PDB Short entry for 1YI8 HEADER LIGASE 11-JAN-05 1YI8 TITLE CRYSTAL STRUCTURE OF TRYPTOPHANYL TRRNA SYNTHETASE II FROM DEINOCOCCUS TITLE 2 RADIODURANS IN COMPLEX WITH L-TRP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPTOPHANYL-TRNA SYNTHETASE; COMPND 3 CHAIN: B, A, C; COMPND 4 FRAGMENT: ENZYME; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 243230; SOURCE 4 STRAIN: R1; SOURCE 5 GENE: DR1093; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS AUXILIARY TRYPTOPHANYL TRNA SYNTHETASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.R.BUDDHA,B.R.CRANE REVDAT 5 14-FEB-24 1YI8 1 REMARK REVDAT 4 13-JUL-11 1YI8 1 VERSN REVDAT 3 24-FEB-09 1YI8 1 VERSN REVDAT 2 10-MAY-05 1YI8 1 JRNL REVDAT 1 22-FEB-05 1YI8 0 JRNL AUTH M.R.BUDDHA,B.R.CRANE JRNL TITL STRUCTURE AND ACTIVITY OF AN AMINOACYL-TRNA SYNTHETASE THAT JRNL TITL 2 CHARGES TRNA WITH NITRO-TRYPTOPHAN. JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 274 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 15723076 JRNL DOI 10.1038/NSMB907 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.7 REMARK 3 NUMBER OF REFLECTIONS : 54416 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.260 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2760 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3400 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 68 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7587 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 1059 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.70 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YI8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031541. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-04; NULL REMARK 200 TEMPERATURE (KELVIN) : 193; 193 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; CHESS REMARK 200 BEAMLINE : X25; F2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978, 0.979, 0.92; 0.9789 REMARK 200 MONOCHROMATOR : SI 111; SI 111 REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72160 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : 0.05600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.18200 REMARK 200 R SYM FOR SHELL (I) : 0.21000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG4K, 0.2M DIAMMONIUM HYDROGEN REMARK 280 PHOSPHATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 105.90000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 105.90000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.25000 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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: DIMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 211.80000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 B 1 REMARK 465 PRO B 2 REMARK 465 PHE B 3 REMARK 465 VAL B 4 REMARK 