HEADER TRANSFERASE 25-MAR-12 4EBY TITLE CRYSTAL STRUCTURE OF THE ECTODOMAIN OF A RECEPTOR LIKE KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITIN ELICITOR RECEPTOR KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 25-230; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: CERK1, AT3G21630, AT3G21630; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF-21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PFASTBAC 1 KEYWDS PATHOGEN-ASSOCIATED MOLECULAR PATTERNS, PATTERN RECOGNITION KEYWDS 2 RECEPTORS, CHITIN ELICITOR RECEPTOR KINASE 1, LYSM, LYSINE MOTIF, KEYWDS 3 CHITIN OLIGOMER, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.CHAI,T.LIU,Z.HAN,J SHE,J.WANG REVDAT 2 29-JUL-20 4EBY 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 LINK SITE ATOM REVDAT 1 27-JUN-12 4EBY 0 JRNL AUTH T.LIU,Z.LIU,C.SONG,Y.HU,Z.HAN,J.SHE,F.FAN,J.WANG,C.JIN, JRNL AUTH 2 J.CHANG,J.M.ZHOU,J.CHAI JRNL TITL CHITIN-INDUCED DIMERIZATION ACTIVATES A PLANT IMMUNE JRNL TITL 2 RECEPTOR. JRNL REF SCIENCE V. 336 1160 2012 JRNL REFN ISSN 0036-8075 JRNL PMID 22654057 JRNL DOI 10.1126/SCIENCE.1218867 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_596) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 35917 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1788 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.2153 - 3.8742 0.94 2639 141 0.1852 0.2049 REMARK 3 2 3.8742 - 3.0773 1.00 2671 152 0.1562 0.1502 REMARK 3 3 3.0773 - 2.6890 1.00 2650 148 0.1761 0.1851 REMARK 3 4 2.6890 - 2.4434 1.00 2655 145 0.1657 0.2110 REMARK 3 5 2.4434 - 2.2684 1.00 2639 118 0.1698 0.1992 REMARK 3 6 2.2684 - 2.1348 1.00 2645 127 0.1584 0.1771 REMARK 3 7 2.1348 - 2.0279 1.00 2607 156 0.1629 0.1877 REMARK 3 8 2.0279 - 1.9397 1.00 2618 135 0.1562 0.1995 REMARK 3 9 1.9397 - 1.8651 1.00 2615 130 0.1601 0.1815 REMARK 3 10 1.8651 - 1.8007 1.00 2622 136 0.1691 0.2019 REMARK 3 11 1.8007 - 1.7445 1.00 2585 140 0.1769 0.2043 REMARK 3 12 1.7445 - 1.6946 1.00 2593 123 0.2024 0.2298 REMARK 3 13 1.6946 - 1.6500 1.00 2590 137 0.2304 0.2646 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 51.56 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14520 REMARK 3 B22 (A**2) : -6.34010 REMARK 3 B33 (A**2) : 6.19500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1732 REMARK 3 ANGLE : 1.281 2353 REMARK 3 CHIRALITY : 0.083 278 REMARK 3 PLANARITY : 0.007 300 REMARK 3 DIHEDRAL : 14.469 664 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 1.2693 -10.2439 -9.4443 REMARK 3 T TENSOR REMARK 3 T11: 0.1222 T22: 0.1094 REMARK 3 T33: 0.1103 T12: 0.0032 REMARK 3 T13: -0.0034 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.4746 L22: 1.2579 REMARK 3 L33: 1.0743 L12: 0.0503 REMARK 3 L13: -0.1890 L23: -0.5596 REMARK 3 S TENSOR REMARK 3 S11: 0.0048 S12: 0.0588 S13: 0.0473 REMARK 3 S21: -0.0018 S22: 0.0111 S23: 0.0433 REMARK 3 S31: -0.0323 S32: 0.0093 S33: -0.0006 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4EBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071425. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 298.00 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35917 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.642 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CACODYLATE PH6.5, 0.2M REMARK 280 SODIUM ACETATE, 30% (V/V) PEG 8000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 28.41450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.38050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.56400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.38050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.41450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.56400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 225 REMARK 465 LYS A 226 REMARK 465 GLN A 227 REMARK 465 ASP A 228 REMARK 465 GLY A 229 REMARK 465 VAL A 230 REMARK 465 HIS A 231 REMARK 465 HIS A 232 REMARK 465 HIS A 233 REMARK 465 HIS A 234 REMARK 465 HIS A 235 REMARK 465 HIS A 236 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 60 -0.41 67.60 REMARK 500 SER A 119 -65.01 -109.93 REMARK 500 ASP A 157 110.07 -160.