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- PDB-7qxr: Azacoelenterazine-bound Renilla-type luciferase (AncFT) -

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Basic information

Entry
Database: PDB / ID: 7qxr
TitleAzacoelenterazine-bound Renilla-type luciferase (AncFT)
ComponentsFragment transplantation onto a hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
KeywordsOXIDOREDUCTASE / luciferase / azacoelenterazine / substrate analogue / Renilla-like / engineered ancestor
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-NSW
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.052 Å
AuthorsMarek, M. / Schenkmayerova, A. / Janin, Y.L.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation22-09853S Czech Republic
CitationJournal: Nat Catal / Year: 2023
Title: Catalytic mechanism for Renilla-type luciferases
Authors: Schenkmayerova, A. / Toul, M. / Pluskal, D. / Baatallah, R. / Gagnot, G. / Pinto, G.P. / Santana, V.T. / Stuchla, M. / Neugebauer, P. / Chaiyen, P. / Damborsky, J. / Bednar, D. / Janin, Y.L. ...Authors: Schenkmayerova, A. / Toul, M. / Pluskal, D. / Baatallah, R. / Gagnot, G. / Pinto, G.P. / Santana, V.T. / Stuchla, M. / Neugebauer, P. / Chaiyen, P. / Damborsky, J. / Bednar, D. / Janin, Y.L. / Prokop, Z. / Marek, M.
History
DepositionJan 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 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: Fragment transplantation onto a hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
B: Fragment transplantation onto a hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
C: Fragment transplantation onto a hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2126
Polymers101,9353
Non-polymers1,2763
Water5,459303
1
A: Fragment transplantation onto a hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4042
Polymers33,9781
Non-polymers4251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fragment transplantation onto a hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4042
Polymers33,9781
Non-polymers4251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fragment transplantation onto a hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4042
Polymers33,9781
Non-polymers4251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.284, 87.549, 102.693
Angle α, β, γ (deg.)90.000, 93.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fragment transplantation onto a hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)


Mass: 33978.387 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NSW / 3-(4-hydroxyphenyl)-8-[(4-hydroxyphenyl)methyl]-5-(phenylmethyl)-1$l^{4},4,7,8-tetrazabicyclo[4.3.0]nona-1(6),2,4-trien-9-one


Mass: 425.459 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H21N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: magnesium chloride, Bis-tris, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→46.944 Å / Num. obs: 56440 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.997 / Net I/σ(I): 9.8
Reflection shellResolution: 2.05→2.11 Å / Num. unique obs: 4304 / CC1/2: 0.591

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S97

6s97


Resolution: 2.052→46.944 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 2852 5.06 %
Rwork0.1924 53532 -
obs0.1952 56384 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.85 Å2 / Biso mean: 37.4412 Å2 / Biso min: 16.12 Å2
Refinement stepCycle: final / Resolution: 2.052→46.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7164 0 96 303 7563
Biso mean--32.81 37.29 -
Num. residues----882
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.052-2.08720.30561270.2997257797
2.0872-2.12520.33771150.2869270199
2.1252-2.16610.34241360.2753264699
2.1661-2.21030.31291290.2576268999
2.2103-2.25830.30351620.2593264599
2.2583-2.31090.33331620.2475264299
2.3109-2.36870.33631520.2324266599
2.3687-2.43270.32431520.23792660100
2.4327-2.50430.31441400.2276266599
2.5043-2.58510.34211520.23682672100
2.5851-2.67750.29851510.22852660100
2.6775-2.78470.29041270.21392663100
2.7847-2.91140.24941340.2057269799
2.9114-3.06490.31061260.21032726100
3.0649-3.25690.23791250.19532696100
3.2569-3.50820.24571460.1857267899
3.5082-3.86110.231720.17382676100
3.8611-4.41950.18461360.14482704100
4.4195-5.56670.17591710.14012686100
5.5667-46.9440.20591370.16382784100

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