HEADER TRANSFERASE 23-JUN-18 6A5D TITLE CRYSTAL STRUCTURE OF PLANT GLYCOSYLPHOSPHATIDYLINOSITOL-ANCHORED TITLE 2 PROTEIN LLG1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GPI-ANCHORED PROTEIN LLG1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 24-159; COMPND 5 SYNONYM: LORELEI-LIKE-GPI-ANCHORED PROTEIN 1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: LLG1; SOURCE 6 EXPRESSION_SYSTEM: INSECT CELL EXPRESSION VECTOR PTIE1; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 266783 KEYWDS A PLANT RECEPTOR L1, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.XIAO,J.CHAI REVDAT 4 22-NOV-23 6A5D 1 HETSYN LINK REVDAT 3 29-JUL-20 6A5D 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 15-JAN-20 6A5D 1 JRNL REVDAT 1 26-JUN-19 6A5D 0 JRNL AUTH Y.XIAO,M.STEGMANN,Z.HAN,T.A.DEFALCO,K.PARYS,L.XU, JRNL AUTH 2 Y.BELKHADIR,C.ZIPFEL,J.CHAI JRNL TITL MECHANISMS OF RALF PEPTIDE PERCEPTION BY A HETEROTYPIC JRNL TITL 2 RECEPTOR COMPLEX. JRNL REF NATURE V. 572 270 2019 JRNL REFN ESSN 1476-4687 JRNL PMID 31291642 JRNL DOI 10.1038/S41586-019-1409-7 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC (1.10.1_2155: ???) REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 35275 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1774 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1438 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 226 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6A5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1300008178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35300 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09600 REMARK 200 FOR THE DATA SET : 26.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.96900 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6A5E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 23.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 6.5, 28% POLYETHYLENE REMARK 280 GLYCOL 2,000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 33.25800 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 24 REMARK 465 PHE A 25 REMARK 465 ILE A 26 REMARK 465 SER A 27 REMARK 465 ASP A 28 REMARK 465 GLY A 29 REMARK 465 VAL A 30 REMARK 465 PHE A 31 REMARK 465 GLU A 32 REMARK 465 SER A 33 REMARK 465 GLN A 34 REMARK 465 SER A 35 REMARK 465 LEU A 36 REMARK 465 VAL A 37 REMARK 465 LEU A 38 REMARK 465 GLY A 39 REMARK 465 ARG A 40 REMARK 465 ASN A 41 REMARK 465 LEU A 42 REMARK 465 LEU A 43 REMARK 465 GLN A 44 REMARK 465 THR A 45 REMARK 465 THR A 139 REMARK 465 SER A 140 REMARK 465 ALA A 141 REMARK 465 GLU A 142 REMARK 465 VAL A 143 REMARK 465 ASN A 144 REMARK 465 ALA A 145 REMARK 465 ALA A 146 REMARK 465 THR A 147 REMARK 465 THR A 148 REMARK 465 SER A 149 REMARK 465 SER A 150 REMARK 465 SER A 151 REMARK 465 ARG A 152 REMARK 465 LEU A 153 REMARK 465 TRP A 154 REMARK 465 LEU A 155 REMARK 465 THR A 156 REMARK 465 VAL A 157 REMARK 465 SER A 158 REMARK 465 ALA A 159 REMARK 465 SER B 24 REMARK 465 PHE B 25 REMARK 465 ILE B 26 REMARK 465 SER B 27 REMARK 465 ASP B 28 REMARK 465 GLY B 29 REMARK 465 VAL B 30 REMARK 465 PHE B 31 REMARK 465 GLU B 32 REMARK 465 SER B 33 REMARK 465 GLN B 34 REMARK 465 SER B 35 REMARK 465 LEU B 36 REMARK 465 VAL B 37 REMARK 465 LEU B 38 REMARK 465 GLY B 39 REMARK 465 ARG B 40 REMARK 465 ASN B 41 REMARK 465 LEU B 42 REMARK 465 LEU B 43 REMARK 465 GLN B 44 REMARK 465 THR B 45 REMARK 465 THR B 139 REMARK 465 SER B 140 REMARK 465 ALA B 141 