HEADER DNA BINDING PROTEIN/DNA 31-DEC-24 9L9W TITLE STRUCTURE OF SPARTA IN COMPLEX WITH GUIDE DNA AND A 19NT TARGET DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIWI DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TIR DOMAIN-CONTAINING PROTEIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'- COMPND 11 D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)- COMPND 12 3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'- COMPND 17 D(*T*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*AP*T)-3'); COMPND 18 CHAIN: D; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOFLAVIFILUM THERMOPHILUM; SOURCE 3 ORGANISM_TAXID: 1393122; SOURCE 4 GENE: SAMN05660895_1671; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: THERMOFLAVIFILUM THERMOPHILUM; SOURCE 9 ORGANISM_TAXID: 1393122; SOURCE 10 GENE: SAMN05660895_1670; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: THERMOFLAVIFILUM THERMOPHILUM; SOURCE 16 ORGANISM_TAXID: 1393122; SOURCE 17 MOL_ID: 4; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: THERMOFLAVIFILUM THERMOPHILUM; SOURCE 20 ORGANISM_TAXID: 1393122 KEYWDS AGO, TIR-APAZ, DNA, NADASE, DNA BINDING PROTEIN/DNA, DNA BINDING KEYWDS 2 PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.HU,C.GUO,X.LIU,J.CHEN,L.LIU REVDAT 1 12-MAR-25 9L9W 0 JRNL AUTH R.HU,C.GUO,X.LIU,Y.LIN,Z.YANG,Z.LI,Y.YANG,E.MA,Y.LI,J.CHEN, JRNL AUTH 2 L.LIU JRNL TITL STRUCTURAL BASIS OF SSDNA-GUIDED NADASE ACTIVATION OF JRNL TITL 2 PROKARYOTIC SPARTA SYSTEM. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 39997222 JRNL DOI 10.1093/NAR/GKAF110 REMARK 2 REMARK 2 RESOLUTION. 5.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 5.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 5233 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.263 REMARK 3 R VALUE (WORKING SET) : 0.261 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 265 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 39.3100 - 7.3900 0.99 2529 128 0.2440 0.2555 REMARK 3 2 7.3800 - 5.8700 0.99 2439 137 0.3208 0.3923 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) : 1.051 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.866 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 295.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 317.2 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 : 0.016 8379 REMARK 3 ANGLE : 1.520 11508 REMARK 3 CHIRALITY : 0.069 1249 REMARK 3 PLANARITY : 0.009 1321 REMARK 3 DIHEDRAL : 28.101 3173 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 9L9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 08-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1300055260. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-24 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 : BL10U2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 7.21 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 7.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5233 REMARK 200 RESOLUTION RANGE HIGH (A) : 5.870 REMARK 200 RESOLUTION RANGE LOW (A) : 39.