[English] 日本語
Yorodumi
- PDB-5dbj: Crystal structure of halogenase PltA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dbj
TitleCrystal structure of halogenase PltA
ComponentsFADH2-dependent halogenase PltA
KeywordsFLAVOPROTEIN / halogenase / FAD / Rossmann fold / pyoluteorin
Function / homology
Function and homology information


1H-pyrrole-2-carbonyl-[peptidyl-carrier protein] chlorinase / alkylhalidase activity / nucleotide binding
Similarity search - Function
Flavin-dependent halogenase / Tryptophan halogenase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 1H-pyrrole-2-carbonyl-[peptidyl-carrier protein] chlorinase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPang, A.H. / Tsodikov, O.V.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal structure of halogenase PltA from the pyoluteorin biosynthetic pathway.
Authors: Pang, A.H. / Garneau-Tsodikova, S. / Tsodikov, O.V.
History
DepositionAug 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: FADH2-dependent halogenase PltA
A: FADH2-dependent halogenase PltA
B: FADH2-dependent halogenase PltA
C: FADH2-dependent halogenase PltA
D: FADH2-dependent halogenase PltA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,20219
Polymers256,9555
Non-polymers4,24714
Water1,982110
1
E: FADH2-dependent halogenase PltA
hetero molecules

E: FADH2-dependent halogenase PltA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4958
Polymers102,7822
Non-polymers1,7136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1880 Å2
ΔGint-7 kcal/mol
Surface area33320 Å2
MethodPISA
2
A: FADH2-dependent halogenase PltA
B: FADH2-dependent halogenase PltA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4958
Polymers102,7822
Non-polymers1,7136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-7 kcal/mol
Surface area33420 Å2
MethodPISA
3
C: FADH2-dependent halogenase PltA
D: FADH2-dependent halogenase PltA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4607
Polymers102,7822
Non-polymers1,6775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-9 kcal/mol
Surface area33480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.934, 94.981, 102.145
Angle α, β, γ (deg.)90.00, 91.21, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
FADH2-dependent halogenase PltA


Mass: 51391.062 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477) (bacteria)
Strain: Pf-5 / ATCC BAA-477 / Gene: pltA, PFL_2787 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4KCZ0, alkylhalidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-Tris propane, pH 7.0, 50 mM magnesium sulfate heptahydrate, 20% w/v PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 56814 / % possible obs: 95.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.6
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.59

-
Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NIX

3nix


Resolution: 2.75→40 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.887 / SU B: 51.317 / SU ML: 0.447 / Cross valid method: THROUGHOUT / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29165 2916 5.1 %RANDOM
Rwork0.23886 ---
obs0.24147 54814 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.222 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å20 Å21.24 Å2
2--1.28 Å20 Å2
3----5.23 Å2
Refinement stepCycle: LAST / Resolution: 2.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17370 0 274 110 17754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01918062
X-RAY DIFFRACTIONr_bond_other_d0.0060.0216915
X-RAY DIFFRACTIONr_angle_refined_deg1.231.96224463
X-RAY DIFFRACTIONr_angle_other_deg0.882338903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83252169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04724.048872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.779153043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.20315107
X-RAY DIFFRACTIONr_chiral_restr0.0670.22628
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220333
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024297
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.634.5358699
X-RAY DIFFRACTIONr_mcbond_other0.634.5358698
X-RAY DIFFRACTIONr_mcangle_it1.1596.80210861
X-RAY DIFFRACTIONr_mcangle_other1.1596.80210862
X-RAY DIFFRACTIONr_scbond_it0.3954.5679362
X-RAY DIFFRACTIONr_scbond_other0.3954.5679363
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7726.82613602
X-RAY DIFFRACTIONr_long_range_B_refined3.16936.17720826
X-RAY DIFFRACTIONr_long_range_B_other3.16736.16720820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 245 -
Rwork0.313 3976 -
obs--95.33 %
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)
11.44330.28430.11441.2010.9793.16130.1490.06970.30580.14360.1094-0.23310.15150.1158-0.25850.2764-0.0137-0.07660.02040.03260.386436.4546-37.37195.1423
21.98570.0450.9941.3215-0.56963.0763-0.4628-0.79820.4744-0.00540.2003-0.1337-0.6459-1.39740.26250.36850.3205-0.16360.7753-0.25860.21455.2148-26.0778-24.7667
31.41150.4475-0.21141.3287-0.08931.24950.0117-0.1853-0.22310.09470.00330.06870.0776-0.0524-0.0150.3970.0392-0.14950.06390.04870.194581.8006-41.402531.1515
43.2394-0.17240.61061.10560.30330.9482-0.08090.410.0319-0.38050.10770.1049-0.09270.1612-0.02680.5957-0.0703-0.10510.07160.0030.162882.001-36.3491-12.6601
51.98190.54220.04491.33940.01171.3047-0.11780.089-0.31460.02230.0571-0.15120.04850.28910.06070.30170.0473-0.00990.0767-0.01450.217421.0712-57.238847.8346
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 438
2X-RAY DIFFRACTION2B2 - 438
3X-RAY DIFFRACTION3C2 - 438
4X-RAY DIFFRACTION4D2 - 438
5X-RAY DIFFRACTION5E2 - 438

+
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://pdbjlvh1.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