[English] 日本語
Yorodumi
- PDB-6y1w: Xcc4156, a flavin-dependent halogenase from Xanthomonas campestris -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y1w
TitleXcc4156, a flavin-dependent halogenase from Xanthomonas campestris
ComponentsPutative tryptophan halogenase
KeywordsFLAVOPROTEIN / flavin-dependent halogenase
Function / homology
Function and homology information


monooxygenase activity / nucleotide binding
Similarity search - Function
Flavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / : / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Meso-2,3-Butanediol / (2S,3S)-butane-2,3-diol / PHOSPHATE ION / L(+)-TARTARIC ACID / Tryptophan halogenase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWidmann, C. / Ismail, M. / Sewald, N. / Niemann, H.H.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structure of apo flavin-dependent halogenase Xcc4156 hints at a reason for cofactor-soaking difficulties.
Authors: Widmann, C. / Ismail, M. / Sewald, N. / Niemann, H.H.
History
DepositionFeb 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative tryptophan halogenase
B: Putative tryptophan halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,00022
Polymers116,3672
Non-polymers2,63320
Water20,8971160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint11 kcal/mol
Surface area38410 Å2
Unit cell
Length a, b, c (Å)119.960, 119.960, 70.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLYGLY(chain 'A' and (resid 11 through 22 or resid 24...AA11 - 2114 - 24
12ALAALAALAALA(chain 'A' and (resid 11 through 22 or resid 24...AA24 - 3027 - 33
13SERSERGLNGLN(chain 'A' and (resid 11 through 22 or resid 24...AA33 - 3936 - 42
14ILEILEGLUGLU(chain 'A' and (resid 11 through 22 or resid 24...AA42 - 7145 - 74
15GLUGLUTRPTRP(chain 'A' and (resid 11 through 22 or resid 24...AA74 - 12177 - 124
16ALAALAARGARG(chain 'A' and (resid 11 through 22 or resid 24...AA124 - 131127 - 134
17PHEPHEGLUGLU(chain 'A' and (resid 11 through 22 or resid 24...AA133 - 145136 - 148
18PHEPHETYRTYR(chain 'A' and (resid 11 through 22 or resid 24...AA148 - 167151 - 170
19PHEPHEILEILE(chain 'A' and (resid 11 through 22 or resid 24...AA170 - 187173 - 190
110VALVALVALVAL(chain 'A' and (resid 11 through 22 or resid 24...AA190 - 232193 - 235
111GLUGLUTHRTHR(chain 'A' and (resid 11 through 22 or resid 24...AA235 - 251238 - 254
112VALVALSERSER(chain 'A' and (resid 11 through 22 or resid 24...AA254 - 287257 - 290
113TYRTYRVALVAL(chain 'A' and (resid 11 through 22 or resid 24...AA290 - 299293 - 302
114HISHISARGARG(chain 'A' and (resid 11 through 22 or resid 24...AA302 - 313305 - 316
115PROPROPROPRO(chain 'A' and (resid 11 through 22 or resid 24...AA319322
116ARGARGTRPTRP(chain 'A' and (resid 11 through 22 or resid 24...AA322 - 326325 - 329
117ASNASNLEULEU(chain 'A' and (resid 11 through 22 or resid 24...AA329 - 335332 - 338
118GLYGLYGLUGLU(chain 'A' and (resid 11 through 22 or resid 24...AA338 - 341341 - 344
119GLUGLULEULEU(chain 'A' and (resid 11 through 22 or resid 24...AA344 - 359347 - 362
120PHEPHEPROPRO(chain 'A' and (resid 11 through 22 or resid 24...AA362 - 363365 - 366
121ILEILEASPASP(chain 'A' and (resid 11 through 22 or resid 24...AA366 - 406369 - 409
122SERSERSERSER(chain 'A' and (resid 11 through 22 or resid 24...AA409 - 415412 - 418
123HISHISARGARG(chain 'A' and (resid 11 through 22 or resid 24...AA418 - 419421 - 422