465 ASP B 5 REMARK 465 LEU B 6 REMARK 465 GLU B 7 REMARK 465 VAL B 8 REMARK 465 PRO B 9 REMARK 465 THR B 10 REMARK 465 MET B 11 REMARK 465 THR B 12 REMARK 465 THR B 13 REMARK 465 PRO B 14 REMARK 465 THR B 15 REMARK 465 PRO B 16 REMARK 465 ALA B 17 REMARK 465 ALA B 18 REMARK 465 THR B 19 REMARK 465 PRO B 20 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 PHE A 3 REMARK 465 VAL A 4 REMARK 465 ASP A 5 REMARK 465 LEU A 6 REMARK 465 GLU A 7 REMARK 465 VAL A 8 REMARK 465 PRO A 9 REMARK 465 THR A 10 REMARK 465 MET A 11 REMARK 465 THR A 12 REMARK 465 THR A 13 REMARK 465 PRO A 14 REMARK 465 THR A 15 REMARK 465 PRO A 16 REMARK 465 ALA A 17 REMARK 465 ALA A 18 REMARK 465 THR A 19 REMARK 465 PRO A 20 REMARK 465 MET C 1 REMARK 465 PRO C 2 REMARK 465 PHE C 3 REMARK 465 VAL C 4 REMARK 465 ASP C 5 REMARK 465 LEU C 6 REMARK 465 GLU C 7 REMARK 465 VAL C 8 REMARK 465 PRO C 9 REMARK 465 THR C 10 REMARK 465 MET C 11 REMARK 465 THR C 12 REMARK 465 THR C 13 REMARK 465 PRO C 14 REMARK 465 THR C 15 REMARK 465 PRO C 16 REMARK 465 ALA C 17 REMARK 465 ALA C 18 REMARK 465 THR C 19 REMARK 465 PRO C 20 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 ARG A 22 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 24 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 25 CG1 CG2 REMARK 470 ASP A 93 CG OD1 OD2 REMARK 470 GLN A 198 CG CD OE1 NE2 REMARK 470 VAL A 204 CG1 CG2 REMARK 470 ARG A 206 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 213 CG CD OE1 NE2 REMARK 470 ARG C 49 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 203 CG CD NE CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG B 185 CG REMARK 480 THR B 242 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LEU A 60 N ASP A 62 2.13 REMARK 500 NE2 GLN C 154 OXT TRP C 3000 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CA ARG A 235 O HOH C 2021 1554 0.49 REMARK 500 O HOH C 1200 O HOH C 1789 4546 0.74 REMARK 500 NH1 ARG C 315 O HOH C 1771 4556 0.82 REMARK 500 CZ ARG A 235 O HOH B 1589 1554 0.84 REMARK 500 NH1 ARG B 322 O HOH A 1468 1546 0.88 REMARK 500 CB ARG A 235 O HOH C 2021 1554 1.14 REMARK 500 NH2 ARG A 235 O HOH B 1589 1554 1.32 REMARK 500 NH1 ARG A 235 O HOH B 1589 1554 1.34 REMARK 500 NE ARG C 315 O HOH C 1613 4556 1.36 REMARK 500 CD ARG C 315 O HOH C 1613 4556 1.59 REMARK 500 CD ARG A 235 O HOH C 1529 1554 1.60 REMARK 500 NE ARG A 235 O HOH C 1529 1554 1.62 REMARK 500 N ARG A 235 O HOH C 2021 1554 1.64 REMARK 500 O HOH A 1790 O HOH A 1956 2655 1.71 REMARK 500 O HOH C 1118 O HOH C 1754 4546 1.80 REMARK 500 N LEU B 201 NE2 GLN A 341 2655 1.81 REMARK 500 NH1 ARG C 322 O HOH C 1537 4546 1.81 REMARK 500 O LEU B 201 OE1 GLN A 341 2655 1.86 REMARK 500 C ARG A 235 O HOH C 2021 1554 1.93 REMARK 500 NH1 ARG B 235 O GLY C 245 4535 1.96 REMARK 500 NE ARG A 