[English] 日本語
Yorodumi
- PDB-2weu: Crystal structure of tryptophan 5-halogenase (PyrH) complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2weu
TitleCrystal structure of tryptophan 5-halogenase (PyrH) complex with substrate tryptophan
ComponentsTRYPTOPHAN 5-HALOGENASE
KeywordsANTIFUNGAL PROTEIN / REGIOSELECTIVITY / TRYPTOPHAN 5-HALOGENASE
Function / homology
Function and homology information


tryptophan 5-halogenase / antibiotic biosynthetic process / monooxygenase activity / nucleotide binding
Similarity search - Function
Flavin-dependent tryptophan halogenase / 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
TRYPTOPHAN / Tryptophan 5-halogenase PyrH
Similarity search - Component
Biological speciesSTREPTOMYCES RUGOSPORUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLeang, K. / Zhu, X. / Naismith, J.H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural Insights in the Regioselectivity in the Enzymatic Chlorination of Tryptophan.
Authors: Zhu, X. / De Laurentis, W. / Leang, K. / Herrmann, J. / Ihlefeld, K. / Van Pee, K.H. / Naismith, J.H.
History
DepositionApr 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: TRYPTOPHAN 5-HALOGENASE
B: TRYPTOPHAN 5-HALOGENASE
C: TRYPTOPHAN 5-HALOGENASE
D: TRYPTOPHAN 5-HALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,6918
Polymers232,8744
Non-polymers8174
Water26,1581452
1
C: TRYPTOPHAN 5-HALOGENASE
D: TRYPTOPHAN 5-HALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8454
Polymers116,4372
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-7.72 kcal/mol
Surface area36620 Å2
MethodPISA
2
A: TRYPTOPHAN 5-HALOGENASE
B: TRYPTOPHAN 5-HALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8454
Polymers116,4372
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-7.16 kcal/mol
Surface area36290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.700, 141.080, 122.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22C
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLNGLN1AA1 - 5111 - 511
211METMETGLNGLN1DD1 - 5111 - 511
121TRPTRPTRPTRP1AE1512
221TRPTRPTRPTRP1DH1512
112METMETGLNGLN1BB1 - 5111 - 511
212METMETGLNGLN1CC1 - 5111 - 511
122TRPTRPTRPTRP1BF1512
222TRPTRPTRPTRP1CG1512
113METMETGLNGLN4AA1 - 5111 - 511
213METMETGLNGLN4BB1 - 5111 - 511
123TRPTRPTRPTRP4AE1512
223TRPTRPTRPTRP4BF1512

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
TRYPTOPHAN 5-HALOGENASE / TRYPTOPHAN 5-HALOGENASE PYRH


Mass: 58218.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SUBSTRATE TRYPTOPHAN IN THE ACTIVE SITE / Source: (gene. exp.) STREPTOMYCES RUGOSPORUS (bacteria) / Strain: LL-42D005 / Production host: PSEUDOMONAS FLUORESCENS (bacteria) / Strain (production host): BL915 / References: UniProt: A4D0H5
#2: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1452 / 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: 2.75 Å3/Da / Density % sol: 55.3 % / Description: NONE
Crystal growpH: 6.2
Details: 0.05M SODIUM CACODYLATE BUFFER PH6.2, 1.4M LI2SO4 0.01M MGCL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 228784 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 1.7→1.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.3 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AQJ

2aqj


Resolution: 1.7→100.5 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.327 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 12099 5 %RANDOM
Rwork0.215 ---
obs0.216 228784 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.87 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.7→100.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15984 0 60 1452 17496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02116499
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211337
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.93922378
X-RAY DIFFRACTIONr_angle_other_deg0.925327166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94651981
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.222.606852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.347152607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.60415163
X-RAY DIFFRACTIONr_chiral_restr0.0860.22321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02118655
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023780
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_it0.6361.59910
X-RAY DIFFRACTIONr_mcbond_other0.211.54053
X-RAY DIFFRACTIONr_mcangle_it1.139215869
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.91336589
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0644.56509
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A6767tight positional0.040.05
12D6767tight positional0.040.05
21B6819tight positional0.040.05
22C6819tight positional0.040.05
31A6760medium positional0.260.5
32B6760medium positional0.260.5
11A6767tight thermal0.140.5
12D6767tight thermal0.140.5
21B6819tight thermal0.150.5
22C6819tight thermal0.150.5
31A6760medium thermal0.892
32B6760medium thermal0.892
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 648 -
Rwork0.322 12251 -
obs--64.62 %
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)
10.6867-0.03170.10250.3951-0.02770.5358-0.0142-0.07710.00660.06220.0104-0.0718-0.03710.0210.00380.0175-0.0056-0.00950.0178-0.0040.0136-0.0348-20.4619-11.3883
20.6109-0.18490.17620.5351-0.1750.3510.00780.0042-0.1280.00530.01940.01080.0806-0.0588-0.02720.0253-0.0192-0.00230.0223-0.00280.0458-22.718-41.4942-35.3028
30.4479-0.2151-0.06660.44630.1430.31560.0280.04470.0455-0.0142-0.0127-0.11-0.02930.0543-0.01530.0084-0.01070.00480.03650.00850.04844.823-11.9881-57.0921
40.46260.0046-0.07030.44150.05960.714-0.00120.0614-0.0866-0.0542-0.0179-0.0110.0957-0.02750.01910.0227-0.00630.00190.0537-0.00630.0171-14.8439-35.8833-81.3471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 511
2X-RAY DIFFRACTION1A1512
3X-RAY DIFFRACTION2B1 - 511
4X-RAY DIFFRACTION2B1512
5X-RAY DIFFRACTION3C1 - 511
6X-RAY DIFFRACTION3C1512
7X-RAY DIFFRACTION4D1 - 511
8X-RAY DIFFRACTION4D1512

+
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