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- PDB-7bbm: Mutant nitrobindin M75L/H76L/Q96C/M148L (NB4H) from Arabidopsis t... -

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Basic information

Entry
Database: PDB / ID: 7bbm
TitleMutant nitrobindin M75L/H76L/Q96C/M148L (NB4H) from Arabidopsis thaliana with cofactor MnPPIX
ComponentsUPF0678 fatty acid-binding protein-like protein At1g79260
KeywordsTRANSPORT PROTEIN / beta-barrel / intracellular transport / metal cofactor / porphyrin cofactor / mnppix / nitrobindin
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
Similarity search - Domain/homology
MANGANESE PROTOPORPHYRIN IX / Peroxynitrite isomerase Rv2717c
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsMinges, A. / Sauer, D.F. / Wittwer, M. / Markel, U. / Spiertz, M. / Schiffels, J. / Davari, M.D. / Okuda, J. / Schwaneberg, U. / Groth, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031B0297 Germany
Citation
Journal: Catalysis Science And Technology / Year: 2021
Title: Chemogenetic engineering of nitrobindin toward an artificial epoxygenase
Authors: Sauer, D.F. / Wittwer, M. / Markel, U. / Minges, A. / Spiertz, M. / Schiffels, J. / Davari, M.D. / Groth, G. / Okuda, J. / Schwaneberg, U.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2011
Title: Data processing and analysis with the autoPROC toolbox.
Authors: Vonrhein, C. / Flensburg, C. / Keller, P. / Sharff, A. / Smart, O. / Paciorek, W. / Womack, T. / Bricogne, G.
#3: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / ...Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / Prisant, M.G. / Read, R.J. / Richardson, J.S. / Richardson, D.C. / Sammito, M.D. / Sobolev, O.V. / Stockwell, D.H. / Terwilliger, T.C. / Urzhumtsev, A.G. / Videau, L.L. / Williams, C.J. / Adams, P.D.
History
DepositionDec 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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)19,4108
Polymers18,4221
Non-polymers9887
Water3,549197
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)38,82016
Polymers36,8442
Non-polymers1,97614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)59.900, 79.547, 36.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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


Mass: 18421.908 Da / Num. of mol.: 1 / Mutation: M75L, H76L, Q96C, M148L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g79260, YUP8H12R.14 / Production host: Escherichia coli (E. coli) / References: UniProt: O64527
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MNH / MANGANESE PROTOPORPHYRIN IX


Mass: 615.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32MnN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 285.15 K / Method: microbatch / pH: 8.6
Details: 1:1 mixture (2 uL total volume) of protein (20 mg/mL) and precipitant solution containing 100 mM Tris/HCl pH 8.6, 18 % (w/v) PEG 2000; 30% (v/v) Ethylene glycol were added as cryo-protectant ...Details: 1:1 mixture (2 uL total volume) of protein (20 mg/mL) and precipitant solution containing 100 mM Tris/HCl pH 8.6, 18 % (w/v) PEG 2000; 30% (v/v) Ethylene glycol were added as cryo-protectant before harvesting and flash freezing in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976253 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2020
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976253 Å / Relative weight: 1
ReflectionResolution: 1.1375→39.774 Å / Num. obs: 64928 / % possible obs: 99.94 % / Redundancy: 12.2 % / Biso Wilson estimate: 14.83 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.022 / Rrim(I) all: 0.078 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.1375-1.15710.931.0372.16431900.81070.3251.088100
1.157-1.17811.130.9612.39532260.8350.2981.007100
1.178-1.20111.080.8712.62231560.85450.270.91399.94
1.201-1.22511.50.812.91832330.86130.2470.84899.97
1.225-1.25212.150.7023.42931950.90950.2080.733100
1.252-1.28112.50.5674.24831920.94350.1650.591100
1.281-1.31312.70.4895.01632330.95520.1410.509100
1.313-1.34912.490.4295.68932360.95960.1250.447100
1.349-1.38811.950.3586.53331910.97380.1070.374100
1.388-1.43312.580.2898.15832290.98330.0840.301100
1.433-1.48412.40.2379.84232190.98550.070.248100
1.484-1.54412.80.18512.47132340.99140.0530.192100
1.544-1.61412.70.14715.25532300.99430.0430.153100
1.614-1.69912.090.12617.24432410.99430.0380.132100
1.699-1.80512.540.10221.52132600.99640.030.10799.97
1.805-1.94512.70.08127.03732710.9970.0240.085100
1.945-2.14112.620.0731.54732700.99730.0210.073100
2.141-2.45120.06733.37133020.99740.020.07100
2.45-3.08712.670.06336.88233300.99730.0180.06599.88
3.087-39.77411.720.06237.59534900.99740.0180.06499.77

