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

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Basic information

Entry
Database: PDB / ID: 6xak
TitleCrystal structure of NzeB in complex with cyclo-(L-Trp-L-Pro) and cyclo-(L-Trp-L-Trp)
ComponentsNzeB
KeywordsOXIDOREDUCTASE / monooxygenase / dimerase / P450
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / Chem-QRP / Chem-UYM
Function and homology information
Biological speciesStreptomyces sp. NRRL F-5053 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.479 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

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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)90,34011
Polymers87,6092
Non-polymers2,7319
Water12,953719
1
A: NzeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2016
Polymers43,8041
Non-polymers1,3965
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NzeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1395
Polymers43,8041
Non-polymers1,3344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.067, 56.131, 58.476
Angle α, β, γ (deg.)91.360, 93.040, 101.090
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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)

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Non-polymers , 5 types, 728 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C16H17N3O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antifungal*YM
#4: Chemical ChemComp-UYM / (3S,6S)-3,6-bis[(1H-indol-3-yl)methyl]piperazine-2,5-dione


Mass: 372.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H20N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.05 Å3/Da / Density % sol: 40.08 %
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: 1.479→41.224 Å / Num. obs: 94423 / % possible obs: 80.96 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.036 / Net I/σ(I): 20.64
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 1.81 / Num. unique obs: 2902 / CC1/2: 0.851 / Rrim(I) all: 0.398 / % possible all: 24.95

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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: 1.479→41.224 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 33.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 4788 5.07 %
Rwork0.1923 89613 -
obs0.1945 94401 80.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.31 Å2 / Biso mean: 28.5606 Å2 / Biso min: 12.62 Å2
Refinement stepCycle: final / Resolution: 1.479→41.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6050 0 211 719 6980
Biso mean--23.15 34.37 -
Num. residues----793
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4793-1.49610.5098250.362946313
1.4961-1.51370.3988470.3428107428
1.5137-1.53220.3676520.313124134
1.5322-1.55160.3593780.2978143039
1.5516-1.5720.3042960.2804161644
1.572-1.59350.3736990.2847182250
1.5935-1.61630.31141160.2832205456
1.6163-1.64040.31371090.2702245365
1.6404-1.66610.30951350.263298880
1.6661-1.69340.30031990.2532333790
1.6934-1.72260.32562040.2435333692
1.7226-1.75390.26351610.2514355695
1.7539-1.78760.2841830.2513350095
1.7876-1.82410.2761820.2396356196
1.8241-1.86380.28481710.2419356896
1.8638-1.90710.27052080.2384347696
1.9071-1.95480.27961940.2453359896
1.9548-2.00770.26122160.24350896
2.0077-2.06680.28132190.2273351496
2.0668-2.13350.26731970.2186357597
2.1335-2.20970.27912060.2084353597
2.2097-2.29820.2491840.2026358297
2.2982-2.40280.22621970.1976357497
2.4028-2.52940.24121760.1968362297
2.5294-2.68790.21922040.1969357597
2.6879-2.89540.24561910.1982357097
2.8954-3.18660.21511630.196361097
3.1866-3.64750.25462040.1707362298
3.6475-4.59450.17882090.1414361598
4.5945-41.2240.17571630.1516363898

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