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- PDB-2jl1: Structural insight into bioremediation of triphenylmethane dyes b... -

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Basic information

Entry
Database: PDB / ID: 2jl1
TitleStructural insight into bioremediation of triphenylmethane dyes by Citrobacter sp. triphenylmethane reductase
ComponentsTRIPHENYLMETHANE REDUCTASE
KeywordsOXIDOREDUCTASE / TRIPHENYLMETHANE REDUCTASE / BIOREMEDIATION / TRIPHENYLMETHANE
Function / homology
Function and homology information


: / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Triphenylmethane reductase
Similarity search - Component
Biological speciesCITROBACTER SP. MY-5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsKim, Y. / Park, H.J. / Kwak, S.N. / Kim, M.H.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Insight Into Bioremediation of Triphenylmethane Dyes by Citrobacter Sp. Triphenylmethane Reductase
Authors: Kim, M.H. / Kim, Y. / Park, H.J. / Lee, J.S. / Kwak, S.N. / Jung, W.H. / Lee, S.G. / Kim, D. / Lee, Y.C. / Oh, T.K.
History
DepositionSep 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIPHENYLMETHANE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2257
Polymers31,0211
Non-polymers1,2046
Water3,009167
1
A: TRIPHENYLMETHANE REDUCTASE
hetero molecules

A: TRIPHENYLMETHANE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,45014
Polymers62,0422
Non-polymers2,40812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2240 Å2
ΔGint-20.1 kcal/mol
Surface area28260 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.262, 140.384, 76.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2025-

HOH

21A-2069-

HOH

31A-2146-

HOH

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Components

#1: Protein TRIPHENYLMETHANE REDUCTASE


Mass: 31021.043 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CITROBACTER SP. MY-5 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSSETA GAMI (DE3) / References: UniProt: Q2TNI4
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMET1 WAS REPLACED WITH PHENYLALANINE IN THE COORDINATE FILE BECAUSE OF CLONING PROCEDURE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.4 % / Description: NONE
Crystal growpH: 8 / Details: 0.05 M KH2PO4, 18% PEG8000, 10 MM NADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 22401 / % possible obs: 95.9 % / Observed criterion σ(I): -0.5 / Redundancy: 11.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28.85
Reflection shellResolution: 1.96→2.02 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.81 / % possible all: 83.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VRB

2vrb


Resolution: 1.96→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.076 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1142 5.1 %RANDOM
Rwork0.179 ---
obs0.182 21246 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å20 Å20 Å2
2---1.33 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 78 167 2434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222319
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9893155
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01925.31994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35215372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.537157
X-RAY DIFFRACTIONr_chiral_restr0.090.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021690
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.21071
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21618
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8831.51471
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30422312
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2113949
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4324.5843
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 73
Rwork0.223 1284
Refinement TLS params.Method: refined / Origin x: -5.809 Å / Origin y: -18.991 Å / Origin z: 0.639 Å
111213212223313233
T-0.0147 Å20.0157 Å2-0.006 Å2--0.0708 Å2-0.0328 Å2---0.0552 Å2
L0.9252 °2-0.18 °20.3582 °2-1.0808 °2-0.1536 °2--0.6919 °2
S0.0247 Å °0.0979 Å °-0.1053 Å °-0.0628 Å °0.0074 Å °0.0135 Å °0.1077 Å °0.0617 Å °-0.032 Å °

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