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

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Basic information

Entry
Database: PDB / ID: 2vrc
TitleCrystal structure of the Citrobacter sp. triphenylmethane reductase complexed with NADP(H)
Components(TRIPHENYLMETHANE REDUCTASE) x 2
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
Triphenylmethane reductase
Similarity search - Component
Biological speciesCITROBACTER SP. MY-5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIPHENYLMETHANE REDUCTASE
B: TRIPHENYLMETHANE REDUCTASE
C: TRIPHENYLMETHANE REDUCTASE
D: TRIPHENYLMETHANE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)124,1944
Polymers124,1944
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-28.6 kcal/mol
Surface area57760 Å2
MethodPQS
Unit cell
Length a, b, c (Å)75.957, 76.954, 272.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRIPHENYLMETHANE REDUCTASE


Mass: 31051.574 Da / Num. of mol.: 3 / Mutation: YES
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: Protein TRIPHENYLMETHANE REDUCTASE


Mass: 31039.520 Da / Num. of mol.: 1 / Mutation: YES
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 21 TO MSE ENGINEERED RESIDUE IN CHAIN A, LYS 22 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, LEU 21 TO MSE ENGINEERED RESIDUE IN CHAIN A, LYS 22 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 23 TO ALA ENGINEERED RESIDUE IN CHAIN A, LEU 235 TO MSE ENGINEERED RESIDUE IN CHAIN B, LEU 21 TO MSE ENGINEERED RESIDUE IN CHAIN B, LYS 22 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 23 TO ALA ENGINEERED RESIDUE IN CHAIN B, LEU 235 TO MSE ENGINEERED RESIDUE IN CHAIN C, LEU 21 TO MSE ENGINEERED RESIDUE IN CHAIN C, LYS 22 TO ALA ENGINEERED RESIDUE IN CHAIN C, LYS 23 TO ALA ENGINEERED RESIDUE IN CHAIN C, LEU 235 TO MSE ENGINEERED RESIDUE IN CHAIN D, LEU 21 TO MSE ENGINEERED RESIDUE IN CHAIN D, LYS 22 TO ALA ENGINEERED RESIDUE IN CHAIN D, LYS 23 TO ALA ENGINEERED RESIDUE IN CHAIN D, LEU 235 TO MSE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 8
Details: 0.3M NAH2PO4,1.2M KH2PO4,0.2M NACL, 0.1M IMIDAZOLE(PH 8.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.97947
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 56316 / % possible obs: 100 % / Observed criterion σ(I): -2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 42.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 8.45 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.5→29.36 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.174 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2747 5.1 %RANDOM
Rwork0.19 ---
obs0.192 51196 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.55 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å20 Å20 Å2
2--4.81 Å20 Å2
3----2.55 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8647 0 0 242 8889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228825
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.94812021
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75651142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.38925.307375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.39151428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.21528
X-RAY DIFFRACTIONr_chiral_restr0.0960.21432
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026628
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.24101
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.26153
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2371
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1131.55796
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21929151
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.24533342
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3254.52870
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: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 184 -
Rwork0.237 3350 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.30820.162-0.11191.0814-0.29712.30070.0034-0.0524-0.1569-0.1915-0.0166-0.20460.24310.07860.0133-0.08630.05040.079-0.24710.03310.017-19.686-3.8266.247
22.9197-0.5539-0.17310.78070.37580.89510.11930.32460.3231-0.1375-0.1211-0.2437-0.13450.00610.0018-0.06150.01070.0798-0.09140.0247-0.0201-22.15631.71953.106
32.3101-0.0784-0.91491.64271.03284.0879-0.1827-0.2996-0.14380.21680.1859-0.22660.64730.6941-0.0031-0.07150.0737-0.04170.17050.0499-0.175111.6978.92916.62
41.5546-0.54260.59821.2438-1.37762.9343-0.1808-0.09870.05090.23680.05820.0935-0.3066-0.44150.1225-0.03740.020.00190.1231-0.0613-0.1451-24.48422.12720.663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 285
2X-RAY DIFFRACTION2B1 - 285
3X-RAY DIFFRACTION3C1 - 285
4X-RAY DIFFRACTION4D1 - 285

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