5EX8

Structure of P450 StaF from glycopeptide antibiotic A47934 biosynthesis; ethylene glycol cryo

> Summary

Summary for 5EX8

DescriptorCytochrome P450, PROTOPORPHYRIN IX CONTAINING FE, 1,2-ETHANEDIOL, ... (4 entities in total)
Functional Keywordscytochrome p450, monooxygenase, phenolic coupling, glycopeptide antibiotic biosynthesis, oxidoreductase
Biological sourceStreptomyces toyocaensis
Total number of polymer chains1
Total molecular weight48947.18
Authors
Cryle, M.J.,Ulrich, V. (deposition date: 2015-11-23, release date: 2017-01-11, Last modification date: 2017-03-01)
Primary citation
Ulrich, V.,Brieke, C.,Cryle, M.J.
Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934.
Beilstein J Org Chem, 12:2849-2864, 2016
PubMed: 28144358 (PDB entries with the same primary citation)
DOI: 10.3762/bjoc.12.284
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.1 Å)
?

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.22980.5%0.9%4.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5ex8
no rotation
Molmil generated image of 5ex8
rotated about x axis by 90°
Molmil generated image of 5ex8
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ACytochrome P450polymer42447337.61
UniProt (Q8KLL7)
Pfam (PF00067)
Streptomyces toyocaensisStaF
PROTOPORPHYRIN IX CONTAINING FEnon-polymer616.51
1,2-ETHANEDIOLnon-polymer62.116
waterwater18.0268

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight47337.6
Non-Polymers*Number of molecules17
Total molecular weight1609.6
All*Total molecular weight48947.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.1 Å)

Cell axes110.050110.05093.650
Cell angles90.0090.00120.00
SpacegroupP 31 2 1
Resolution limits47.67 - 2.10
the highest resolution shell value2.155 - 2.100
R-factor0.19565
R-work0.19392
the highest resolution shell value0.225
R-free0.22900
the highest resolution shell value0.286
RMSD bond length0.009
RMSD bond angle1.193

Data Collection Statistics

Resolution limits50.00 - 2.10
the highest resolution shell value -
Number of reflections36757
Rmerge_l_obs0.072
the highest resolution shell value0.308
Completeness95.1
Redundancy6.2
the highest resolution shell value6

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP5.2277

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

?

Functional Information from GO Data

ChainGOidnamespacecontents
A0020037molecular_functionheme binding
A0005506molecular_functioniron ion binding
A0004497molecular_functionmonooxygenase activity
A0016705molecular_functionoxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
?

Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC123binding site for residue HEM A 401
ChainResidue
ALEU85
ATHR86
AHIS93
AARG97
APHE228
AALA233
AGLN236
AVAL237
AASP279
ATHR282
AHIS283
AARG285
ALEU308
AALA334
APHE335
AGLY336
AHIS340
ACYS342
AGLY344
AEDO402
AEDO407
AHOH557
AHOH566

AC28binding site for residue EDO A 402
ChainResidue
ALEU-15
APHE228
AALA232
AALA233
AGLN236
AHEM401
AEDO407
AHOH757

AC34binding site for residue EDO A 403
ChainResidue
AHIS337
AGLY338
AHOH541
AHOH580

AC45binding site for residue EDO A 404
ChainResidue
AARG18
AGLU250
ALEU368
APRO371
AARG373

AC52binding site for residue EDO A 405
ChainResidue
AASP162
AILE166

AC63binding site for residue EDO A 406
ChainResidue
AARG259
AHIS361
APRO364

AC77binding site for residue EDO A 407
ChainResidue
APHE228
AGLN236
AASP279
AHIS283
AHEM401
AEDO402
AHOH757

AC85binding site for residue EDO A 408
ChainResidue
AASP370
AARG373
AGLU374
ALEU388
AHOH509

AC95binding site for residue EDO A 409
ChainResidue
AVAL137
ATRP142
AASP235
AARG239
AHOH505

AD15binding site for residue EDO A 410
ChainResidue
AARG58
AGLN59
AGLY62
ASER63
AHIS337

AD25binding site for residue EDO A 411
ChainResidue
AGLN110
AARG113
ALYS353
AHOH536
AHOH574

AD33binding site for residue EDO A 412
ChainResidue
AARG115
AASP122
AARG157

AD42binding site for residue EDO A 413
ChainResidue
AASP64
ALYS65

AD55binding site for residue EDO A 414
ChainResidue
AILE79
ATYR88
AGLU221
AHOH529
AHOH693

AD66binding site for residue EDO A 415
ChainResidue
ALEU-18
ATRP81
APRO82
AMET187
AALA220
AGLY224

AD74binding site for residue EDO A 416
ChainResidue
AGLY131
AGLY132
AASP390
ATRP391

AD82binding site for residue EDO A 417
ChainResidue
AARG165
ASER201

?

Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
EDO_5ex8_A_404101,2-ETHANEDIOL binding site
ChainResidueligand
AARG18EDO: 1,2-ETHANEDIOL
ATRP246EDO: 1,2-ETHANEDIOL
AGLU250EDO: 1,2-ETHANEDIOL
ALEU368EDO: 1,2-ETHANEDIOL
AASP370-ILE375EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_41051,2-ETHANEDIOL binding site
ChainResidueligand
AARG58-GLN59EDO: 1,2-ETHANEDIOL
AGLY62-SER63EDO: 1,2-ETHANEDIOL
AHIS337EDO: 1,2-ETHANEDIOL

