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- PDB-6g75: Crystal structure of the common ancestor of haloalkane dehalogena... -

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Basic information

Entry
Database: PDB / ID: 6g75
TitleCrystal structure of the common ancestor of haloalkane dehalogenases and Renilla luciferase (AncHLD-RLuc)
ComponentsCommon ancestor of haloalkane dehalogenase and Renilla luciferase (AncHLD-RLuc)
KeywordsHYDROLASE / Haloalkane dehalogenase / Renilla luciferase / oxygen-bound
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / OXYGEN MOLECULE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.391 Å
AuthorsChaloupkova, R. / Waterman, J. / Marek, M. / Damborsky, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic16-24223S Czech Republic
CitationJournal: Acs Catalysis / Year: 2019
Title: Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts
Authors: Chaloupkova, R. / Liskova, V. / Toul, M. / Markova, K. / Sebestova, E. / Hernychova, L. / Marek, M. / Pinto, G.P. / Pluskal, D. / Waterman, J. / Prokop, Z. / Damborsky, J.
History
DepositionApr 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: 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 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Common ancestor of haloalkane dehalogenase and Renilla luciferase (AncHLD-RLuc)
B: Common ancestor of haloalkane dehalogenase and Renilla luciferase (AncHLD-RLuc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6288
Polymers68,0832
Non-polymers5456
Water8,377465
1
A: Common ancestor of haloalkane dehalogenase and Renilla luciferase (AncHLD-RLuc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3144
Polymers34,0421
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Common ancestor of haloalkane dehalogenase and Renilla luciferase (AncHLD-RLuc)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3144
Polymers34,0421
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.549, 60.510, 123.630
Angle α, β, γ (deg.)90.000, 90.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Common ancestor of haloalkane dehalogenase and Renilla luciferase (AncHLD-RLuc)


Mass: 34041.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7.0 and 10% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.39→21.76 Å / Num. obs: 122192 / % possible obs: 93.1 % / Redundancy: 2.5 % / Biso Wilson estimate: 11.25 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.079 / Rrim(I) all: 0.134 / Net I/σ(I): 4.5 / Num. measured all: 301152 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.39-1.412.50.7271495058910.4310.5630.9241.491.5
7.62-21.762.70.05522098150.9920.0380.0679.195.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimless0.2.17data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2psf

2psf


Resolution: 1.391→21.619 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1896 6022 4.93 %
Rwork0.1499 116096 -
obs0.1518 122118 92.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.23 Å2 / Biso mean: 18.6127 Å2 / Biso min: 5.09 Å2
Refinement stepCycle: final / Resolution: 1.391→21.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 0 36 465 5301
Biso mean--46.68 32.87 -
Num. residues----591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055053
X-RAY DIFFRACTIONf_angle_d0.8216871
X-RAY DIFFRACTIONf_chiral_restr0.083717
X-RAY DIFFRACTIONf_plane_restr0.006883
X-RAY DIFFRACTIONf_dihedral_angle_d2.5953072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.391-1.40680.30121800.24993755393591
1.4068-1.42340.3032170.24533775399291
1.4234-1.44070.2762020.22753803400591
1.4407-1.45890.26531960.21613780397693
1.4589-1.47810.24691740.20813849402391
1.4781-1.49840.25111860.19733810399691
1.4984-1.51980.27342130.19153751396491
1.5198-1.54250.23692200.18063764398490
1.5425-1.56660.22692420.16613705394791
1.5666-1.59220.18492240.14593769399390
1.5922-1.61970.22032120.14483779399193
1.6197-1.64910.21162060.1433860406692
1.6491-1.68080.19712110.13963844405593
1.6808-1.71510.18171590.13673880403991
1.7151-1.75240.19921700.12993838400893
1.7524-1.79310.1971950.13153841403691
1.7931-1.8380.17741900.13353806399692
1.838-1.88760.17781960.13283787398391
1.8876-1.94310.17511850.12823871405692
1.9431-2.00580.15881760.13043867404393
2.0058-2.07750.18891970.13653917411493
2.0775-2.16060.17152480.13593885413394
2.1606-2.25880.17881670.13973945411294
2.2588-2.37770.17682160.14173984420095
2.3777-2.52650.18292090.14844012422196
2.5265-2.72120.18241900.15164013420396
2.7212-2.99440.21082200.15924049426996
2.9944-3.42630.1821760.15034011418794
3.4263-4.31110.16452200.13474025424596
4.3111-21.62180.15392250.14834121434696

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