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- PDB-4ymy: Crystal structure of mutant nitrobindin M75A/H76L/Q96C/M148L/H158... -

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Basic information

Entry
Database: PDB / ID: 4ymy
TitleCrystal structure of mutant nitrobindin M75A/H76L/Q96C/M148L/H158A (NB11) from Arabidopsis thaliana
ComponentsUPF0678 fatty acid-binding protein-like protein At1g79260
KeywordsTRANSPORT PROTEIN / beta-barrel / intracellular transport / hydrophobic ligand / Cytoplasm
Function / homology
Function and homology information


Isomerases; Other isomerases / isomerase activity / metal ion binding / cytosol
Similarity search - Function
Nitrobindin family / THAP4-like, heme-binding beta-barrel domain / 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 Å
AuthorsMizohata, E. / Himiyama, T. / Tachikawa, K. / Oohora, K. / Onoda, A. / Hayashi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
MEXTarea 2204 Japan
CitationJournal: Acs Catalysis / Year: 2015
Title: A Highly Active Biohybrid Catalyst for Olefin Metathesis in Water: Impact of a Hydrophobic Cavity in a beta-Barrel Protein
Authors: Sauer, D.F. / Himiyama, T. / Tachikawa, K. / Fukumoto, K. / Onoda, A. / Mizohata, E. / Inoue, T. / Bocola, M. / Schwaneberg, U. / Hayashi, T. / Okuda, J.
History
DepositionMar 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7235
Polymers19,3551
Non-polymers3684
Water3,513195
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)39,44710
Polymers38,7102
Non-polymers7378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area3740 Å2
ΔGint-14 kcal/mol
Surface area14850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.654, 79.285, 36.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-378-

HOH

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Components

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


Mass: 19354.908 Da / Num. of mol.: 1 / Fragment: UNP residues 2-166 / Mutation: M75A/H76L/Q96C/M148L/H158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g79260, 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: Tris-HCl buffer, polyethylene glycol 2000

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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 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 92122 / % possible obs: 98.3 % / Redundancy: 10.3 % / Rsym value: 0.051 / Net I/σ(I): 42.7
Reflection shellResolution: 1→1.04 Å / Mean I/σ(I) obs: 4.2 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data processing
PHASERphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A13

2a13


Resolution: 1→47.67 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.458 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13593 4620 5 %RANDOM
Rwork0.12312 ---
obs0.12375 87472 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.747 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0 Å2
2--0.09 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 24 195 1409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021321
X-RAY DIFFRACTIONr_bond_other_d0.0010.021292
X-RAY DIFFRACTIONr_angle_refined_deg2.022.0011803
X-RAY DIFFRACTIONr_angle_other_deg1.77333017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8845176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09623.58553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.74715236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.272159
X-RAY DIFFRACTIONr_chiral_restr0.1390.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211459
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02278
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_it1.3131.391635
X-RAY DIFFRACTIONr_mcbond_other1.3141.391634
X-RAY DIFFRACTIONr_mcangle_it1.7012.102798
X-RAY DIFFRACTIONr_mcangle_other1.72.102799
X-RAY DIFFRACTIONr_scbond_it3.281.898686
X-RAY DIFFRACTIONr_scbond_other3.2761.898686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1212.658994
X-RAY DIFFRACTIONr_long_range_B_refined4.76213.4621496
X-RAY DIFFRACTIONr_long_range_B_other4.20612.5171418
X-RAY DIFFRACTIONr_rigid_bond_restr5.83332613
X-RAY DIFFRACTIONr_sphericity_free35.242577
X-RAY DIFFRACTIONr_sphericity_bonded11.12452694
LS refinement shellResolution: 1.001→1.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 333 -
Rwork0.222 6099 -
obs--93.53 %

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