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- PDB-6y9f: Crystal structure of putative ancestral haloalkane dehalogenase A... -

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Basic information

Entry
Database: PDB / ID: 6y9f
TitleCrystal structure of putative ancestral haloalkane dehalogenase AncHLD3 (node 3)
ComponentsAncestral haloalkane dehalogenase AncHLD3
KeywordsHYDROLASE / Haloalkane dehalogenase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.26 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 AncHLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4883
Polymers34,0741
Non-polymers4152
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint9 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.420, 71.420, 225.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-532-

HOH

21A-726-

HOH

31A-771-

HOH

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Components

#1: Protein Ancestral haloalkane dehalogenase AncHLD3


Mass: 34073.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: Sodium citrate tribasic, CHES

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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: 1.26→61.852 Å / Num. obs: 92642 / % possible obs: 99.8 % / Redundancy: 17 % / CC1/2: 1 / Net I/σ(I): 25.7
Reflection shellResolution: 1.26→1.29 Å / Num. unique obs: 6558 / CC1/2: 0.564

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.1-3865refinement
XDSdata reduction
xia2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K2A

4k2a


Resolution: 1.26→61.852 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1687 4591 4.96 %
Rwork0.1466 87912 -
obs0.1477 92503 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.35 Å2 / Biso mean: 24.7953 Å2 / Biso min: 11.33 Å2
Refinement stepCycle: final / Resolution: 1.26→61.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 26 272 2560
Biso mean--42.85 39.86 -
Num. residues----288
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.26-1.27430.29091610.2886280497
1.2743-1.28930.32081360.2581277098
1.2893-1.3050.28041420.244285499
1.305-1.32160.26521510.2181291299
1.3216-1.3390.23841440.19652846100
1.339-1.35730.20031450.1782906100
1.3573-1.37670.20761680.16632892100
1.3767-1.39720.2081570.14722846100
1.3972-1.41910.18491480.14172906100
1.4191-1.44230.1641480.1442898100
1.4423-1.46720.19131340.13842914100
1.4672-1.49390.16481640.13322880100
1.4939-1.52260.17481310.12212943100
1.5226-1.55370.14351260.11452919100
1.5537-1.58750.13111550.11122928100
1.5875-1.62440.14481560.11272891100
1.6244-1.66510.15771400.11132923100
1.6651-1.71010.13331460.1132922100
1.7101-1.76040.14371720.11712886100
1.7604-1.81720.1521530.11982956100
1.8172-1.88220.14491720.12482924100
1.8822-1.95750.1621380.12172929100
1.9575-2.04660.15241630.12422957100
2.0466-2.15460.12571590.12572937100
2.1546-2.28950.14841570.13032971100
2.2895-2.46630.16341750.14552970100
2.4663-2.71450.18751560.16672995100
2.7145-3.10730.1921560.16923054100
3.1073-3.91480.15671800.14313062100
3.9148-61.8520.18031580.16193317100

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