REMARK 465 GLU B 142 REMARK 465 VAL B 143 REMARK 465 ASN B 144 REMARK 465 ALA B 145 REMARK 465 ALA B 146 REMARK 465 THR B 147 REMARK 465 THR B 148 REMARK 465 SER B 149 REMARK 465 SER B 150 REMARK 465 SER B 151 REMARK 465 ARG B 152 REMARK 465 LEU B 153 REMARK 465 TRP B 154 REMARK 465 LEU B 155 REMARK 465 THR B 156 REMARK 465 VAL B 157 REMARK 465 SER B 158 REMARK 465 ALA B 159 DBREF 6A5D A 24 159 UNP Q9FKT1 LLG1_ARATH 24 159 DBREF 6A5D B 24 159 UNP Q9FKT1 LLG1_ARATH 24 159 SEQRES 1 A 136 SER PHE ILE SER ASP GLY VAL PHE GLU SER GLN SER LEU SEQRES 2 A 136 VAL LEU GLY ARG ASN LEU LEU GLN THR LYS LYS THR CYS SEQRES 3 A 136 PRO VAL ASN PHE GLU PHE MET ASN TYR THR ILE ILE THR SEQRES 4 A 136 SER LYS CYS LYS GLY PRO LYS TYR PRO PRO LYS GLU CYS SEQRES 5 A 136 CYS GLY ALA PHE LYS ASP PHE ALA CYS PRO TYR THR ASP SEQRES 6 A 136 GLN LEU ASN ASP LEU SER SER ASP CYS ALA THR THR MET SEQRES 7 A 136 PHE SER TYR ILE ASN LEU TYR GLY LYS TYR PRO PRO GLY SEQRES 8 A 136 LEU PHE ALA ASN GLN CYS LYS GLU GLY LYS GLU GLY LEU SEQRES 9 A 136 GLU CYS PRO ALA GLY SER GLN LEU PRO PRO GLU THR SER SEQRES 10 A 136 ALA GLU VAL ASN ALA ALA THR THR SER SER SER ARG LEU SEQRES 11 A 136 TRP LEU THR VAL SER ALA SEQRES 1 B 136 SER PHE ILE SER ASP GLY VAL PHE GLU SER GLN SER LEU SEQRES 2 B 136 VAL LEU GLY ARG ASN LEU LEU GLN THR LYS LYS THR CYS SEQRES 3 B 136 PRO VAL ASN PHE GLU PHE MET ASN TYR THR ILE ILE THR SEQRES 4 B 136 SER LYS CYS LYS GLY PRO LYS TYR PRO PRO LYS GLU CYS SEQRES 5 B 136 CYS GLY ALA PHE LYS ASP PHE ALA CYS PRO TYR THR ASP SEQRES 6 B 136 GLN LEU ASN ASP LEU SER SER ASP CYS ALA THR THR MET SEQRES 7 B 136 PHE SER TYR ILE ASN LEU TYR GLY LYS TYR PRO PRO GLY SEQRES 8 B 136 LEU PHE ALA ASN GLN CYS LYS GLU GLY LYS GLU GLY LEU SEQRES 9 B 136 GLU CYS PRO ALA GLY SER GLN LEU PRO PRO GLU THR SER SEQRES 10 B 136 ALA GLU VAL ASN ALA ALA THR THR SER SER SER ARG LEU SEQRES 11 B 136 TRP LEU THR VAL SER ALA HET NAG C 1 14 HET FUC C 2 10 HET FUC C 3 10 HET NAG D 1 14 HET FUC D 2 10 HET FUC D 3 10 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 3 FUC 4(C6 H12 O5) FORMUL 5 HOH *226(H2 O) HELIX 1 AA1 ASN A 52 MET A 56 5 5 HELIX 2 AA2 TYR A 58 SER A 63 1 6 HELIX 3 AA3 PRO A 71 CYS A 84 1 14 HELIX 4 AA4 TYR A 86 ASN A 91 1 6 HELIX 5 AA5 ASP A 96 LYS A 110 1 15 HELIX 6 AA6 GLY A 114 GLY A 123 1 10 HELIX 7 AA7 ASN B 52 MET B 56 5 5 HELIX 8 AA8 TYR B 58 SER B 63 1 6 HELIX 9 AA9 PRO B 71 CYS B 84 1 14 HELIX 10 AB1 TYR B 86 ASN B 91 1 6 HELIX 11 AB2 ASP B 96 LYS B 110 1 15 HELIX 12 AB3 GLY B 114 CYS B 120 1 7 SSBOND 1 CYS A 49 CYS A 97 1555 1555 2.08 SSBOND 2 CYS A 65 CYS A 75 1555 1555 2.03 SSBOND 3 CYS A 76 CYS A 120 1555 1555 2.04 SSBOND 4 CYS A 84 CYS A 129 1555 1555 2.03 SSBOND 5 CYS B 49 CYS B 97 1555 1555 2.14 SSBOND 6 CYS B 65 CYS B 75 1555 1555 2.03 SSBOND 7 CYS B 76 CYS B 120 1555 1555 2.08 SSBOND 8 CYS B 84 CYS B 129 1555 1555 2.03 LINK ND2 ASN A 57 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN B 57 C1 NAG D 1 1555 1555 1.45 LINK O3 NAG C 1 C1 FUC C 2 1555 1555 1.44 LINK O6 NAG C 1 C1 FUC C 3 1555 1555 1.44 LINK O3 NAG D 1 C1 FUC D 2 1555 1555 1.44 LINK O6 NAG D 1 C1 FUC D 3 1555 1555 1.44 CISPEP 1 GLY A 67 PRO A 68 0 7.31 CISPEP 2 GLY B 67 PRO B 68 0 7.36 CRYST1 35.212 66.516 43.686 90.00 111.13 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.028399 0.000000 0.010976 0.00000 SCALE2 0.000000 0.015034 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024541 0.00000