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

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Basic information

Entry
Database: PDB / ID: 6xai
TitleCrystal structure of NzeB in complex with cyclo-(L-Trp-L-Pro)
ComponentsNzeB
KeywordsOXIDOREDUCTASE / monooxygenase / dimerase / P450
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / Chem-QRP
Function and homology information
Biological speciesStreptomyces sp. NRRL F-5053 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.489 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 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NzeB
B: NzeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,28613
Polymers87,6092
Non-polymers2,67711
Water12,448691
1
A: NzeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1747
Polymers43,8041
Non-polymers1,3696
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NzeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1126
Polymers43,8041
Non-polymers1,3075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.122, 56.285, 58.779
Angle α, β, γ (deg.)91.130, 92.930, 101.000
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NzeB


Mass: 43804.465 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-QRP / (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione / Brevianamide F / cyclo-L-Trp-L-Pro


Mass: 283.325 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H17N3O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antifungal*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 40.77 %
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: Dec 13, 2017
RadiationMonochromator: mirros / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.489→41.299 Å / Num. obs: 109037 / % possible obs: 94.48 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.046 / Net I/σ(I): 16.78
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 10046 / CC1/2: 0.85 / Rrim(I) all: 0.439 / % possible all: 87.34

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MR-Rosetta

Resolution: 1.489→41.299 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 5444 4.99 %
Rwork0.1671 103585 -
obs0.1693 109029 94.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.38 Å2 / Biso mean: 27.5064 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 1.489→41.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6090 0 190 691 6971
Biso mean--19.5 36.01 -
Num. residues----798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056464
X-RAY DIFFRACTIONf_angle_d0.9278834
X-RAY DIFFRACTIONf_chiral_restr0.071963
X-RAY DIFFRACTIONf_plane_restr0.0051165
X-RAY DIFFRACTIONf_dihedral_angle_d5.9423736
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.489-1.50590.3811240.3647291479
1.5059-1.52360.31961540.2767337490
1.5236-1.54220.33811610.243329692
1.5422-1.56170.30431810.2309346294
1.5617-1.58220.28842060.2068341894
1.5822-1.60390.26161860.1882345695
1.6039-1.62680.24841750.1726340895
1.6268-1.65110.21731720.1746350795
1.6511-1.67690.23011760.1663349295
1.6769-1.70440.24122100.1686350295
1.7044-1.73380.22321800.1678338795
1.7338-1.76530.23311690.1648351695
1.7653-1.79930.20851880.1669350295
1.7993-1.8360.22911480.1685351095
1.836-1.87590.22731780.1769352595
1.8759-1.91960.2341980.1728341695
1.9196-1.96760.21261840.1716348595
1.9676-2.02080.26172230.1763348895
2.0208-2.08020.23522110.1771344696
2.0802-2.14740.22761850.174347396
2.1474-2.22410.23832080.1703348496
2.2241-2.31310.22681800.1652351095
2.3131-2.41840.18731820.1623347295
2.4184-2.54590.19611730.1618353796
2.5459-2.70540.19761900.1654348196
2.7054-2.91420.22421810.1722347896
2.9142-3.20740.20451640.1739351595
3.2074-3.67120.20161930.1593348095
3.6712-4.62440.16872040.1395352597
4.6244-41.2990.19251600.1586352696

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