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 17.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 5.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 6.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 <I/SIGMA(I)> 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: PHENIX 1.17.1_3660 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE, PH=8.5, 4.4% PEG4000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 116.61267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.30633 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 58.30633 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 116.61267 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 LYS A 170 REMARK 465 SER A 171 REMARK 465 LYS A 172 REMARK 465 ALA A 173 REMARK 465 LYS A 174 REMARK 465 SER A 175 REMARK 465 PHE A 176 REMARK 465 ARG A 177 REMARK 465 TYR A 178 REMARK 465 THR A 179 REMARK 465 PRO A 180 REMARK 465 THR A 181 REMARK 465 LEU A 182 REMARK 465 PHE A 183 REMARK 465 GLU A 184 REMARK 465 GLU A 185 REMARK 465 PHE A 186 REMARK 465 ASN A 187 REMARK 465 LYS A 188 REMARK 465 LYS A 189 REMARK 465 LEU A 190 REMARK 465 LYS A 191 REMARK 465 GLU A 192 REMARK 465 VAL A 193 REMARK 465 GLU A 194 REMARK 465 LYS A 195 REMARK 465 GLU A 196 REMARK 465 ALA A 197 REMARK 465 LYS A 198 REMARK 465 THR A 199 REMARK 465 TYR A 200 REMARK 465 ASN A 201 REMARK 465 TYR A 202 REMARK 465 SER B 420 REMARK 465 GLU B 421 REMARK 465 DT D 2 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 LYS A 392 CG CD CE NZ REMARK 470 ARG B 114 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 160 CG ND1 CD2 CE1 NE2 REMARK 470 ASP B 161 CG OD1 OD2 REMARK 470 LYS B 162 CG CD CE NZ REMARK 470 ILE B 165 CG1 CG2 CD1 REMARK 470 GLU B 166 CG CD OE1 OE2 REMARK 470 LYS B 167 CG CD CE NZ REMARK 470 GLU B 168 CG CD OE1 OE2 REMARK 470 ARG B 193 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 289 CG CD CE NZ REMARK 470 LYS B 366 CG CD CE NZ REMARK 470 LYS B 409 CG CD CE NZ REMARK 470 PHE B 411 CG CD1 CD2 CE1 CE2 CZ REMARK 470 DA D 3 P OP1 OP2 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 OG1 THR A 399 O THR B 170 1.94 REMARK 500 OE2 GLU A 344 OH TYR A 353 1.95 REMARK 500 OH TYR A 262 OD1 ASP A 309 1.99 REMARK 500 NZ LYS A 59 OE1 GLU A 249 2.01 REMARK 500 O GLU B 184 NH2 ARG B 186 2.04 REMARK 500 NE2 GLN A 302 O THR A 479 2.04 REMARK 500 OG1 THR A 432 O SER A 434 2.04 REMARK 500 O PRO A 404 OH TYR B 416 2.05 REMARK 500 O6 DG C 12 N4 DC D 9 2.08 REMARK 500 OE1 GLU A 9 NZ LYS A 464 2.08 REMARK 500 O SER B 65 ND2 ASN B 69 2.12 REMARK 500 O TRP A 254 OG1 THR A 258 2.13 REMARK 500 NE ARG A 225 OG SER A 227 2.13 REMARK 500 OE2 GLU A 327 NE2 HIS A 329 2.14 REMARK 500 O ASP B 44 N THR B 48 2.15 REMARK 500 O THR B 18 OG SER B 22 2.17 REMARK 500 O ALA A 253 OG SER A 257 2.17 REMARK 500 O LYS A 336 OG1 THR A 340 2.18 REMARK 500 NZ LYS B 4 OE1 GLU B 52 2.18 REMARK 500 O SER A 257 N TYR A 261 2.18 REMARK 500 O ALA B 81 N LYS B 85 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER B 360 