235 O HOH B 1589 1554 1.97 REMARK 500 OE2 GLU B 177 CG PRO A 192 2655 1.98 REMARK 500 CZ ARG B 322 O HOH A 1468 1546 1.99 REMARK 500 CZ ARG C 315 O HOH C 1613 4556 2.00 REMARK 500 CG ARG A 235 O HOH C 1529 1554 2.02 REMARK 500 O HOH B 1248 O HOH A 1154 2655 2.05 REMARK 500 O HOH C 1588 O HOH C 1691 1545 2.11 REMARK 500 CG ARG A 235 O HOH C 2021 1554 2.12 REMARK 500 OD1 ASP B 170 O HOH A 1031 2655 2.12 REMARK 500 CZ ARG C 315 O HOH C 1771 4556 2.12 REMARK 500 O HOH B 1371 O HOH A 1175 2655 2.15 REMARK 500 CA ARG C 315 O HOH C 1808 4556 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ARG B 22 -88.40 -168.64 REMARK 500 PRO B 31 99.74 -66.72 REMARK 500 HIS B 36 -169.54 -126.82 REMARK 500 LEU B 40 -70.75 -56.23 REMARK 500 SER B 43 -44.05 -172.13 REMARK 500 ALA B 54 -177.21 -175.19 REMARK 500 ALA B 61 61.05 -62.75 REMARK 500 ARG B 142 43.50 -84.47 REMARK 500 TYR B 190 -81.21 -93.43 REMARK 500 ARG B 203 -70.20 -94.46 REMARK 500 ARG B 206 107.75 -37.48 REMARK 500 ASN B 222 43.39 -109.22 REMARK 500 THR B 242 -93.87 -127.61 REMARK 500 ALA B 249 -74.14 -34.86 REMARK 500 SER B 250 -61.85 -22.33 REMARK 500 ASP B 251 154.75 -39.55 REMARK 500 ASP B 279 -70.64 -72.82 REMARK 500 ALA B 283 -90.45 -79.98 REMARK 500 HIS B 294 -74.85 -59.22 REMARK 500 PHE B 349 134.04 -39.10 REMARK 500 PRO A 31 85.95 -51.02 REMARK 500 LEU A 37 -39.79 -27.27 REMARK 500 ALA A 61 61.47 -35.06 REMARK 500 PRO A 73 -76.38 -39.13 REMARK 500 GLU A 74 -15.33 -46.88 REMARK 500 ALA A 191 123.53 -22.90 REMARK 500 PRO A 192 66.14 -62.21 REMARK 500 ARG A 206 118.03 -21.18 REMARK 500 PRO A 208 -170.56 -56.54 REMARK 500 ASP A 211 44.51 -106.52 REMARK 500 GLN A 213 141.47 -34.14 REMARK 500 LYS A 215 -156.27 -134.79 REMARK 500 ASN A 222 51.75 -109.78 REMARK 500 LEU A 226 5.86 -68.41 REMARK 500 THR A 242 -97.87 -76.94 REMARK 500 ALA A 249 -9.51 -51.91 REMARK 500 ASN A 258 94.57 -48.04 REMARK 500 GLN A 275 4.34 -69.81 REMARK 500 ALA A 283 -80.55 -102.69 REMARK 500 VAL A 291 -71.97 -59.07 REMARK 500 LYS A 293 -30.05 -39.82 REMARK 500 LEU A 295 -14.41 -49.66 REMARK 500 ARG C 22 -85.20 -114.10 REMARK 500 SER C 43 -37.09 -149.22 REMARK 500 ARG C 72 57.43 -140.93 REMARK 500 TYR C 190 -90.56 -113.13 REMARK 500 PRO C 192 71.84 -65.28 REMARK 500 SER C 202 -178.31 43.41 REMARK 500 ARG C 203 21.12 -151.99 REMARK 500 VAL C 204 151.47 64.13 REMARK 500 REMARK 500 THIS ENTRY HAS 55 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 139 0.07 SIDE CHAIN REMARK 500 TYR A 150 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRP C 3000 DBREF 1YI8 A 21 351 UNP Q9RVD6 SYW2_DEIRA 21 351 DBREF 1YI8 B 21 351 UNP Q9RVD6 SYW2_DEIRA 21 351 DBREF 1YI8 C 21 351 UNP Q9RVD6 SYW2_DEIRA 21 351 SEQRES 1 B 351 MET PRO PHE VAL ASP LEU GLU VAL PRO THR MET THR THR SEQRES 2 B 351 PRO THR PRO ALA