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- PDB-6xfo: Orthorhombic crystal form of Striga hermonthica Dwarf14 (ShD14) -

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Basic information

Entry
Database: PDB / ID: 6xfo
TitleOrthorhombic crystal form of Striga hermonthica Dwarf14 (ShD14)
ComponentsD14
KeywordsHYDROLASE / Strigolactone receptor / Alpha/beta hydrolase
Function / homologyAlpha/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 / ACETATE ION / D14
Function and homology information
Biological speciesStriga hermonthica (purple witchweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsHamiaux, C. / Snowden, K.C.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden FundPAF1301 New Zealand
CitationJournal: To Be Published
Title: To be published
Authors: Hamiaux, C. / Zhang, Y. / Snowden, K.C. / Bouwmeester, H.J.
History
DepositionJun 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 / pdbx_struct_conn_angle / struct_conn
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D14
B: D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6074
Polymers58,5232
Non-polymers832
Water7,819434
1
A: D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2862
Polymers29,2621
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3212
Polymers29,2621
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.230, 83.330, 86.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D14


Mass: 29261.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Striga hermonthica (purple witchweed) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta Gami2 / References: UniProt: A0A2U8XQ45
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris/Acetate pH 8.5, 0.2 M MgCl2, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.58→46.18 Å / Num. obs: 72148 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 17.596 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.02 / Rrim(I) all: 0.077 / Net I/σ(I): 21.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.58-1.6113.21.0392.335430.8310.2961.081100
8.66-46.1810.60.0314860.9990.0110.03295.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.37 Å38.43 Å
Translation5.37 Å38.43 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.3.6data scaling
PHASER2.5.6phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DNP

4dnp


Resolution: 1.58→38.46 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.779 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0853 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 3564 4.9 %RANDOM
Rwork0.1757 ---
obs0.1771 68492 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.85 Å2 / Biso mean: 27.199 Å2 / Biso min: 10.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0 Å2-0 Å2
2---0.39 Å20 Å2
3---0.73 Å2
Refinement stepCycle: final / Resolution: 1.58→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 5 434 4543
Biso mean--36.35 33.53 -
Num. residues----530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0134230
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174010
X-RAY DIFFRACTIONr_angle_refined_deg2.0741.6315761
X-RAY DIFFRACTIONr_angle_other_deg1.6071.579217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.22220.088228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50915676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5491541
X-RAY DIFFRACTIONr_chiral_restr0.1020.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024809
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02966
LS refinement shellResolution: 1.581→1.622 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 270 -
Rwork0.252 5005 -
all-5275 -
obs--99.98 %
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)
12.0095-0.9819-0.13872.4325-0.1580.59930.1381-0.0526-0.0691-0.1541-0.09570.14180.04480.0429-0.04240.04320.0048-0.03810.0101-0.00780.066830.37826.82101.416
21.9249-1.1888-0.21764.1254-0.46961.05380.0489-0.07510.15620.0059-0.0431-0.4191-0.0080.0466-0.00590.02190.0067-0.0040.01060.00280.082830.52626.08758.308
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 266
2X-RAY DIFFRACTION2B3 - 266

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