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EBZ RELATED DB: PDB DBREF 4EBY A 25 230 UNP A8R7E6 A8R7E6_ARATH 25 230 SEQADV 4EBY HIS A 231 UNP A8R7E6 EXPRESSION TAG SEQADV 4EBY HIS A 232 UNP A8R7E6 EXPRESSION TAG SEQADV 4EBY HIS A 233 UNP A8R7E6 EXPRESSION TAG SEQADV 4EBY HIS A 234 UNP A8R7E6 EXPRESSION TAG SEQADV 4EBY HIS A 235 UNP A8R7E6 EXPRESSION TAG SEQADV 4EBY HIS A 236 UNP A8R7E6 EXPRESSION TAG SEQRES 1 A 212 CYS ARG THR SER CYS PRO LEU ALA LEU ALA SER TYR TYR SEQRES 2 A 212 LEU GLU ASN GLY THR THR LEU SER VAL ILE ASN GLN ASN SEQRES 3 A 212 LEU ASN SER SER ILE ALA PRO TYR ASP GLN ILE ASN PHE SEQRES 4 A 212 ASP PRO ILE LEU ARG TYR ASN SER ASN ILE LYS ASP LYS SEQRES 5 A 212 ASP ARG ILE GLN MET GLY SER ARG VAL LEU VAL PRO PHE SEQRES 6 A 212 PRO CYS GLU CYS GLN PRO GLY ASP PHE LEU GLY HIS ASN SEQRES 7 A 212 PHE SER TYR SER VAL ARG GLN GLU ASP THR TYR GLU ARG SEQRES 8 A 212 VAL ALA ILE SER ASN TYR ALA ASN LEU THR THR MET GLU SEQRES 9 A 212 SER LEU GLN ALA ARG ASN PRO PHE PRO ALA THR ASN ILE SEQRES 10 A 212 PRO LEU SER ALA THR LEU ASN VAL LEU VAL ASN CYS SER SEQRES 11 A 212 CYS GLY ASP GLU SER VAL SER LYS ASP PHE GLY LEU PHE SEQRES 12 A 212 VAL THR TYR PRO LEU ARG PRO GLU ASP SER LEU SER SER SEQRES 13 A 212 ILE ALA ARG SER SER GLY VAL SER ALA ASP ILE LEU GLN SEQRES 14 A 212 ARG TYR ASN PRO GLY VAL ASN PHE ASN SER GLY ASN GLY SEQRES 15 A 212 ILE VAL TYR VAL PRO GLY ARG ASP PRO ASN GLY ALA PHE SEQRES 16 A 212 PRO PRO PHE LYS SER SER LYS GLN ASP GLY VAL HIS HIS SEQRES 17 A 212 HIS HIS HIS HIS MODRES 4EBY ASN A 52 ASN GLYCOSYLATION SITE MODRES 4EBY ASN A 40 ASN GLYCOSYLATION SITE MODRES 4EBY ASN A 123 ASN GLYCOSYLATION SITE MODRES 4EBY ASN A 152 ASN GLYCOSYLATION SITE MODRES 4EBY ASN A 102 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET NAG A 810 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE FORMUL 2 NAG 9(C8 H15 N O6) FORMUL 5 BMA C6 H12 O6 FORMUL 7 HOH *348(H2 O) HELIX 1 1 THR A 43 LEU A 51 1 9 HELIX 2 2 PHE A 63 ARG A 68 1 6 HELIX 3 3 THR A 112 SER A 119 1 8 HELIX 4 4 THR A 126 ASN A 134 1 9 HELIX 5 5 SER A 177 GLY A 186 1 10 HELIX 6 6 SER A 188 ASN A 196 1 9 SHEET 1 A 4 ARG A 84 PHE A 89 0 SHEET 2 A 4 ALA A 32 TYR A 37 -1 N TYR A 36 O VAL A 85 SHEET 3 A 4 PHE A 167 PRO A 171 1 O THR A 169 N LEU A 33 SHEET 4 A 4 ILE A 207 PRO A 211 -1 O VAL A 210 N VAL A 168 SHEET 1 B 3 GLU A 92 GLN A 94 0 SHEET 2 B 3 PHE A 98 SER A 106 -1 O PHE A 98 N GLN A 94 SHEET 3 B 3 THR A 146 ASN A 152 -1 O VAL A 149 N PHE A 103 SSBOND 1 CYS A 25 CYS A 93 1555 1555 2.05 SSBOND 2 CYS A 29 CYS A 155 1555 1555 2.03 SSBOND 3 CYS A 91 CYS A 153 1555 1555 2.03 LINK ND2 ASN A 40 C1 NAG A 810 1555 1555 1.45 LINK ND2 ASN A 52 C1 NAG B 1 1555 1555 1.45 LINK ND2 ASN A 102 C1 NAG E 1 1555 1555 1.45 LINK ND2 ASN A 123 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN A 152 C1 NAG D 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.46 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.47 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.46 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.46 CRYST1 56.829 71.128 72.761 90.00 90.00 90.00 P 21 21 21 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 0.017597 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014059 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013744 0.00000