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
Coot0.9.2model building
BUCCANEER1.6.10model building
PHASER2.8.3phasing
Aimless0.7.4data scaling
XDS20200417data reduction
MxCuBE3data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WJB

3wjb


Resolution: 1.14→39.77 Å / SU ML: 0.0989 / SU R Cruickshank DPI: 0.039 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.1703
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1581 3158 4.89 %
Rwork0.1445 117741 -
obs0.1451 64903 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.64 Å2
Refine analyzeLuzzati coordinate error obs: 0.2065 Å
Refinement stepCycle: LAST / Resolution: 1.14→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 67 197 1462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221474
X-RAY DIFFRACTIONf_angle_d1.33952029
X-RAY DIFFRACTIONf_chiral_restr0.1204209
X-RAY DIFFRACTIONf_plane_restr0.0157264
X-RAY DIFFRACTIONf_dihedral_angle_d12.3489231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.25252250.22463937X-RAY DIFFRACTION99.95
1.15-1.160.21462080.21693830X-RAY DIFFRACTION100
1.16-1.180.25351740.21434053X-RAY DIFFRACTION99.95
1.18-1.190.25691910.20853864X-RAY DIFFRACTION100
1.19-1.210.26812100.20493921X-RAY DIFFRACTION99.83
1.21-1.230.25792090.18953956X-RAY DIFFRACTION100
1.23-1.240.18681860.19023898X-RAY DIFFRACTION100
1.24-1.260.22082120.17073982X-RAY DIFFRACTION99.98
1.26-1.280.17511950.16493870X-RAY DIFFRACTION100
1.28-1.30.17212130.15354004X-RAY DIFFRACTION100
1.3-1.320.17422000.14933871X-RAY DIFFRACTION100
1.32-1.350.18841890.1463994X-RAY DIFFRACTION99.95
1.35-1.370.15992200.13633859X-RAY DIFFRACTION100
1.37-1.40.16521920.12873995X-RAY DIFFRACTION100
1.4-1.430.12931850.12243906X-RAY DIFFRACTION99.93
1.43-1.470.16652010.11563965X-RAY DIFFRACTION100
1.47-1.50.13392150.11093871X-RAY DIFFRACTION100
1.5-1.540.12062320.10323905X-RAY DIFFRACTION100
1.54-1.590.1362030.1063945X-RAY DIFFRACTION100
1.59-1.640.12651980.10483889X-RAY DIFFRACTION100
1.64-1.70.13651820.11353965X-RAY DIFFRACTION100
1.7-1.770.15891950.11573964X-RAY DIFFRACTION99.98
1.77-1.850.13021820.11853959X-RAY DIFFRACTION100
1.85-1.940.1312180.1163907X-RAY DIFFRACTION100
1.94-2.070.11872130.11213913X-RAY DIFFRACTION100
2.07-2.230.14131890.11533924X-RAY DIFFRACTION99.95
2.23-2.450.15412000.13373952X-RAY DIFFRACTION99.95
2.45-2.80.14512280.15263911X-RAY DIFFRACTION99.52
2.81-3.530.15651960.15713871X-RAY DIFFRACTION98.98
3.53-39.770.18421930.17583860X-RAY DIFFRACTION97.95

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