ALA THR PRO ALA ARG PRO ARG VAL LEU SEQRES 3 B 351 THR GLY ASP ARG PRO THR GLY ALA LEU HIS LEU GLY HIS SEQRES 4 B 351 LEU ALA GLY SER LEU GLN ASN ARG VAL ARG LEU GLN ASP SEQRES 5 B 351 GLU ALA GLU LEU PHE VAL LEU LEU ALA ASP VAL GLN ALA SEQRES 6 B 351 LEU THR ASP HIS PHE ASP ARG PRO GLU GLN VAL ARG GLU SEQRES 7 B 351 ASN VAL LEU ALA VAL ALA LEU ASP TYR LEU ALA ALA GLY SEQRES 8 B 351 LEU ASP PRO GLN LYS THR THR CYS VAL VAL GLN SER ALA SEQRES 9 B 351 VAL PRO GLU LEU ALA GLU LEU THR VAL TYR PHE LEU ASN SEQRES 10 B 351 LEU VAL THR VAL SER HIS LEU ARG GLN ASN PRO THR VAL SEQRES 11 B 351 LYS ALA GLU ILE ALA GLN LYS GLY TYR GLY GLU ARG VAL SEQRES 12 B 351 PRO ALA GLY PHE PHE VAL TYR PRO VAL SER GLN ALA ALA SEQRES 13 B 351 ASP ILE ALA ALA PHE GLY ALA THR LEU VAL PRO VAL GLY SEQRES 14 B 351 ASP ASP GLN LEU PRO MET LEU GLU GLN THR ARG GLU ILE SEQRES 15 B 351 VAL ARG ARG PHE ASN ALA LEU TYR ALA PRO VAL LEU ALA SEQRES 16 B 351 GLU PRO GLN ALA GLN LEU SER ARG VAL PRO ARG LEU PRO SEQRES 17 B 351 GLY LEU ASP GLY GLN ALA LYS MET SER LYS SER LEU GLY SEQRES 18 B 351 ASN ALA ILE ALA LEU GLY ASP SER ALA ASP GLU VAL ALA SEQRES 19 B 351 ARG LYS VAL MET GLY MET TYR THR ASP PRO GLY HIS LEU SEQRES 20 B 351 ARG ALA SER ASP PRO GLY ARG VAL GLU GLY ASN PRO VAL SEQRES 21 B 351 PHE THR PHE LEU ASP ALA PHE ASP PRO ASP PRO ALA ARG SEQRES 22 B 351 VAL GLN ALA LEU LYS ASP GLN TYR ARG ALA GLY GLY LEU SEQRES 23 B 351 GLY ASP VAL LYS VAL LYS LYS HIS LEU ILE ASP VAL LEU SEQRES 24 B 351 ASN GLY VAL LEU ALA PRO ILE ARG THR ARG ARG ALA GLU SEQRES 25 B 351 TYR GLU ARG ASP PRO ASP ALA VAL LEU ARG PHE VAL THR SEQRES 26 B 351 GLU GLY THR ALA ARG GLY ARG GLU VAL ALA ALA GLN THR SEQRES 27 B 351 LEU GLY GLN VAL ARG ARG ALA MET ARG LEU PHE GLY HIS SEQRES 1 A 351 MET PRO PHE VAL ASP LEU GLU VAL PRO THR MET THR THR SEQRES 2 A 351 PRO THR PRO ALA ALA THR PRO ALA ARG PRO ARG VAL LEU SEQRES 3 A 351 THR GLY ASP ARG PRO THR GLY ALA LEU HIS LEU GLY HIS SEQRES 4 A 351 LEU ALA GLY SER LEU GLN ASN ARG VAL ARG LEU GLN ASP SEQRES 5 A 351 GLU ALA GLU LEU PHE VAL LEU LEU ALA ASP VAL GLN ALA SEQRES 6 A 351 LEU THR ASP HIS PHE ASP ARG PRO GLU GLN VAL ARG GLU SEQRES 7 A 351 ASN VAL LEU ALA VAL ALA LEU ASP TYR LEU ALA ALA GLY SEQRES 8 A 351 LEU ASP PRO GLN LYS THR THR CYS VAL VAL GLN SER ALA SEQRES 9 A 351 VAL PRO GLU LEU ALA GLU LEU THR VAL TYR PHE LEU ASN SEQRES 10 A 351 LEU VAL THR VAL SER HIS LEU ARG GLN ASN PRO THR VAL SEQRES 11 A 351 LYS ALA GLU ILE ALA GLN LYS GLY TYR GLY GLU ARG VAL SEQRES 12 A 351 PRO ALA GLY PHE PHE VAL TYR PRO VAL SER GLN ALA ALA SEQRES 13 A 351 ASP ILE ALA ALA PHE GLY ALA THR LEU VAL PRO VAL GLY SEQRES 14 A 351 ASP ASP GLN LEU PRO MET LEU GLU GLN THR ARG GLU ILE SEQRES 15 A 351 VAL ARG ARG PHE ASN ALA LEU TYR ALA PRO VAL LEU ALA SEQRES 16 A 351 GLU PRO