.0760.240.74398.5
1.88-1.939.40.2146590.9810.0710.2260.92398.5
1.93-1.999.60.1726280.9810.0570.1810.96598.1
1.99-2.059.50.1456500.9890.0480.1531.197.6
2.05-2.139.60.1386350.9920.0450.1451.26196.9
2.13-2.219.50.1186410.9910.0390.1241.34697.4
2.21-2.319.60.126450.9920.040.1271.47696.6
2.31-2.439.60.1066430.9940.0340.1111.74196.4
2.43-2.599.50.0956460.9950.0310.11.7495.8
2.59-2.799.50.0866380.9970.0280.091.82995.5
2.79-3.079.50.0756600.9970.0250.0791.71895.1
3.07-3.519.30.0656490.9970.0220.0691.74595
3.51-4.429.40.0526560.9980.0170.0551.43593.6
4.42-5090.0376950.9980.0130.040.76689.2

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6D8I

6d8i


Resolution: 1.63→30.276 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.183 1286 9.96 %Random selection
Rwork0.1628 11631 --
obs0.1649 12917 96.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146 Å2 / Biso mean: 25.1454 Å2 / Biso min: 12.26 Å2
Refinement stepCycle: final / Resolution: 1.63→30.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms590 0 46 131 767
Biso mean--43.45 35.37 -
Num. residues----79
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006643
X-RAY DIFFRACTIONf_angle_d0.761875
X-RAY DIFFRACTIONf_chiral_restr0.049105
X-RAY DIFFRACTIONf_plane_restr0.005113
X-RAY DIFFRACTIONf_dihedral_angle_d13.586394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6296-1.69480.20961400.18941267140799
1.6948-1.7720.21521420.18541294143699
1.772-1.86540.19271450.17231283142899
1.8654-1.98220.1941460.16761293143999
1.9822-2.13520.1781460.14821274142098
2.1352-2.350.16651350.15281294142997
2.35-2.68990.19351450.16461277142296
2.6899-3.38830.19311400.16511300144095
3.3883-30.28120.16821470.161349149693
Refinement TLS params.Method: refined / Origin x: 43.7057 Å / Origin y: 22.3604 Å / Origin z: 12.1276 Å
111213212223313233
T0.1503 Å20.005 Å2-0.004 Å2-0.1473 Å20.0033 Å2--0.1428 Å2
L1.381 °20.8135 °2-0.706 °2-0.6883 °20.0183 °2--1.3652 °2
S-0.0468 Å °0.0851 Å °0.0394 Å °-0.0849 Å °0.0711 Å °-0.015 Å °-0.0621 Å °-0.0412 Å °0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA15 - 93
2X-RAY DIFFRACTION1allB1 - 5
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 131
5X-RAY DIFFRACTION1allD1

+
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