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- PDB-3wjf: Crystal structure of mutant nitrobindin M75L/H76L/Q96C/V128W/M148... -

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Basic information

Entry
Database: PDB / ID: 3wjf
TitleCrystal structure of mutant nitrobindin M75L/H76L/Q96C/V128W/M148L/H158L (NB9) from Arabidopsis thaliana
ComponentsUPF0678 fatty acid-binding protein-like protein At1g79260
KeywordsTRANSPORT PROTEIN / beta-barrel / intracellular transport / hydrophobic ligands
Function / homology
Function and homology information


Isomerases; Other isomerases / isomerase activity / metal ion binding / cytosol
Similarity search - Function
THAP4-like, heme-binding beta-barrel domain / Nitrobindin family / THAP4-like, heme-binding beta-barrel domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peroxynitrite isomerase Rv2717c
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMizohata, E. / Fukumoto, K. / Onoda, A. / Bocola, M. / Arlt, M. / Inoue, T. / Schwaneberg, U. / Hayashi, T.
CitationJournal: CHEMCATCHEM / Year: 2014
Title: A Rhodium Complex-linked Hybrid Biocatalyst: Stereo-controlled Phenylacetylene Polymerization within an Engineered Protein Cavity
Authors: Fukumoto, K. / Onoda, A. / Mizohata, E. / Bocola, M. / Inoue, T. / Schwaneberg, U. / Hayashi, T.
History
DepositionOct 8, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: UPF0678 fatty acid-binding protein-like protein At1g79260
B: UPF0678 fatty acid-binding protein-like protein At1g79260


Theoretical massNumber of molelcules
Total (without water)39,0522
Polymers39,0522
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-11 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.604, 73.266, 59.518
Angle α, β, γ (deg.)90.00, 111.75, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.749949, 0.332924, 0.57161), (0.330225, -0.937164, 0.11258), (0.573173, 0.10433, -0.812766)-3.9949, -6.10531, 15.90104

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Components

#1: Protein UPF0678 fatty acid-binding protein-like protein At1g79260 / Nitrobindin


Mass: 19526.146 Da / Num. of mol.: 2 / Mutation: M75L, H76L, Q96C, V128W, M148L, H158L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g79260, At1g79260.1, YUP8H12R.14 / Plasmid: pET42b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: O64527
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 5mM MES, 200mM NaCl, 1mM dithioerythritol, 100mM Tris-HCl, 18-20% polyethylene glycol 2000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17383 / % possible obs: 95.1 % / Rsym value: 0.05 / Net I/σ(I): 23
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.294 / % possible all: 90.3

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.909 / SU B: 14.334 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27103 881 5.1 %RANDOM
Rwork0.20588 ---
obs0.20927 16290 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.309 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å20.33 Å2
2---0.56 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 0 72 2478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.9863411
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0815316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35523.73799
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.93515430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.7981514
X-RAY DIFFRACTIONr_chiral_restr0.120.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211876
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 53 -
Rwork0.256 1075 -
obs--88.96 %
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)
13.69860.5673-0.48292.19320.54532.74490.1111-0.1448-0.16450.0171-0.1178-0.14720.11290.22910.00670.03530.0168-0.01650.04690.03550.092518.7489-8.93456.0507
21.7434-0.06480.44982.69680.58382.47210.027-0.39560.09210.5026-0.15160.24080.0564-0.19730.12460.1419-0.03390.0530.1613-0.06860.124210.4789.20820.6864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 166
2X-RAY DIFFRACTION2B14 - 166

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