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- PDB-4fcz: Crystal Structure of Toluene-tolerance protein from Pseudomonas p... -

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Basic information

Entry
Database: PDB / ID: 4fcz
TitleCrystal Structure of Toluene-tolerance protein from Pseudomonas putida (strain KT2440), Northeast Structural Genomics Consortium (NESG) Target PpR99
ComponentsToluene-tolerance protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyTgt2/MlaC / Tgt2/MlaC superfamily / Toluene tolerance Ttg2/phospholipid-binding protein MlaC / MlaC protein / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Toluene tolerance protein
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.604 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target PpR99
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMay 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Toluene-tolerance protein
A: Toluene-tolerance protein


Theoretical massNumber of molelcules
Total (without water)50,2632
Polymers50,2632
Non-polymers00
Water73941
1
A: Toluene-tolerance protein


Theoretical massNumber of molelcules
Total (without water)25,1321
Polymers25,1321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Toluene-tolerance protein


Theoretical massNumber of molelcules
Total (without water)25,1321
Polymers25,1321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.868, 40.883, 82.399
Angle α, β, γ (deg.)90.00, 106.49, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer,24.6 kD,88.3%

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Components

#1: Protein Toluene-tolerance protein


Mass: 25131.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: ttg2D, PP_0961 / References: UniProt: Q88P91
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 14, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.068
ReflectionResolution: 2.6→39.086 Å / Num. obs: 28693 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 10

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Processing

Software
NameVersionClassificationNB
PHENIXdev_1269refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX(AutoSolve)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.604→39.086 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0.13 / Phase error: 30.07 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2976 1574 10.63 %
Rwork0.2326 --
obs0.2367 14803 92.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.825 Å2
Baniso -1Baniso -2Baniso -3
1--7.206 Å2-0 Å2-6.274 Å2
2--1.742 Å20 Å2
3---5.464 Å2
Refinement stepCycle: LAST / Resolution: 2.604→39.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 0 41 2903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092918
X-RAY DIFFRACTIONf_angle_d1.1893939
X-RAY DIFFRACTIONf_dihedral_angle_d16.2321101
X-RAY DIFFRACTIONf_chiral_restr0.076423
X-RAY DIFFRACTIONf_plane_restr0.006529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6067-2.69080.3678920.2827817X-RAY DIFFRACTION56
2.6908-2.78690.37071210.27231034X-RAY DIFFRACTION72
2.7869-2.89840.32191270.26111184X-RAY DIFFRACTION82
2.8984-3.03030.35261340.26451200X-RAY DIFFRACTION85
3.0303-3.18990.29241440.25691249X-RAY DIFFRACTION86
3.1899-3.38960.31641400.23771280X-RAY DIFFRACTION88
3.3896-3.65110.30151520.23251262X-RAY DIFFRACTION88
3.6511-4.0180.2811460.21121293X-RAY DIFFRACTION89
4.018-4.59830.22671440.20621305X-RAY DIFFRACTION89
4.5983-5.7890.2871500.21341311X-RAY DIFFRACTION89
5.789-34.60580.30691520.21881359X-RAY DIFFRACTION89
Refinement TLS params.Method: refined / Origin x: 5.3534 Å / Origin y: 18.1984 Å / Origin z: 53.8285 Å
111213212223313233
T0.3965 Å2-0.0103 Å2-0.0917 Å2-0.0468 Å2-0.0179 Å2--0.3299 Å2
L0.3589 °20.0132 °2-0.0442 °2-1.5014 °2-0.3138 °2--0.4231 °2
S0.0355 Å °-0.0334 Å °0.0348 Å °0.1936 Å °-0.0066 Å °-0.263 Å °-0.002 Å °0.0352 Å °0.0231 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA20 - 206
2X-RAY DIFFRACTION1allB22 - 205

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