124LEULEULEULEU(chain 'A' and (resid 11 through 22 or resid 24...AA422425
125GLYGLYARGARG(chain 'A' and (resid 11 through 22 or resid 24...AA427 - 428430 - 431
126HISHISPHEPHE(chain 'A' and (resid 11 through 22 or resid 24...AA431 - 437434 - 440
127ASNASNGLNGLN(chain 'A' and (resid 11 through 22 or resid 24...AA440 - 449443 - 452
128VALVALHISHIS(chain 'A' and (resid 11 through 22 or resid 24...AA452 - 457455 - 460
129ALAALAPHEPHE(chain 'A' and (resid 11 through 22 or resid 24...AA460 - 471463 - 474
130GLYGLYPHEPHE(chain 'A' and (resid 11 through 22 or resid 24...AA474 - 492477 - 495
131ARGARGPROPRO(chain 'A' and (resid 11 through 22 or resid 24...AA495 - 502498 - 505
232ARGARGGLYGLY(chain 'B' and (resid 11 through 22 or resid 24...BB11 - 2114 - 24
233ALAALAALAALA(chain 'B' and (resid 11 through 22 or resid 24...BB24 - 3027 - 33
234SERSERGLNGLN(chain 'B' and (resid 11 through 22 or resid 24...BB33 - 3936 - 42
235ILEILEGLUGLU(chain 'B' and (resid 11 through 22 or resid 24...BB42 - 7145 - 74
236GLUGLUTRPTRP(chain 'B' and (resid 11 through 22 or resid 24...BB74 - 12177 - 124
237ALAALAARGARG(chain 'B' and (resid 11 through 22 or resid 24...BB124 - 131127 - 134
238PHEPHEGLUGLU(chain 'B' and (resid 11 through 22 or resid 24...BB133 - 145136 - 148
239PHEPHETYRTYR(chain 'B' and (resid 11 through 22 or resid 24...BB148 - 167151 - 170
240PHEPHEILEILE(chain 'B' and (resid 11 through 22 or resid 24...BB170 - 187173 - 190
241VALVALVALVAL(chain 'B' and (resid 11 through 22 or resid 24...BB190 - 232193 - 235
242GLUGLUTHRTHR(chain 'B' and (resid 11 through 22 or resid 24...BB235 - 251238 - 254
243VALVALSERSER(chain 'B' and (resid 11 through 22 or resid 24...BB254 - 287257 - 290
244TYRTYRVALVAL(chain 'B' and (resid 11 through 22 or resid 24...BB290 - 299293 - 302
245HISHISARGARG(chain 'B' and (resid 11 through 22 or resid 24...BB302 - 313305 - 316
246PROPROPROPRO(chain 'B' and (resid 11 through 22 or resid 24...BB319322
247ARGARGTRPTRP(chain 'B' and (resid 11 through 22 or resid 24...BB322 - 326325 - 329
248ASNASNLEULEU(chain 'B' and (resid 11 through 22 or resid 24...BB329 - 335332 - 338
249GLYGLYGLUGLU(chain 'B' and (resid 11 through 22 or resid 24...BB338 - 341341 - 344
250GLUGLULEULEU(chain 'B' and (resid 11 through 22 or resid 24...BB344 - 359347 - 362
251PHEPHEPROPRO(chain 'B' and (resid 11 through 22 or resid 24...BB362 - 363365 - 366
252ILEILEASPASP(chain 'B' and (resid 11 through 22 or resid 24...BB366 - 406369 - 409
253SERSERSERSER(chain 'B' and (resid 11 through 22 or resid 24...BB409 - 415412 - 418
254HISHISARGARG(chain 'B' and (resid 11 through 22 or resid 24...BB418 - 419421 - 422
255LEULEULEULEU(chain 'B' and (resid 11 through 22 or resid 24...BB422425
256GLYGLYARGARG(chain 'B' and (resid 11 through 22 or resid 24...BB427 - 428430 - 431
257HISHISPHEPHE(chain 'B' and (resid 11 through 22 or resid 24...BB431 - 437434 - 440
258ASNASNGLNGLN(chain 'B' and (resid 11 through 22 or resid 24...BB440 - 449443 - 452
259VALVALHISHIS(chain 'B' and (resid 11 through 22 or resid 24...BB452 - 457455 - 460
260ALAALAPHEPHE(chain 'B' and (resid 11 through 22 or resid 24...BB460 - 471463 - 474
261GLYGLYPHEPHE(chain 'B' and (resid 11 through 22 or resid 24...BB474 - 492477 - 495
262ARGARGPROPRO(chain 'B' and (resid 11 through 22 or resid 24...BB495 - 502498 - 505

