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- PDB-3a8r: The structure of the N-terminal regulatory domain of a plant NADP... -

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Basic information

Entry
Database: PDB / ID: 3a8r
TitleThe structure of the N-terminal regulatory domain of a plant NADPH oxidase
ComponentsPutative uncharacterized protein
KeywordsCALCIUM BINDING PROTEIN / EF-hand / Membrane / Oxidoreductase / Transmembrane
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor / NAD(P)H oxidase H2O2-forming activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / calcium ion binding / plasma membrane
Similarity search - Function
NADPH oxidase Respiratory burst / Respiratory burst NADPH oxidase / Cytochrome b245, heavy chain / Ferric reductase, NAD binding domain / : / Ferric reductase NAD binding domain / FAD-binding 8 / FAD-binding domain / Ferric reductase transmembrane component-like domain / Ferric reductase like transmembrane component ...NADPH oxidase Respiratory burst / Respiratory burst NADPH oxidase / Cytochrome b245, heavy chain / Ferric reductase, NAD binding domain / : / Ferric reductase NAD binding domain / FAD-binding 8 / FAD-binding domain / Ferric reductase transmembrane component-like domain / Ferric reductase like transmembrane component / EF-hand / Recoverin; domain 1 / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Respiratory burst oxidase homolog protein B
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsOda, T. / Hashimoto, H. / Kuwabara, N. / Akashi, S. / Hayashi, K. / Kojima, C. / Wong, H.L. / Kawasaki, T. / Shimamoto, K. / Sato, M. / Shimizu, T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The structure of the N-terminal regulatory domain of a plant NADPH oxidase and its functional implications
Authors: Oda, T. / Hashimoto, H. / Kuwabara, N. / Akashi, S. / Hayashi, K. / Kojima, C. / Wong, H.L. / Kawasaki, T. / Shimamoto, K. / Sato, M. / Shimizu, T.
History
DepositionOct 7, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 17, 2014Group: Other
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8294
Polymers39,7492
Non-polymers802
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-68 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.418, 72.162, 118.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein / RbohB / Os01g0360200 protein / Respiratory burst oxidase protein B


Mass: 19874.568 Da / Num. of mol.: 2 / Fragment: EF-hand domain, residues 138-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: B1164G11.26, Os01g0360200, OsJ_01746 / Plasmid: pET32c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: Q5ZAJ0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES-NaOH buffer, pH 7.0 containing 0.6M sodium thiocyanate, 13%(w/v) PEG 8000, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONPhoton Factory BL-5A20.97915, 0.97931, 0.96411
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 9, 2006
ADSC QUANTUM 3152CCDFeb 19, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatoreSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979151
30.979311
40.964111
ReflectionResolution: 2.4→50 Å / Num. all: 21074 / Num. obs: 20590 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 64.3 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 16.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 6 / Num. unique all: 2072 / Rsym value: 0.234 / % possible all: 86

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Processing

Software
NameVersionClassification
beamline sceduring softwaredata collection
SOLVEphasing
REFMAC5.6.0041refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.47 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU B: 17.178 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.319 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1047 5.1 %RANDOM
Rwork0.234 ---
all0.235 19437 --
obs0.235 19437 100 %-
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: 44.754 Å2
Baniso -1Baniso -2Baniso -3
1--2.46 Å20 Å20 Å2
2--1.12 Å20 Å2
3---1.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.242 Å0.319 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 2 77 2698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222647
X-RAY DIFFRACTIONr_bond_other_d0.0050.021828
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9763550
X-RAY DIFFRACTIONr_angle_other_deg0.93834463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6535331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66625.194129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.60615514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.961518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022943
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02525
X-RAY DIFFRACTIONr_mcbond_it0.0460.215181
X-RAY DIFFRACTIONr_mcbond_other0.0370.228664
LS refinement shellResolution: 2.4→2.461 Å / Rfactor Rfree error: 0.242 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 61 -
Rwork0.283 1194 -
obs-1255 100 %
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)
10.5384-0.1124-0.03791.0889-0.29570.6533-0.00050.1845-0.2675-0.25690.0382-0.08810.141-0.1183-0.03770.0758-0.01830.04630.31760.00630.2737-14.7103-7.168913.1868
21.29870.439-0.10211.1054-0.42080.2574-0.05670.04080.134-0.18140.0883-0.09030.0184-0.1375-0.03150.07020.01190.09350.2650.01190.2053-12.801517.803115.9865
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A138 - 303
2X-RAY DIFFRACTION2B138 - 304

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