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- PDB-3wjd: Crystal structure of mutant nitrobindin F44W/M75L/H76L/Q96C/M148L... -

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Basic information

Entry
Database: PDB / ID: 3wjd
TitleCrystal structure of mutant nitrobindin F44W/M75L/H76L/Q96C/M148L/H158L (NB5) 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: 1.1 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0678 fatty acid-binding protein-like protein At1g79260
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5702
Polymers19,4781
Non-polymers921
Water3,585199
1
A: UPF0678 fatty acid-binding protein-like protein At1g79260
hetero molecules

A: UPF0678 fatty acid-binding protein-like protein At1g79260
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1404
Polymers38,9562
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2310 Å2
ΔGint-12 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.849, 79.419, 36.329
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 19478.105 Da / Num. of mol.: 1 / Mutation: F44W, M75L, H76L, Q96C, 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): BL21Start(DE3) / References: UniProt: O64527
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
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: 1.1→50 Å / Num. obs: 70416 / % possible obs: 98.9 % / Rsym value: 0.034 / Net I/σ(I): 56.3
Reflection shellResolution: 1.1→1.14 Å / Mean I/σ(I) obs: 4.7 / Rsym value: 0.293 / % possible all: 98.8

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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: 1.1→40 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.755 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16613 3554 5.1 %RANDOM
Rwork0.14456 ---
obs0.14564 66607 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 6 199 1404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021312
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.251.9931796
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2095174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08223.58553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58515239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.208159
X-RAY DIFFRACTIONr_chiral_restr0.1530.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021983
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_restr8.93531312
X-RAY DIFFRACTIONr_sphericity_free59.589522
X-RAY DIFFRACTIONr_sphericity_bonded20.15751449
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 233 -
Rwork0.225 4614 -
obs--98.36 %
Refinement TLS params.Method: refined / Origin x: 22.5883 Å / Origin y: 9.7437 Å / Origin z: 14.6371 Å
111213212223313233
T0.0074 Å2-0.0018 Å20 Å2-0.0077 Å2-0.0026 Å2--0.012 Å2
L0.1052 °2-0.0347 °2-0.0768 °2-0.0339 °2-0.0097 °2--0.1104 °2
S-0.0019 Å °0.019 Å °-0.0011 Å °-0.0026 Å °-0.0028 Å °-0.0023 Å °0.0064 Å °-0.0194 Å °0.0047 Å °

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