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- PDB-7nfz: Crystal structure of haloalkane dehalogenase LinB57 mutant (H272F... -

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Basic information

Entry
Database: PDB / ID: 7nfz
TitleCrystal structure of haloalkane dehalogenase LinB57 mutant (H272F) from Sphingobium japonicum UT26
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Haloalkane dehalogenase
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / periplasmic space
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.551 Å
AuthorsMarek, M.
CitationJournal: To Be Published
Title: Crystal structure of haloalkane dehalogenase LinB57 mutant (H272F) from Sphingobium japonicum UT26
Authors: Marek, M. / Damborsky, J.
History
DepositionFeb 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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

Downloads & links

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,40011
Polymers33,9831
Non-polymers1,41810
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint20 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.496, 65.448, 90.171
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Haloalkane dehalogenase / 1 / 3 / 4 / 6-tetrachloro-1 / 4-cyclohexadiene halidohydrolase / 4-TCDN halidohydrolase


Mass: 33982.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium japonicum (strain DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S) (bacteria)
Strain: DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S
Gene: linB, SJA_C1-19590 / Production host: Escherichia coli (E. coli) / References: UniProt: D4Z2G1, haloalkane dehalogenase

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Non-polymers , 6 types, 256 molecules

#2: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 44.98 % / Description: plate-like shape
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: sodium di-hydrogen phosphate, di-potassium hydrogen phosphate, lithium sulphate, CAPS

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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: 1.55→45.09 Å / Num. obs: 44672 / % possible obs: 99.5 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.193 / Net I/σ(I): 11.1
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 1.907 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2129 / CC1/2: 0.593 / % possible all: 97.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.19.1-4122refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MJ5

1mj5


Resolution: 1.551→44.718 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1897 2168 4.86 %
Rwork0.1643 42434 -
obs0.1656 44602 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.77 Å2 / Biso mean: 16.7984 Å2 / Biso min: 6 Å2
Refinement stepCycle: final / Resolution: 1.551→44.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 102 247 2664
Biso mean--34.62 29.28 -
Num. residues----294
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5511-1.58720.26551280.2588274398
1.5872-1.62690.29851280.2318278498
1.6269-1.67080.26181280.2097279199
1.6708-1.720.23041560.1926276099
1.72-1.77550.19551420.1903279699
1.7755-1.8390.2321610.182275799
1.839-1.91260.23821450.1845281099
1.9126-1.99970.21471370.16032820100
1.9997-2.10510.18581380.15152822100
2.1051-2.2370.18141470.14612844100
2.237-2.40970.18651450.15032829100
2.4097-2.65220.1951340.15582879100
2.6522-3.03590.15931440.14922878100
3.0359-3.82450.17171630.1372895100
3.8245-44.7180.15941720.16893026100
Refinement TLS params.Method: refined / Origin x: -19.0822 Å / Origin y: -0.1855 Å / Origin z: 4.1442 Å
111213212223313233
T0.0801 Å20.0039 Å20.0004 Å2-0.0671 Å2-0.0032 Å2--0.0801 Å2
L0.3358 °2-0.0547 °2-0.1567 °2-0.3794 °20.0878 °2--1.0134 °2
S-0.0232 Å °0.0004 Å °-0.0253 Å °0.0252 Å °-0.0037 Å °0.0132 Å °0.2144 Å °-0.0071 Å °-0.0235 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 353
2X-RAY DIFFRACTION1allA400 - 700
3X-RAY DIFFRACTION1allB1 - 246

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