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- PDB-5los: Piriformospora indica PIIN_05872 -

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Basic information

Entry
Database: PDB / ID: 5los
TitlePiriformospora indica PIIN_05872
ComponentsPIIN_05872
KeywordsMETAL BINDING PROTEIN / histidine zipper / antiparallel coiled coil
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPiriformospora indica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHartmann, M.D. / Albrecht, R. / Martin, J. / Lupas, A.N.
CitationJournal: New Phytol. / Year: 2020
Title: A secreted fungal histidine- and alanine-rich protein regulates metal ion homeostasis and oxidative stress.
Authors: Nostadt, R. / Hilbert, M. / Nizam, S. / Rovenich, H. / Wawra, S. / Martin, J. / Kupper, H. / Mijovilovich, A. / Ursinus, A. / Langen, G. / Hartmann, M.D. / Lupas, A.N. / Zuccaro, A.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PIIN_05872
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1653
Polymers13,0031
Non-polymers1612
Water1,51384
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-41 kcal/mol
Surface area5880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.370, 52.370, 198.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein PIIN_05872


Mass: 13003.274 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piriformospora indica (fungus) / Strain: DSM 11827 / Gene: PIIN_05872 / Production host: Escherichia coli (E. coli) / References: UniProt: G4TKU4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium sulfate, 100 mM sodium citrate pH 5.6, 15%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→37 Å / Num. obs: 9761 / % possible obs: 98.9 % / Redundancy: 3.47 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 16.66
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.32 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→34.69 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.061 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24461 729 7.5 %RANDOM
Rwork0.20403 ---
obs0.20711 9031 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.969 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å2-0 Å2
2---0.54 Å20 Å2
3---1.08 Å2
Refinement stepCycle: 1 / Resolution: 2→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms696 0 6 84 786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.018716
X-RAY DIFFRACTIONr_bond_other_d0.0020.02656
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.87969
X-RAY DIFFRACTIONr_angle_other_deg0.96131486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.334588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75722.85742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24815109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.626157
X-RAY DIFFRACTIONr_chiral_restr0.1310.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02848
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02199
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_it2.6472.937355
X-RAY DIFFRACTIONr_mcbond_other2.6342.931354
X-RAY DIFFRACTIONr_mcangle_it3.2694.361442
X-RAY DIFFRACTIONr_mcangle_other3.2694.368443
X-RAY DIFFRACTIONr_scbond_it3.8013.426361
X-RAY DIFFRACTIONr_scbond_other3.7923.392357
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5854.935522
X-RAY DIFFRACTIONr_long_range_B_refined7.93825.519864
X-RAY DIFFRACTIONr_long_range_B_other7.79524.689835
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 47 -
Rwork0.249 619 -
obs--94.74 %
Refinement TLS params.Method: refined / Origin x: 6.864 Å / Origin y: 4.0268 Å / Origin z: 18.1717 Å
111213212223313233
T0.0244 Å2-0.0014 Å2-0.0039 Å2-0.0426 Å20.0087 Å2--0.0071 Å2
L0.386 °20.3058 °2-0.1615 °2-4.9763 °2-5.5926 °2--8.3892 °2
S0.068 Å °-0.0818 Å °-0.0096 Å °0.0555 Å °-0.3024 Å °-0.1834 Å °-0.1905 Å °0.1461 Å °0.2344 Å °

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