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- PDB-5z7y: Crystal structure of Striga hermonthica HTL7 (ShHTL7) -

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Basic information

Entry
Database: PDB / ID: 5z7y
TitleCrystal structure of Striga hermonthica HTL7 (ShHTL7)
ComponentsHyposensitive to light 7
KeywordsHYDROLASE / Hydrolase Activity / putative receptor of strigolactone
Function / homology
Function and homology information


response to karrikin / metal ion binding
Similarity search - Function
Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Hyposensitive to light 7
Similarity search - Component
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsXu, Y. / Miyakawa, T. / Nakamura, A. / Tanokura, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Platform for Drug Discovery, Informatics, and Structural Life Science from the Ministry of Education, Culture, Sports, Science and Technology of Japan Japan
Core Research for Evolutional Science and Technology Program of Japan Science and Technology Agency Japan
Grant-in-Aid for Scientific Research on Innovative Areas from the Japan Society for the Promotion of Science (JSPS)JP17H05835 Japan
JSPS KAKENHIJP15H05621 Japan
CitationJournal: Nat Commun / Year: 2018
Title: Structural analysis of HTL and D14 proteins reveals the basis for ligand selectivity in Striga.
Authors: Xu, Y. / Miyakawa, T. / Nosaki, S. / Nakamura, A. / Lyu, Y. / Nakamura, H. / Ohto, U. / Ishida, H. / Shimizu, T. / Asami, T. / Tanokura, M.
History
DepositionJan 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hyposensitive to light 7
B: Hyposensitive to light 7
C: Hyposensitive to light 7
D: Hyposensitive to light 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,31813
Polymers125,8974
Non-polymers4229
Water12,827712
1
A: Hyposensitive to light 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6114
Polymers31,4741
Non-polymers1373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11650 Å2
MethodPISA
2
B: Hyposensitive to light 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4982
Polymers31,4741
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area11370 Å2
MethodPISA
3
C: Hyposensitive to light 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5613
Polymers31,4741
Non-polymers862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-9 kcal/mol
Surface area11720 Å2
MethodPISA
4
D: Hyposensitive to light 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6494
Polymers31,4741
Non-polymers1743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.086, 72.609, 81.122
Angle α, β, γ (deg.)97.69, 95.39, 107.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Hyposensitive to light 7 / Hydrolase / alpha/beta fold family protein


Mass: 31474.127 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Striga hermonthica (purple witchweed) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3PNA2
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 90mM Tris-HCl (pH 8.5), 27% (w/v) PEG 5000, 180mM MgCl2, 3.5% 1,4-dioxane

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 72978 / % possible obs: 93.8 % / Redundancy: 2.3 % / CC1/2: 0.994 / Rrim(I) all: 0.123 / Net I/σ(I): 7.9
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10951 / CC1/2: 0.787 / Rrim(I) all: 0.478 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z7X

5z7x


Resolution: 1.9→43.617 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 27.99
RfactorNum. reflection% reflection
Rfree0.2531 3608 4.95 %
Rwork0.2107 --
obs0.2128 72939 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→43.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8331 0 25 712 9068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048549
X-RAY DIFFRACTIONf_angle_d0.66311627
X-RAY DIFFRACTIONf_dihedral_angle_d13.3295125
X-RAY DIFFRACTIONf_chiral_restr0.0461341
X-RAY DIFFRACTIONf_plane_restr0.0041481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8996-1.92450.341030.30052043X-RAY DIFFRACTION72
1.9245-1.95090.3571310.29962402X-RAY DIFFRACTION85
1.9509-1.97880.32481430.29322689X-RAY DIFFRACTION94
1.9788-2.00830.34181540.27812698X-RAY DIFFRACTION95
2.0083-2.03970.28461340.2722676X-RAY DIFFRACTION95
2.0397-2.07310.30341360.25212751X-RAY DIFFRACTION96
2.0731-2.10890.28261510.2532746X-RAY DIFFRACTION95
2.1089-2.14720.30561400.24852657X-RAY DIFFRACTION95
2.1472-2.18850.30111240.23942747X-RAY DIFFRACTION95
2.1885-2.23320.28821230.23142664X-RAY DIFFRACTION95
2.2332-2.28180.26181400.23592705X-RAY DIFFRACTION95
2.2818-2.33480.2761370.22342724X-RAY DIFFRACTION95
2.3348-2.39320.27871290.2192715X-RAY DIFFRACTION96
2.3932-2.45790.26581390.22462732X-RAY DIFFRACTION95
2.4579-2.53020.28421460.22292735X-RAY DIFFRACTION96
2.5302-2.61190.28961370.2172713X-RAY DIFFRACTION95
2.6119-2.70520.27391430.21382720X-RAY DIFFRACTION95
2.7052-2.81350.27261530.20632662X-RAY DIFFRACTION95
2.8135-2.94160.2731410.2062725X-RAY DIFFRACTION96
2.9416-3.09660.25191320.21182754X-RAY DIFFRACTION96
3.0966-3.29060.21081410.19912719X-RAY DIFFRACTION95
3.2906-3.54450.23971410.18722654X-RAY DIFFRACTION94
3.5445-3.9010.21631490.17222663X-RAY DIFFRACTION94
3.901-4.4650.20151480.16882675X-RAY DIFFRACTION94
4.465-5.62360.21191440.18162646X-RAY DIFFRACTION93
5.6236-43.62850.22861490.20632716X-RAY DIFFRACTION96

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