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- PDB-6y9g: Crystal structure of putative ancestral haloalkane dehalogenase A... -

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Basic information

Entry
Database: PDB / ID: 6y9g
TitleCrystal structure of putative ancestral haloalkane dehalogenase AncHLD5 (node 5)
ComponentsAncestral haloalkane dehalogenase AncHLD5
KeywordsHYDROLASE / Haloalkane dehalogenase
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.748 Å
AuthorsChaloupkova, R. / Damborsky, J. / Marek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
European CommissionMSCA-IF-2017 792772 Czech Republic
CitationJournal: Comput Struct Biotechnol J / Year: 2020
Title: Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics.
Authors: Babkova, P. / Dunajova, Z. / Chaloupkova, R. / Damborsky, J. / Bednar, D. / Marek, M.
History
DepositionMar 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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: Ancestral haloalkane dehalogenase AncHLD5
B: Ancestral haloalkane dehalogenase AncHLD5


Theoretical massNumber of molelcules
Total (without water)68,8442
Polymers68,8442
Non-polymers00
Water3,171176
1
A: Ancestral haloalkane dehalogenase AncHLD5


Theoretical massNumber of molelcules
Total (without water)34,4221
Polymers34,4221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ancestral haloalkane dehalogenase AncHLD5


Theoretical massNumber of molelcules
Total (without water)34,4221
Polymers34,4221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.871, 51.365, 78.419
Angle α, β, γ (deg.)90.000, 94.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ancestral haloalkane dehalogenase AncHLD5


Mass: 34421.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.86 Å3/Da / Density % sol: 34.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 8000, magnesium chloride, Tris base

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.748→47.06 Å / Num. obs: 50947 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.998 / Net I/σ(I): 13.5
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 2588 / CC1/2: 0.789

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.14-3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K2A

4k2a


Resolution: 1.748→39.988 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.78
RfactorNum. reflection% reflection
Rfree0.2154 2528 4.96 %
Rwork0.1831 --
obs0.1847 50921 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.57 Å2 / Biso mean: 26.0117 Å2 / Biso min: 12.1 Å2
Refinement stepCycle: final / Resolution: 1.748→39.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 0 178 4723
Biso mean---29.55 -
Num. residues----570
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7482-1.78190.27791150.271250493
1.7819-1.81820.28961410.23612702100
1.8182-1.85780.27311470.222682100
1.8578-1.9010.25751400.1994272299
1.901-1.94850.2541360.2013268299
1.9485-2.00120.20321320.17842701100
2.0012-2.06010.25061300.18252722100
2.0601-2.12660.22991630.18182661100
2.1266-2.20260.21361610.16862700100
2.2026-2.29080.21541370.1793268799
2.2908-2.3950.22941300.18092706100
2.395-2.52130.24251640.18292671100
2.5213-2.67920.21881310.18222730100
2.6792-2.8860.22191370.1884270499
2.886-3.17630.20621330.1838271899
3.1763-3.63570.19391520.171268098
3.6357-4.57950.18741480.1644267597
4.5795-39.9880.20471310.1885274697

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