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- PDB-6y1w: Xcc4156, a flavin-dependent halogenase from Xanthomonas campestris -

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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


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 / Putative 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

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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

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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

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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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

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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

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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

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