CB SER B 360 OG -0.200 REMARK 500 DT C 1 P DT C 1 OP3 -0.127 REMARK 500 DT C 1 C1' DT C 1 N1 0.123 REMARK 500 DG C 2 C8 DG C 2 N9 0.061 REMARK 500 DA C 7 O3' DA C 7 C3' -0.048 REMARK 500 DT C 16 O3' DT C 16 C3' 0.096 REMARK 500 DA C 17 N9 DA C 17 C4 0.054 REMARK 500 DT C 21 C1' DT C 21 N1 0.078 REMARK 500 DT D 4 C1' DT D 4 N1 0.099 REMARK 500 DC D 6 C1' DC D 6 N1 0.091 REMARK 500 DA D 8 O3' DA D 8 C3' 0.087 REMARK 500 DA D 15 O3' DA D 15 C3' -0.046 REMARK 500 DC D 16 O3' DC D 16 C3' -0.050 REMARK 500 DT D 18 C5 DT D 18 C6 -0.051 REMARK 500 DT D 18 C6 DT D 18 N1 -0.057 REMARK 500 DT D 18 C2 DT D 18 O2 0.053 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 132 CB - CG - OD2 ANGL. DEV. = 7.5 DEGREES REMARK 500 CYS B 34 CA - CB - SG ANGL. DEV. = 9.0 DEGREES REMARK 500 PHE B 176 CG - CD1 - CE1 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG B 276 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG B 276 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 LEU B 335 CA - CB - CG ANGL. DEV. = -20.4 DEGREES REMARK 500 DG C 2 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT C 6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG C 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT C 13 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG C 15 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT C 16 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DT C 21 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC D 6 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA D 7 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC D 9 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC D 13 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES 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 PHE A 14 -169.72 -117.35 REMARK 500 CYS A 20 -154.09 -141.58 REMARK 500 CYS A 151 31.86 -98.36 REMARK 500 LEU A 214 4.72 -64.37 REMARK 500 LEU A 305 -87.84 -107.11 REMARK 500 SER A 391 -167.77 -63.04 REMARK 500 LYS A 392 66.12 -117.92 REMARK 500 GLU A 436 -157.86 -103.51 REMARK 500 ILE A 445 78.69 -66.30 REMARK 500 ASN B 3 -31.18 -131.99 REMARK 500 LYS B 41 14.70 -148.62 REMARK 500 GLU B 55 -66.46 -92.39 REMARK 500 HIS B 147 -19.55 -46.88 REMARK 500 ILE B 157 -72.43 -86.59 REMARK 500 GLU B 166 87.31 -58.03 REMARK 500 ARG B 189 62.57 -66.58 REMARK 500 ASP B 191 -124.13 60.73 REMARK 500 ALA B 204 11.85 49.75 REMARK 500 LYS B 211 -133.03 54.59 REMARK 500 GLU B 220 -36.57 -36.26 REMARK 500 LEU B 227 80.71 -152.45 REMARK 500 GLU B 231 9.18 -68.54 REMARK 500 LYS B 280 22.62 -155.75 REMARK 500 ASN B 281 22.73 84.61 REMARK 500 LYS B 307 -9.93 85.78 REMARK 500 LYS B 315 -131.90 53.72 REMARK 500 ASP B 387 -167.51 -161.72 REMARK 500 MET B 414 112.42 103.