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- PDB-6xam: Crystal structure of NzeB in complex with cyclo-(L-Trp-L-homoalanine) -

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Basic information

Entry
Database: PDB / ID: 6xam
TitleCrystal structure of NzeB in complex with cyclo-(L-Trp-L-homoalanine)
ComponentsNzeB
KeywordsOXIDOREDUCTASE / monooxygenase / dimerase / P450
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / Chem-WMA
Function and homology information
Biological speciesStreptomyces sp. NRRL F-5053 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.481 Å
AuthorsShende, V.V. / Khatri, Y. / Newmister, S.A. / Sanders, J.N. / Lindovska, P. / Yu, F. / Doyon, T.J. / Kim, J. / Movassaghi, M. / Houk, K.N. / Sherman, D.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1700982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM118101 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Structure and Function of NzeB, a Versatile C-C and C-N Bond-Forming Diketopiperazine Dimerase.
Authors: Shende, V.V. / Khatri, Y. / Newmister, S.A. / Sanders, J.N. / Lindovska, P. / Yu, F. / Doyon, T.J. / Kim, J. / Houk, K.N. / Movassaghi, M. / Sherman, D.H.
History
DepositionJun 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NzeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0265
Polymers43,8041
Non-polymers1,2214
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.607, 56.203, 56.058
Angle α, β, γ (deg.)90.000, 101.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NzeB


Mass: 43804.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. NRRL F-5053 (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-WMA / (3S,6S)-3-ethyl-6-[(1H-indol-3-yl)methyl]piperazine-2,5-dione


Mass: 271.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 23% PEG 3350, 100 mM DL-malic acid, 2.5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2018
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.481→39.261 Å / Num. obs: 50302 / % possible obs: 89.27 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02968 / Rrim(I) all: 0.0322 / Net I/σ(I): 31.27
Reflection shellResolution: 1.481→1.534 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3031 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 2484 / CC1/2: 0.834 / Rrim(I) all: 0.3933 / % possible all: 44.42

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6xai

6xai


Resolution: 1.481→39.261 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 2464 4.9 %
Rwork0.1879 47833 -
obs0.1894 50297 89.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.87 Å2 / Biso mean: 26.2657 Å2 / Biso min: 11.55 Å2
Refinement stepCycle: final / Resolution: 1.481→39.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 87 378 3496
Biso mean--18.56 33.05 -
Num. residues----395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.481-1.50910.2873560.2986103435
1.5091-1.53990.3256750.2671163155
1.5399-1.57340.2358800.2504189864
1.5734-1.610.25271110.2312221974
1.61-1.65030.27711680.2395252186
1.6503-1.69490.26341280.2321283595
1.6949-1.74480.27611590.2318289198
1.7448-1.80110.29391880.2265291499
1.8011-1.86540.27561700.2183292999
1.8654-1.94010.26741590.2217295199
1.9401-2.02840.23011460.21832968100
2.0284-2.13540.25511450.21122984100
2.1354-2.26910.22711290.20282990100
2.2691-2.44430.23871290.2023013100
2.4443-2.69020.23391800.20212942100
2.6902-3.07940.24181370.18363035100
3.0794-3.87920.18811590.15872985100
3.8792-39.2610.1611450.14863093100

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