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- PDB-2vrb: Crystal structure of the Citrobacter sp. triphenylmethane reducta... -

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Basic information

Entry
Database: PDB / ID: 2vrb
TitleCrystal structure of the Citrobacter sp. triphenylmethane reductase complexed with NADP(H)
ComponentsTRIPHENYLMETHANE REDUCTASE
KeywordsOXIDOREDUCTASE / REDUCTASE / SDR FAMILY / TRIPHENYLMETHANE REDUCTION
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: 2 Å
AuthorsKim, Y. / Park, H.J. / Kwak, S.N. / Lee, J.S. / Oh, T.K. / 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
DepositionMar 31, 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 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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)31,7182
Polymers30,9751
Non-polymers7431
Water2,450136
1
A: TRIPHENYLMETHANE REDUCTASE
hetero molecules

A: TRIPHENYLMETHANE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4374
Polymers61,9502
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2060 Å2
ΔGint-19.3 kcal/mol
Surface area28220 Å2
MethodPQS
Unit cell
Length a, b, c (Å)58.800, 141.645, 75.811
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-2121-

HOH

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Components

#1: Protein TRIPHENYLMETHANE REDUCTASE


Mass: 30975.039 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 0.05M KH2PO4,18% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 21741 / % possible obs: 99.7 % / Observed criterion σ(I): -2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.466 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1106 5.1 %RANDOM
Rwork0.2 ---
obs0.202 20569 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2---2.6 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 48 136 2343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222266
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9813097
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0445287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.825.37693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78815365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.362157
X-RAY DIFFRACTIONr_chiral_restr0.1150.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021679
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21050
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21588
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1381.51460
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52822296
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8153904
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.114.5801
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 94
Rwork0.241 1462
Refinement TLS params.Method: refined / Origin x: 5.417 Å / Origin y: 19.116 Å / Origin z: 0.862 Å
111213212223313233
T-0.0741 Å20.0353 Å20.0873 Å2--0.094 Å20.0631 Å2---0.1447 Å2
L1.8544 °2-0.1692 °2-0.6137 °2-3.121 °20.1028 °2--1.1884 °2
S0.1421 Å °0.2088 Å °0.2185 Å °-0.3345 Å °-0.0258 Å °-0.072 Å °-0.24 Å °-0.1468 Å °-0.1163 Å °

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