HEADER SIGNALING PROTEIN 24-AUG-14 4W8G TITLE CRYSTAL STRUCTURE OF THE TIR DOMAIN OF THE TOLL-RELATED RECEPTOR TRR-2 TITLE 2 FROM THE LOWER METAZOAN HYDRA MAGNIPAPILLATA (CRYSTAL FORM I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOLL-RECEPTOR-RELATED 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 95-221; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HYDRA VULGARIS; SOURCE 3 ORGANISM_COMMON: HYDRA; SOURCE 4 ORGANISM_TAXID: 6087; SOURCE 5 GENE: TRR-2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: CODONPLUS RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET19B KEYWDS FLAVODOXIN-LIKE, TOLL/INTERLEUKIN RECEPTOR TIR DOMAIN, SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.H.-J.WEISSE,A.J.SCHEIDIG REVDAT 3 10-JAN-24 4W8G 1 REMARK REVDAT 2 07-MAR-18 4W8G 1 REMARK REVDAT 1 09-SEP-15 4W8G 0 JRNL AUTH A.J.SCHEIDIG,R.H.-J.WEISSE JRNL TITL CRYSTAL STRUCTURE OF THE TIR DOMAIN OF THE TOLL-RELATED JRNL TITL 2 RECEPTOR TRR-2 FROM THE LOWER METAZOAN HYDRA MAGNIPAPILLATA JRNL TITL 3 (CRYSTAL FORM I) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 9127 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.252 REMARK 3 R VALUE (WORKING SET) : 0.250 REMARK 3 FREE R VALUE : 0.302 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 444 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 54.7766 - 2.8126 1.00 3025 156 0.2119 0.2751 REMARK 3 2 2.8126 - 2.2324 1.00 2875 135 0.3139 0.3148 REMARK 3 3 2.2324 - 1.9502 0.98 2783 153 0.3941 0.4457 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 43.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 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 : 0.006 1070 REMARK 3 ANGLE : 1.216 1456 REMARK 3 CHIRALITY : 0.059 159 REMARK 3 PLANARITY : 0.008 189 REMARK 3 DIHEDRAL : 13.328 395 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4W8G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000203375. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.239530 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS MARCH 30, 2013 REMARK 200 DATA SCALING SOFTWARE : XSCALE NOVEMBER 3, 2014, AIMLESS REMARK 200 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9188 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 54.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : 0.19300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.80 REMARK 200 R MERGE FOR SHELL (I) : 5.03500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.0.05 REMARK 200 STARTING MODEL: TRUNCATED FORM OF 1FYV REMARK 200 REMARK 200 REMARK: LONG, NEEDLE-LIKE APPEARANCE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NAOAC BUFFER PH 5.6, 310 MM REMARK 280 MGCL2, 20% (W/V) PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 16.13000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.75500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.75500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.75500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.13000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.75500 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 MET A 93 REMARK 465 GLY A 94 REMARK 465 LYS A 95 REMARK 465 ASN A 221 REMARK 465 HIS A 222 REMARK 465 HIS A 223 REMARK 465 HIS A 224 REMARK 465 HIS A 225 REMARK 465 HIS A 226 REMARK 465 HIS A 227 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 177 CG ND1 CD2 CE1 NE2 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 HIS A 177 -135.68 -129.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4W8H RELATED DB: PDB REMARK 900 DETAILS: TIR DOMAIN OF HYDRA MAGNIPAPILLATA TRR-2 IN CRYSTAL FORM REMARK 900 II. DBREF 4W8G A 95 221 UNP A6M946 A6M946_HYDVU 95 221 SEQADV 4W8G MET A 93 UNP A6M946 INITIATING METHIONINE SEQADV 4W8G GLY A 94 UNP A6M946 EXPRESSION TAG SEQADV 4W8G LYS A 118 UNP A6M946 GLU 118 CONFLICT SEQADV 4W8G LEU A 119 UNP A6M946 VAL 119 CONFLICT SEQADV 4W8G HIS A 222 UNP A6M946 EXPRESSION TAG SEQADV 4W8G HIS A 223 UNP A6M946 EXPRESSION TAG SEQADV 4W8G HIS A 224 UNP A6M946 EXPRESSION TAG SEQADV 4W8G HIS A 225 UNP A6M946 EXPRESSION TAG SEQADV 4W8G HIS A 226 UNP A6M946 EXPRESSION TAG SEQADV 4W8G HIS A 227 UNP A6M946 EXPRESSION TAG SEQRES 1 A 135 MET GLY LYS THR TYR ASP VAL ASN ILE CYS TYR ALA PRO SEQRES 2 A 135 GLU ASP ARG GLU TRP VAL ILE ASN THR LEU VAL PHE LYS SEQRES 3 A 135 LEU GLU ARG ALA GLY ILE LYS THR PHE VAL ASN ILE ARG SEQRES 4 A 135 ASP ASP THR PRO GLY ASN PHE PHE ALA GLU ASN ILE MET SEQRES 5 A 135 ASP ALA ILE GLU ASN SER ASN ARG THR ILE VAL VAL MET SEQRES 6 A 135 SER PRO ASP PHE PHE LYS ASN ASN ILE CYS ASP LYS THR SEQRES 7 A 135 LEU GLN ILE GLY LEU SER HIS GLN ILE ILE PRO ILE LEU SEQRES 8 A 135 TYR ARG PRO CYS GLU VAL PRO TYR PHE LEU ASN HIS MET SEQRES 9 A 135 THR TYR LEU ASP TRP CYS ASP LYS ASP VAL ARG PRO VAL SEQRES 10 A 135 PHE TRP ARG ASN LEU PHE ARG ASP ILE ARG ASN ASN HIS SEQRES 11 A 135 HIS HIS HIS HIS HIS FORMUL 2 HOH *7(H2 O) HELIX 1 AA1 ALA A 104 GLU A 106 5 3 HELIX 2 AA2 ASP A 107 THR A 114 1 8 HELIX 3 AA3 THR A 114 ALA A 122 1 9 HELIX 4 AA4 VAL A 128 ASP A 133 1 6 HELIX 5 AA5 PHE A 138 ASN A 149 1 12 HELIX 6 AA6 ASP A 160 LYS A 163 5 4 HELIX 7 AA7 ASN A 164 LEU A 175 1 12 HELIX 8 AA8 PRO A 190 ASN A 194 5 5 HELIX 9 AA9 ASP A 203 ASP A 205 5 3 HELIX 10 AB1 VAL A 206 ASN A 220 1 15 SHEET 1 AA1 5 THR A 126 PHE A 127 0 SHEET 2 AA1 5 TYR A 97 CYS A 102 1 N VAL A 99 O PHE A 127 SHEET 3 AA1 5 SER A 150 MET A 157 1 O ILE A 154 N ASN A 100 SHEET 4 AA1 5 ILE A 179 LEU A 183 1 O ILE A 182 N VAL A 155 SHEET 5 AA1 5 LEU A 199 ASP A 200 1 O LEU A 199 N LEU A 183 CRYST1 32.260 33.510 109.510 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 0.030998 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029842 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009132 0.00000