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- PDB-4wuj: Structural Biochemistry of a Fungal LOV Domain Photoreceptor Reve... -

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Basic information

Entry
Database: PDB / ID: 4wuj
TitleStructural Biochemistry of a Fungal LOV Domain Photoreceptor Reveals an Evolutionarily Conserved Pathway Integrating Blue-Light and Oxidative Stress
ComponentsGlycoside hydrolase family 15, cellulose signaling associated protein envoy
KeywordsCIRCADIAN CLOCK PROTEIN / LOV domain / blue-light / photoreceptor / circadian clock
Function / homology
Function and homology information


hydrolase activity / nucleotide binding / identical protein binding / nucleus
Similarity search - Function
PAS domain / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Glycoside hydrolase family 15, cellulose signaling associated protein envoy
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsHopkins, H.C. / Lokhandwala, J. / Zoltowski, B.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Herman Frasch Foundation739-HF12 United States
CitationJournal: Structure / Year: 2015
Title: Structural Biochemistry of a Fungal LOV Domain Photoreceptor Reveals an Evolutionarily Conserved Pathway Integrating Light and Oxidative Stress.
Authors: Lokhandwala, J. / Hopkins, H.C. / Rodriguez-Iglesias, A. / Dattenbock, C. / Schmoll, M. / Zoltowski, B.D.
History
DepositionOct 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 15, cellulose signaling associated protein envoy
B: Glycoside hydrolase family 15, cellulose signaling associated protein envoy
C: Glycoside hydrolase family 15, cellulose signaling associated protein envoy
D: Glycoside hydrolase family 15, cellulose signaling associated protein envoy
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,23514
Polymers63,8334
Non-polymers2,40210
Water4,522251
1
C: Glycoside hydrolase family 15, cellulose signaling associated protein envoy
hetero molecules

A: Glycoside hydrolase family 15, cellulose signaling associated protein envoy
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1177
Polymers31,9172
Non-polymers1,2015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_746-x+2,y-1/2,-z+11
Buried area5160 Å2
ΔGint-78 kcal/mol
Surface area14090 Å2
MethodPISA
2
B: Glycoside hydrolase family 15, cellulose signaling associated protein envoy
D: Glycoside hydrolase family 15, cellulose signaling associated protein envoy
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1177
Polymers31,9172
Non-polymers1,2015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-78 kcal/mol
Surface area13720 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-144 kcal/mol
Surface area29460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.342, 102.225, 71.550
Angle α, β, γ (deg.)90.000, 91.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycoside hydrolase family 15, cellulose signaling associated protein envoy


Mass: 15958.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea jecorina (fungus) / Strain: QM6a / Gene: env1, TRIREDRAFT_81609 / Plasmid: pGST / Production host: Escherichia coli (E. coli) / References: UniProt: G0RUC2
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Hepes pH 7.5 buffer, 6% (v/v) Peg400 and 1.4M ammonium sulfate
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 30153 / % possible obs: 96.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.047 / Χ2: 2.669 / Net I/av σ(I): 46.174 / Net I/σ(I): 25.6 / Num. measured all: 121511
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.23-2.273.20.11812062.28878.3
2.27-2.313.40.11515372.35497
2.31-2.353.50.10914852.28696.9
2.35-2.43.80.10315122.39597.2
2.4-2.4540.09615662.50997.7
2.45-2.514.20.0915262.67498.8
2.51-2.574.20.0815332.6498.2
2.57-2.644.20.07615422.7698.5
2.64-2.724.30.06615362.54298.5
2.72-2.814.30.06415452.66898.2
2.81-2.914.20.05815212.66698.4
2.91-3.034.20.05315632.6998.9
3.03-3.164.20.0515512.80498.7
3.16-3.334.20.04515362.71998.5
3.33-3.544.20.0415412.65998.7
3.54-3.814.10.03915602.7698.1
3.81-4.24.10.03815362.72897.5
4.2-4.840.03614612.70692.6
4.8-6.0540.03715332.79796.6
6.05-503.80.04413633.56884.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000phasing
Cootmodel building
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D72

3d72


Resolution: 2.23→44.334 Å / FOM work R set: 0.7969 / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 1514 5.03 %Random Selection
Rwork0.206 28588 --
obs0.2087 30102 96.68 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.759 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso max: 110.19 Å2 / Biso mean: 40.3 Å2 / Biso min: 14.02 Å2
Baniso -1Baniso -2Baniso -3
1--4.8911 Å2-0 Å26.0038 Å2
2---8.8425 Å2-0 Å2
3---13.7335 Å2
Refinement stepCycle: final / Resolution: 2.23→44.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4309 0 230 251 4790
Biso mean--31.4 41.73 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144564
X-RAY DIFFRACTIONf_angle_d1.4856244
X-RAY DIFFRACTIONf_chiral_restr0.076695
X-RAY DIFFRACTIONf_plane_restr0.008794
X-RAY DIFFRACTIONf_dihedral_angle_d18.2671654
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2291-2.30110.32991390.2292509264894
2.3011-2.38330.30021450.22562582272797
2.3833-2.47870.26541330.22342638277198
2.4787-2.59150.26491320.21212634276698
2.5915-2.72810.25981450.21592622276799
2.7281-2.8990.31291160.21232655277198
2.899-3.12280.29011650.21422645281099
3.1228-3.4370.27091260.20712659278599
3.437-3.93410.26111370.20772641277898
3.9341-4.95550.21981370.17222561269895
4.9555-44.3430.22761390.21352442258189

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