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- PDB-6azb: Crystal structure of Physcomitrella patens KAI2-like E -

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Basic information

Entry
Database: PDB / ID: 6azb
TitleCrystal structure of Physcomitrella patens KAI2-like E
ComponentsPp-KAI2-like E
KeywordsHYDROLASE / alpha/beta hydrolase / strigolactone binding
Function / homologyalpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / AB hydrolase-1 domain-containing protein
Function and homology information
Biological speciesPhyscomitrella patens subsp. patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.00003537274 Å
AuthorsBurger, M. / Lee, H.J. / Chory, J.
CitationJournal: Cell Rep / Year: 2019
Title: Structural Basis of Karrikin and Non-natural Strigolactone Perception in Physcomitrella patens.
Authors: Burger, M. / Mashiguchi, K. / Lee, H.J. / Nakano, M. / Takemoto, K. / Seto, Y. / Yamaguchi, S. / Chory, J.
History
DepositionSep 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pp-KAI2-like E
B: Pp-KAI2-like E


Theoretical massNumber of molelcules
Total (without water)59,7902
Polymers59,7902
Non-polymers00
Water3,531196
1
A: Pp-KAI2-like E


Theoretical massNumber of molelcules
Total (without water)29,8951
Polymers29,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pp-KAI2-like E


Theoretical massNumber of molelcules
Total (without water)29,8951
Polymers29,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.860, 45.900, 146.550
Angle α, β, γ (deg.)90.000, 97.400, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 6 - 267 / Label seq-ID: 8 - 269

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22chain 'B'BB

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Components

#1: Protein Pp-KAI2-like E


Mass: 29895.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrella patens subsp. patens (plant)
Gene: PHYPADRAFT_215526 / Plasmid: pGEX4T3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A9ST85, Hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 52.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 10% PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2016 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→72.67 Å / Num. obs: 40640 / % possible obs: 96.22 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.09026 / Rpim(I) all: 0.05544 / Net I/σ(I): 10.89
Reflection shellResolution: 2→2.072 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.3019 / Mean I/σ(I) obs: 4.48 / Num. unique obs: 3966 / CC1/2: 0.762 / Rpim(I) all: 0.1847 / % possible all: 95.84

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JYP

4jyp


Resolution: 2.00003537274→72.6647044236 Å / Cross valid method: FREE R-VALUE / σ(F): 14.0596932612 / Phase error: 32.7258986441
RfactorNum. reflection% reflection
Rfree0.253943247082 1742 4.28641732283 %
Rwork0.221130195416 --
obs0.22950736493 40640 96.2257896482 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.2902908994 Å2
Refinement stepCycle: LAST / Resolution: 2.00003537274→72.6647044236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 0 196 4276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002582298860684180
X-RAY DIFFRACTIONf_angle_d0.6060075705925690
X-RAY DIFFRACTIONf_chiral_restr0.0434431205888654
X-RAY DIFFRACTIONf_plane_restr0.0037380090963734
X-RAY DIFFRACTIONf_dihedral_angle_d4.732219119322464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05890.2787963055341300.2652130491473194X-RAY DIFFRACTION92.2588099365
2.0589-2.12530.2692049635261380.2530829286873197X-RAY DIFFRACTION91.5521191294
2.1253-2.20130.2693064311441370.2504254906113227X-RAY DIFFRACTION92.49068501
2.2013-2.28940.2677149030191390.2451028128993203X-RAY DIFFRACTION91.9873635841
2.2894-2.39360.2844111577471400.2440186416973249X-RAY DIFFRACTION92.8020565553
2.3936-2.51980.2667188570371380.2385883996033277X-RAY DIFFRACTION93.0173147885
2.5198-2.67770.2313168215341390.2452133281083233X-RAY DIFFRACTION92.8756104568
2.6777-2.88440.2526745237241390.2415529266223282X-RAY DIFFRACTION93.1592392847
2.8844-3.17450.2432153256481380.222411237563253X-RAY DIFFRACTION92.8897772701
3.1745-3.63370.2276290965481390.2073888480353273X-RAY DIFFRACTION92.0416197975
3.6337-4.57720.2463355388991350.2079574540393240X-RAY DIFFRACTION91.1136107987
4.5772-42.70520.2927267900861430.2164906713753352X-RAY DIFFRACTION91.5846994536

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