5EX9

Structure of P450 StaF from glycopeptide antibiotic A47934 biosynthesis; glycerol cryo

> Summary

Summary for 5EX9

Related5EX8
DescriptorCytochrome P450, PROTOPORPHYRIN IX CONTAINING FE, GLYCEROL, ... (4 entities in total)
Functional Keywordscytochrome p450, monooxygenase, phenolic coupling, glycopeptide antibiotic biosynthesis, oxidoreductase
Biological sourceStreptomyces toyocaensis
Total number of polymer chains1
Total molecular weight48690.84
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 (2.2 Å)
?

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.21440.5%1.8%3.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5ex9
no rotation
Molmil generated image of 5ex9
rotated about x axis by 90°
Molmil generated image of 5ex9
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
GLYCEROLnon-polymer92.18
waterwater18.0216

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight47337.6
Non-Polymers*Number of molecules9
Total molecular weight1353.2
All*Total molecular weight48690.8
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.2 Å)

Cell axes109.700109.70093.900
Cell angles90.0090.00120.00
SpacegroupP 31 2 1
Resolution limits47.51 - 2.20
the highest resolution shell value2.257 - 2.200
R-factor0.1922
R-work0.19076
the highest resolution shell value0.218
R-free0.22011
the highest resolution shell value0.245
RMSD bond length0.008
RMSD bond angle1.071

Data Collection Statistics

Resolution limits50.00 - 2.20
the highest resolution shell value -
Number of reflections33006
Rmerge_l_obs0.090
the highest resolution shell value0.400
Completeness98.4
Redundancy9.6
the highest resolution shell value10.3

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
AILE339
AHIS340
ACYS342
ALEU343
AGLY344
AHOH512
AHOH563

AC24binding site for residue GOL A 402
ChainResidue
ATYR189
AGLN192
AHIS193
AGLN196

AC37binding site for residue GOL A 403
ChainResidue
ASER-13
ALYS281
ATHR282
AHIS283
APRO284
AHOH555
AHOH559

AC43binding site for residue GOL A 404
ChainResidue
AASP159
AASP162
ATYR189

AC54binding site for residue GOL A 405
ChainResidue
AGLY336
AHIS337
AGLY338
AHIS341

AC67binding site for residue GOL A 406
ChainResidue
ASER27
ALYS30
AARG198
AARG199
AASP219
AHOH534
AHOH594

AC75binding site for residue GOL A 407
ChainResidue
AARG97
AVAL101
AHIS341
AHOH545
AHOH629

AC84binding site for residue GOL A 408
ChainResidue
AASP215
ATHR376
AGLU385
AHOH554

AC92binding site for residue GOL A 409
ChainResidue
AARG58
AHOH558

?

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

site_idNumber of ResiduesDetails
GOL_5ex9_A_4092GLYCEROL binding site
ChainResidueligand
AARG58GOL: GLYCEROL
AHIS337GOL: GLYCEROL

GOL_5ex9_A_4056GLYCEROL binding site
ChainResidueligand
AARG58GOL: GLYCEROL
ALEU333GOL: GLYCEROL
AGLY336-GLY338GOL: GLYCEROL
AHIS341GOL: GLYCEROL

HEM_5ex9_A_40131PROTOPORPHYRIN 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
ATHR278-ASP279HEM: PROTOPORPHYRIN IX CONTAINING FE
ATHR282-HIS283HEM: PROTOPORPHYRIN IX CONTAINING FE
AARG285HEM: PROTOPORPHYRIN IX CONTAINING FE
ALEU308HEM: PROTOPORPHYRIN IX CONTAINING FE
AALA334-GLY336HEM: PROTOPORPHYRIN IX CONTAINING FE
AILE339-GLY344HEM: PROTOPORPHYRIN IX CONTAINING FE
AMET347-ALA348HEM: PROTOPORPHYRIN IX CONTAINING FE

GOL_5ex9_A_4075GLYCEROL binding site
ChainResidueligand
AARG97GOL: GLYCEROL
AVAL101GOL: GLYCEROL
AHIS341-LEU343GOL: GLYCEROL

GOL_5ex9_A_4026GLYCEROL binding site
ChainResidueligand
APRO156GOL: GLYCEROL
AASP159GOL: GLYCEROL
ATYR189GOL: GLYCEROL
AGLN192-HIS193GOL: GLYCEROL
AGLN196GOL: GLYCEROL

GOL_5ex9_A_4047GLYCEROL binding site
ChainResidueligand
AASP158-ASP159GOL: GLYCEROL
AASP162-LEU163GOL: GLYCEROL
AILE166GOL: GLYCEROL
ALYS185GOL: GLYCEROL
ATYR189GOL: GLYCEROL

GOL_5ex9_A_4066GLYCEROL binding site
ChainResidueligand
AALA195GOL: GLYCEROL
AARG198-ARG199GOL: GLYCEROL
AASP215GOL: GLYCEROL
AILE217GOL: GLYCEROL
AASP219GOL: GLYCEROL

GOL_5ex9_A_4035GLYCEROL binding site
ChainResidueligand
ALYS281-PRO284GOL: GLYCEROL
ATHR305GOL: GLYCEROL

GOL_5ex9_A_4083GLYCEROL binding site
ChainResidueligand
ATHR376GOL: GLYCEROL
AGLU385-ALA386GOL: GLYCEROL

?

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