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Putative tryptophan halogenase


Mass: 58183.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain B100) (bacteria)
Gene: XCCB100_4156 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0RXY9

-
Non-polymers , 6 types, 1180 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-BUD / (2S,3S)-butane-2,3-diol


Mass: 90.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-BU9 / Meso-2,3-Butanediol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1160 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.87 % / Description: Thin needles
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.6 M Na/K tartrate; 0.1 M MES pH 6.5 protein concentration 10 mg/mL drop size 3 uL drop ratio (protein : reservoir) 2 :1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.917143 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917143 Å / Relative weight: 1
ReflectionResolution: 1.6→45.66 Å / Num. obs: 149524 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 18.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.031 / Rrim(I) all: 0.099 / Net I/σ(I): 17.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.396 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7328 / CC1/2: 0.604 / Rpim(I) all: 0.476 / Rrim(I) all: 1.476 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSMar 15, 2019data reduction
XSCALEMar 15, 2019data scaling
PHASER2.8.2phasing
PHENIX1.14rc3_3199refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FRL

6frl


Resolution: 1.6→45.66 Å / SU ML: 0.1704 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 19.4028 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1893 7318 4.9 %
Rwork0.158 142174 -
obs0.1596 149492 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.36 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7909 0 169 1160 9238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01118569
X-RAY DIFFRACTIONf_angle_d1.126311686
X-RAY DIFFRACTIONf_chiral_restr0.07371258
X-RAY DIFFRACTIONf_plane_restr0.00791534
X-RAY DIFFRACTIONf_dihedral_angle_d10.16246797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.27622860.25574681X-RAY DIFFRACTION99.98
1.62-1.640.2962320.25014822X-RAY DIFFRACTION99.96
1.64-1.660.28742420.2474661X-RAY DIFFRACTION100
1.66-1.680.30282420.23484747X-RAY DIFFRACTION100
1.68-1.70.25422800.21834697X-RAY DIFFRACTION99.98
1.7-1.720.23232620.21454718X-RAY DIFFRACTION100
1.72-1.750.25992380.20514724X-RAY DIFFRACTION99.98
1.75-1.770.24042820.19834726X-RAY DIFFRACTION99.96
1.77-1.80.22612600.19734711X-RAY DIFFRACTION100
1.8-1.830.27782360.19634797X-RAY DIFFRACTION100
1.83-1.860.23482440.19264643X-RAY DIFFRACTION100
1.86-1.90.23541910.194811X-RAY DIFFRACTION100
1.9-1.930.22872360.18264779X-RAY DIFFRACTION100
1.93-1.970.22012470.17544744X-RAY DIFFRACTION100
1.97-2.020.19152590.17144741X-RAY DIFFRACTION100
2.02-2.060.19882360.16164707X-RAY DIFFRACTION100
2.06-2.110.19812220.16174762X-RAY DIFFRACTION100
2.11-2.170.20342440.15854782X-RAY DIFFRACTION100
2.17-2.240.19792500.1574716X-RAY DIFFRACTION100
2.24-2.310.18432260.15144788X-RAY DIFFRACTION100
2.31-2.390.19432260.15034737X-RAY DIFFRACTION100
2.39-2.490.21492360.15694753X-RAY DIFFRACTION100
2.49-2.60.19712040.15414761X-RAY DIFFRACTION100
2.6-2.740.19412190.1524802X-RAY DIFFRACTION100
2.74-2.910.18422760.15434679X-RAY DIFFRACTION100
2.91-3.130.18962120.14944780X-RAY DIFFRACTION100
3.13-3.450.15132580.13494708X-RAY DIFFRACTION100
3.45-3.950.14532420.12644745X-RAY DIFFRACTION100
3.95-4.970.14172390.12234767X-RAY DIFFRACTION100
4.97-45.660.17292910.16274685X-RAY DIFFRACTION99.9

+
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