GLN ALA GLN LEU SER ARG VAL PRO ARG LEU PRO SEQRES 17 A 351 GLY LEU ASP GLY GLN ALA LYS MET SER LYS SER LEU GLY SEQRES 18 A 351 ASN ALA ILE ALA LEU GLY ASP SER ALA ASP GLU VAL ALA SEQRES 19 A 351 ARG LYS VAL MET GLY MET TYR THR ASP PRO GLY HIS LEU SEQRES 20 A 351 ARG ALA SER ASP PRO GLY ARG VAL GLU GLY ASN PRO VAL SEQRES 21 A 351 PHE THR PHE LEU ASP ALA PHE ASP PRO ASP PRO ALA ARG SEQRES 22 A 351 VAL GLN ALA LEU LYS ASP GLN TYR ARG ALA GLY GLY LEU SEQRES 23 A 351 GLY ASP VAL LYS VAL LYS LYS HIS LEU ILE ASP VAL LEU SEQRES 24 A 351 ASN GLY VAL LEU ALA PRO ILE ARG THR ARG ARG ALA GLU SEQRES 25 A 351 TYR GLU ARG ASP PRO ASP ALA VAL LEU ARG PHE VAL THR SEQRES 26 A 351 GLU GLY THR ALA ARG GLY ARG GLU VAL ALA ALA GLN THR SEQRES 27 A 351 LEU GLY GLN VAL ARG ARG ALA MET ARG LEU PHE GLY HIS SEQRES 1 C 351 MET PRO PHE VAL ASP LEU GLU VAL PRO THR MET THR THR SEQRES 2 C 351 PRO THR PRO ALA ALA THR PRO ALA ARG PRO ARG VAL LEU SEQRES 3 C 351 THR GLY ASP ARG PRO THR GLY ALA LEU HIS LEU GLY HIS SEQRES 4 C 351 LEU ALA GLY SER LEU GLN ASN ARG VAL ARG LEU GLN ASP SEQRES 5 C 351 GLU ALA GLU LEU PHE VAL LEU LEU ALA ASP VAL GLN ALA SEQRES 6 C 351 LEU THR ASP HIS PHE ASP ARG PRO GLU GLN VAL ARG GLU SEQRES 7 C 351 ASN VAL LEU ALA VAL ALA LEU ASP TYR LEU ALA ALA GLY SEQRES 8 C 351 LEU ASP PRO GLN LYS THR THR CYS VAL VAL GLN SER ALA SEQRES 9 C 351 VAL PRO GLU LEU ALA GLU LEU THR VAL TYR PHE LEU ASN SEQRES 10 C 351 LEU VAL THR VAL SER HIS LEU ARG GLN ASN PRO THR VAL SEQRES 11 C 351 LYS ALA GLU ILE ALA GLN LYS GLY TYR GLY GLU ARG VAL SEQRES 12 C 351 PRO ALA GLY PHE PHE VAL TYR PRO VAL SER GLN ALA ALA SEQRES 13 C 351 ASP ILE ALA ALA PHE GLY ALA THR LEU VAL PRO VAL GLY SEQRES 14 C 351 ASP ASP GLN LEU PRO MET LEU GLU GLN THR ARG GLU ILE SEQRES 15 C 351 VAL ARG ARG PHE ASN ALA LEU TYR ALA PRO VAL LEU ALA SEQRES 16 C 351 GLU PRO GLN ALA GLN LEU SER ARG VAL PRO ARG LEU PRO SEQRES 17 C 351 GLY LEU ASP GLY GLN ALA LYS MET SER LYS SER LEU GLY SEQRES 18 C 351 ASN ALA ILE ALA LEU GLY ASP SER ALA ASP GLU VAL ALA SEQRES 19 C 351 ARG LYS VAL MET GLY MET TYR THR ASP PRO GLY HIS LEU SEQRES 20 C 351 ARG ALA SER ASP PRO GLY ARG VAL GLU GLY ASN PRO VAL SEQRES 21 C 351 PHE THR PHE LEU ASP ALA PHE ASP PRO ASP PRO ALA ARG SEQRES 22 C 351 VAL GLN ALA LEU LYS ASP GLN TYR ARG ALA GLY GLY LEU SEQRES 23 C 351 GLY ASP VAL LYS VAL LYS LYS HIS LEU ILE ASP VAL LEU SEQRES 24 C 351 ASN GLY VAL LEU ALA PRO ILE ARG THR ARG ARG ALA GLU SEQRES 25 C 351 TYR GLU ARG ASP PRO ASP ALA VAL LEU ARG PHE VAL THR SEQRES 26 C 351 GLU GLY THR ALA ARG GLY ARG GLU VAL ALA ALA GLN THR SEQRES 27 C 351 LEU GLY GLN VAL ARG ARG ALA MET ARG LEU PHE GLY HIS HET TRP C3000 15 HETNAM TRP TRYPTOPHAN FORMUL 4 TRP C11 H12 N2 O2 FORMUL 5 HOH *1059(H2 O) HELIX 1 1 HIS B 36 SER B 43 1 8 HELIX 2 2 SER B 43 