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- PDB-1j1i: Crystal structure of a His-tagged Serine Hydrolase Involved in th... -

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Basic information

Entry
Database: PDB / ID: 1j1i
TitleCrystal structure of a His-tagged Serine Hydrolase Involved in the Carbazole Degradation (CarC enzyme)
Componentsmeta cleavage compound hydrolase
KeywordsHYDROLASE / Carbazole degradation / meta cleavage product hydrolase / histidine tagged protein / ALPHA/BETA-HYDROLASE / BETA-KETOLASE / DIOXIN / AROMATIC COMPOUNDS / DIBENZOFURAN
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Meta cleavage compound hydrolase
Function and homology information
Biological speciesJanthinobacterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsHabe, H. / Morii, K. / Fushinobu, S. / Nam, J.W. / Ayabe, Y. / Yoshida, T. / Wakagi, T. / Yamane, H. / Nojiri, H. / Omori, T.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: Crystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme).
Authors: Habe, H. / Morii, K. / Fushinobu, S. / Nam, J.W. / Ayabe, Y. / Yoshida, T. / Wakagi, T. / Yamane, H. / Nojiri, H. / Omori, T.
#1: Journal: To be Published
Title: The C-C bond hydrolase from a carbazole-degrader
Authors: Nojiri, H. / Taira, H. / Iwata, K. / Morii, K. / Nam, J.W. / Yoshida, T. / Habe, H. / Nakamura, S. / Shimizu, K. / Yamane, H. / Omori, T.
History
DepositionDec 5, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: meta cleavage compound hydrolase


Theoretical massNumber of molelcules
Total (without water)33,1381
Polymers33,1381
Non-polymers00
Water3,135174
1
A: meta cleavage compound hydrolase

A: meta cleavage compound hydrolase


Theoretical massNumber of molelcules
Total (without water)66,2752
Polymers66,2752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Unit cell
Length a, b, c (Å)130.268, 130.268, 84.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsThe second part of the biological assembly is generated by the two fold axis: -y+1/2, -x+1/2, -z+1/2.

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Components

#1: Protein meta cleavage compound hydrolase / Serine Hydrolase Involved in the Carbazole Degradation / CarC


Mass: 33137.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Janthinobacterium (bacteria) / Genus: Janthinobacterium / Strain: J3 / Gene: CarC / Plasmid: pECJ3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q84II3, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.92 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 6000, citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.2 %PEG60001reservoir
226 mMcitric acid1reservoirpH5.0
315-20 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 14, 2000 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→33.22 Å / Num. all: 30733 / Num. obs: 30496 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.8
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2978 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CrystalClear1.3data collection
CrystalClear1.3data reduction
MOLREPphasing
CNS1.1refinement
CrystalClearV. 1.3 (MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IUP

1iup


Resolution: 1.86→32.57 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1534 5 %RANDOM
Rwork0.215 ---
all0.217 30733 --
obs0.215 30496 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.2113 Å2 / ksol: 0.36267 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å20 Å2
2--1.42 Å20 Å2
3----2.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.86→32.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 0 174 2195
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.531.5
X-RAY DIFFRACTIONc_mcangle_it3.242
X-RAY DIFFRACTIONc_scbond_it4.132
X-RAY DIFFRACTIONc_scangle_it5.72.5
LS refinement shellResolution: 1.86→1.98 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 274 5.5 %
Rwork0.275 4698 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67

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