HEM_5ex8_A_40134PROTOPORPHYRIN IX CONTAINING FE binding site
ChainResidueligand
ALEU61HEM: PROTOPORPHYRIN IX CONTAINING FE
ALEU85-THR86HEM: PROTOPORPHYRIN IX CONTAINING FE
AHIS93HEM: PROTOPORPHYRIN IX CONTAINING FE
AARG97HEM: PROTOPORPHYRIN IX CONTAINING FE
APHE104HEM: PROTOPORPHYRIN IX CONTAINING FE
ATHR149HEM: PROTOPORPHYRIN IX CONTAINING FE
APHE228-VAL229HEM: PROTOPORPHYRIN IX CONTAINING FE
AALA233-ALA234HEM: PROTOPORPHYRIN IX CONTAINING FE
AGLN236-VAL237HEM: PROTOPORPHYRIN IX CONTAINING FE
ALEU240HEM: PROTOPORPHYRIN IX CONTAINING FE
AMET273HEM: PROTOPORPHYRIN IX CONTAINING FE
ATHR278-ASP279HEM: PROTOPORPHYRIN IX CONTAINING FE
ATHR282-HIS283HEM: PROTOPORPHYRIN IX CONTAINING FE
AARG285HEM: PROTOPORPHYRIN IX CONTAINING FE
ALEU308HEM: PROTOPORPHYRIN IX CONTAINING FE
ALEU333-GLY336HEM: PROTOPORPHYRIN IX CONTAINING FE
AILE339-GLY344HEM: PROTOPORPHYRIN IX CONTAINING FE
AMET347-ALA348HEM: PROTOPORPHYRIN IX CONTAINING FE
AMET351HEM: PROTOPORPHYRIN IX CONTAINING FE

EDO_5ex8_A_41321,2-ETHANEDIOL binding site
ChainResidueligand
AASP64-LYS65EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_41461,2-ETHANEDIOL binding site
ChainResidueligand
AILE79EDO: 1,2-ETHANEDIOL
APRO82-GLY83EDO: 1,2-ETHANEDIOL
ATYR88EDO: 1,2-ETHANEDIOL
ALEU96EDO: 1,2-ETHANEDIOL
AGLU221EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_41591,2-ETHANEDIOL binding site
ChainResidueligand
ATRP81-GLY83EDO: 1,2-ETHANEDIOL
AMET187EDO: 1,2-ETHANEDIOL
ALYS191EDO: 1,2-ETHANEDIOL
AALA220-GLU221EDO: 1,2-ETHANEDIOL
ATHR223-GLY224EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_40751,2-ETHANEDIOL binding site
ChainResidueligand
ATHR86EDO: 1,2-ETHANEDIOL
APHE228EDO: 1,2-ETHANEDIOL
AGLN236EDO: 1,2-ETHANEDIOL
AASP279EDO: 1,2-ETHANEDIOL
AHIS283EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_41171,2-ETHANEDIOL binding site
ChainResidueligand
AHIS106EDO: 1,2-ETHANEDIOL
AMET109-GLN110EDO: 1,2-ETHANEDIOL
AARG113EDO: 1,2-ETHANEDIOL
AALA346EDO: 1,2-ETHANEDIOL
ALEU350EDO: 1,2-ETHANEDIOL
ALYS353EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_41271,2-ETHANEDIOL binding site
ChainResidueligand
AARG115EDO: 1,2-ETHANEDIOL
AGLN118-ILE119EDO: 1,2-ETHANEDIOL
AASP122EDO: 1,2-ETHANEDIOL
AALA143EDO: 1,2-ETHANEDIOL
APRO147EDO: 1,2-ETHANEDIOL
AARG157EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_41651,2-ETHANEDIOL binding site
ChainResidueligand
AGLU128EDO: 1,2-ETHANEDIOL
AGLY131-GLY132EDO: 1,2-ETHANEDIOL
AASP390-TRP391EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_40971,2-ETHANEDIOL binding site
ChainResidueligand
AVAL137EDO: 1,2-ETHANEDIOL
ATRP142EDO: 1,2-ETHANEDIOL
AARG171EDO: 1,2-ETHANEDIOL
AASP235EDO: 1,2-ETHANEDIOL
AARG239EDO: 1,2-ETHANEDIOL
AASP383-VAL384EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_40561,2-ETHANEDIOL binding site
ChainResidueligand
AASP159EDO: 1,2-ETHANEDIOL
AASP162-LEU163EDO: 1,2-ETHANEDIOL
AILE166EDO: 1,2-ETHANEDIOL
ALYS185EDO: 1,2-ETHANEDIOL
ATYR189EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_41751,2-ETHANEDIOL binding site
ChainResidueligand
AARG165-ILE166EDO: 1,2-ETHANEDIOL
AALA169EDO: 1,2-ETHANEDIOL
AALA182EDO: 1,2-ETHANEDIOL
ALYS185EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_40251,2-ETHANEDIOL binding site
ChainResidueligand
APHE228EDO: 1,2-ETHANEDIOL
AALA232-ALA233EDO: 1,2-ETHANEDIOL
AGLN236EDO: 1,2-ETHANEDIOL
ACYS342EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_40661,2-ETHANEDIOL binding site
ChainResidueligand
AARG259-GLU260EDO: 1,2-ETHANEDIOL
AALA360-ARG362EDO: 1,2-ETHANEDIOL
APRO364EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_40351,2-ETHANEDIOL binding site
ChainResidueligand
AGLY336-GLY338EDO: 1,2-ETHANEDIOL
AHIS341EDO: 1,2-ETHANEDIOL
AARG345EDO: 1,2-ETHANEDIOL

EDO_5ex8_A_40881,2-ETHANEDIOL binding site
ChainResidueligand
ALEU368EDO: 1,2-ETHANEDIOL
AASP370EDO: 1,2-ETHANEDIOL
AARG373-ILE375EDO: 1,2-ETHANEDIOL
AALA386-LEU388EDO: 1,2-ETHANEDIOL

?

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
?

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
?

Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2017 Protein Data Bank Japan