GLN B 51 1 9 HELIX 3 3 ALA B 61 PHE B 70 1 10 HELIX 4 4 ARG B 72 ALA B 90 1 19 HELIX 5 5 SER B 103 VAL B 105 5 3 HELIX 6 6 PRO B 106 ASN B 117 1 12 HELIX 7 7 THR B 120 GLN B 126 1 7 HELIX 8 8 ASN B 127 GLY B 138 1 12 HELIX 9 9 PRO B 144 GLY B 162 1 19 HELIX 10 10 GLY B 169 ASP B 171 5 3 HELIX 11 11 GLN B 172 TYR B 190 1 19 HELIX 12 12 SER B 229 GLY B 239 1 11 HELIX 13 13 VAL B 260 ASP B 268 1 9 HELIX 14 14 ASP B 270 GLY B 284 1 15 HELIX 15 15 GLY B 287 ARG B 315 1 29 HELIX 16 16 ASP B 316 MET B 346 1 31 HELIX 17 17 HIS A 36 GLY A 42 1 7 HELIX 18 18 GLY A 42 ALA A 54 1 13 HELIX 19 19 ALA A 65 PHE A 70 1 6 HELIX 20 20 ARG A 72 ALA A 90 1 19 HELIX 21 21 SER A 103 VAL A 105 5 3 HELIX 22 22 PRO A 106 LEU A 116 1 11 HELIX 23 23 THR A 120 GLN A 126 1 7 HELIX 24 24 ASN A 127 GLN A 136 1 10 HELIX 25 25 PRO A 144 VAL A 149 1 6 HELIX 26 26 VAL A 149 PHE A 161 1 13 HELIX 27 27 GLY A 169 ASP A 171 5 3 HELIX 28 28 GLN A 172 TYR A 190 1 19 HELIX 29 29 SER A 217 GLY A 221 5 5 HELIX 30 30 SER A 229 MET A 238 1 10 HELIX 31 31 ASN A 258 ASP A 268 1 11 HELIX 32 32 ASP A 270 ARG A 282 1 13 HELIX 33 33 GLY A 287 ARG A 315 1 29 HELIX 34 34 ASP A 316 MET A 346 1 31 HELIX 35 35 HIS C 36 SER C 43 1 8 HELIX 36 36 SER C 43 VAL C 48 1 6 HELIX 37 37 ALA C 61 PHE C 70 1 10 HELIX 38 38 ARG C 72 GLY C 91 1 20 HELIX 39 39 SER C 103 VAL C 105 5 3 HELIX 40 40 PRO C 106 ASN C 117 1 12 HELIX 41 41 THR C 120 ASN C 127 1 8 HELIX 42 42 ASN C 127 GLY C 138 1 12 HELIX 43 43 PRO C 144 VAL C 149 1 6 HELIX 44 44 VAL C 149 GLY C 162 1 14 HELIX 45 45 GLN C 172 TYR C 190 1 19 HELIX 46 46 SER C 229 GLY C 239 1 11 HELIX 47 47 ASN C 258 ASP C 268 1 11 HELIX 48 48 ASP C 270 GLY C 284 1 15 HELIX 49 49 GLY C 287 ASP C 316 1 30 HELIX 50 50 ASP C 316 MET C 346 1 31 SHEET 1 A 3 ARG B 24 ASP B 29 0 SHEET 2 A 3 GLU B 55 LEU B 60 1 O GLU B 55 N VAL B 25 SHEET 3 A 3 THR B 97 VAL B 101 1 O VAL B 100 N LEU B 60 SHEET 1 B 2 LEU B 165 VAL B 168 0 SHEET 2 B 2 GLN B 198 LEU B 201 1 O GLN B 198 N VAL B 166 SHEET 1 C 3 THR A 27 GLY A 28 0 SHEET 2 C 3 LEU A 56 LEU A 60 1 O PHE A 57 N THR A 27 SHEET 3 C 3 THR A 97 VAL A 101 1 O VAL A 100 N LEU A 60 SHEET 1 D 2 PRO A 167 VAL A 168 0 SHEET 2 D 2 GLN A 200 LEU A 201 1 O GLN A 200 N VAL A 168 SHEET 1 E 3 ARG C 24 ASP C 29 0 SHEET 2 E 3 GLU C 55 LEU C 60 1 O GLU C 55 N VAL C 25 SHEET 3 E 3 THR C 97 VAL C 101 1 O VAL C 100 N LEU C 60 SHEET 1 F 2 LEU C 165 VAL C 168 0 SHEET 2 F 2 GLN C 198 LEU C 201 1 O GLN C 198 N VAL C 166 SITE 1 AC1 6 GLY C 28 ALA C 61 GLN C 64 GLN C 154 SITE 2 AC1 6 ASP C 157 ILE C 158 CRYST1 211.800 58.500 88.900 90.00 100.73 90.00 C 1 2 1 12 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 0.004721 0.000000 0.000894 0.00000 SCALE2 0.000000 0.017094 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011449 0.00000