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA B 325 ALA B 326 149.42 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9L9W A 1 507 UNP A0A1I7NFD7_9BACT DBREF2 9L9W A A0A1I7NFD7 1 507 DBREF1 9L9W B 1 421 UNP A0A1I7NFG5_9BACT DBREF2 9L9W B A0A1I7NFG5 1 421 DBREF 9L9W C 1 21 PDB 9L9W 9L9W 1 21 DBREF 9L9W D 2 21 PDB 9L9W 9L9W 2 21 SEQRES 1 A 507 MET LYS GLU LEU ILE TYR ILE GLU GLU PRO SER ILE LEU SEQRES 2 A 507 PHE ALA HIS GLY GLN LYS CYS THR ASP PRO ARG ASP GLY SEQRES 3 A 507 LEU ALA LEU PHE GLY PRO LEU ASN GLN ILE TYR GLY ILE SEQRES 4 A 507 LYS SER GLY VAL VAL GLY THR GLN LYS GLY LEU GLN ILE SEQRES 5 A 507 PHE LYS SER TYR LEU ASP LYS ILE GLN LYS PRO ILE TYR SEQRES 6 A 507 ASN HIS ASN ASN ILE THR ARG PRO MET PHE PRO GLY PHE SEQRES 7 A 507 GLU ALA VAL PHE GLY CYS LYS TRP GLU SER GLN ASN ILE SEQRES 8 A 507 VAL PHE LYS GLU ILE THR ASP GLU GLU ILE ARG ARG TYR SEQRES 9 A 507 LEU PHE ASN ALA SER THR HIS LYS ARG THR TYR ASP LEU SEQRES 10 A 507 VAL THR LEU PHE ASN ASP LYS ILE ILE THR ALA ASN LYS SEQRES 11 A 507 ASN ASP GLU GLU ARG VAL ASP VAL TRP PHE VAL ILE VAL SEQRES 12 A 507 PRO GLU GLU ILE TYR LYS TYR CYS ARG PRO ASN SER VAL SEQRES 13 A 507 LEU PRO ASN GLU LEU VAL GLN THR LYS SER LEU ILE SER SEQRES 14 A 507 LYS SER LYS ALA LYS SER PHE ARG TYR THR PRO THR LEU SEQRES 15 A 507 PHE GLU GLU PHE ASN LYS LYS LEU LYS GLU VAL GLU LYS SEQRES 16 A 507 GLU ALA LYS THR TYR ASN TYR ASP ALA GLN PHE HIS ASP SEQRES 17 A 507 GLN LEU LYS ALA ARG LEU LEU GLU HIS THR ILE PRO THR SEQRES 18 A 507 GLN ILE LEU ARG GLU SER THR LEU ALA TRP ARG ASP PHE SEQRES 19 A 507 LYS ASN THR PHE GLY ALA PRO ILE ARG ASP PHE SER LYS SEQRES 20 A 507 ILE GLU GLY HIS LEU ALA TRP THR ILE SER THR ALA ALA SEQRES 21 A 507 TYR TYR LYS ALA GLY GLY LYS PRO TRP LYS LEU GLY ASP SEQRES 22 A 507 ILE ARG PRO GLY VAL CYS TYR LEU GLY LEU VAL TYR LYS SEQRES 23 A 507 LYS ILE GLU LYS SER LYS ASN PRO GLN ASN ALA CYS CYS SEQRES 24 A 507 ALA ALA GLN MET PHE LEU ASP ASN GLY ASP GLY THR VAL SEQRES 25 A 507 PHE LYS GLY GLU VAL GLY PRO TRP TYR ASN PRO GLU LYS SEQRES 26 A 507 GLY GLU TYR HIS LEU LYS PRO LYS GLU ALA LYS ALA LEU SEQRES 27 A 507 LEU THR GLN ALA LEU GLU SER TYR LYS GLU GLN ASN LYS SEQRES 28 A 507 SER TYR PRO LYS GLU VAL PHE ILE HIS ALA ARG THR ARG SEQRES 29 A 507 PHE ASN ASP GLU GLU TRP ASN ALA PHE ASN GLU VAL THR SEQRES 30 A 507 PRO LYS ASN THR ASN LEU VAL GLY VAL THR ILE THR LYS SEQRES 31 A 507 SER LYS PRO LEU LYS LEU TYR LYS THR GLU GLY ALA PHE SEQRES 32 A 507 PRO ILE MET ARG GLY ASN ALA TYR ILE VAL ASP GLU LYS SEQRES 33 A 507 LYS ALA PHE LEU TRP THR LEU GLY PHE VAL PRO LYS LEU SEQRES 34 A 507 GLN SER THR LEU SER MET GLU VAL PRO ASN PRO ILE PHE SEQRES 35 A 507 ILE GLU ILE ASN LYS GLY GLU ALA GLU ILE GLN GLN VAL SEQRES 36 A 507 LEU LYS ASP ILE LEU ALA LEU THR LYS LEU ASN TYR ASN SEQRES 37 A 507 ALA CYS ILE TYR ALA ASP GLY GLU PRO VAL THR LEU ARG SEQRES 38 A 507 PHE ALA ASN LYS ILE GLY GLU ILE LEU THR ALA SER THR SEQRES 39 A 507 GLU ILE LYS THR PRO PRO LEU ALA PHE LYS TYR TYR ILE SEQRES 1 B 421 MET ARG ASN LYS ILE PHE ILE SER HIS ALA THR PRO GLU SEQRES 2 B 421 ASP ASP ASP PHE THR ARG TRP LEU SER LEU LYS LEU ILE SEQRES 3 B 421 GLY LEU GLY TYR GLU VAL TRP CYS ASP ILE LEU PHE LEU SEQRES 4 B 421 ASP LYS GLY VAL ASP PHE TRP SER THR ILE GLU LYS GLU SEQRES 5 B 421 ILE ARG GLU ASN THR CYS LYS PHE LEU ILE VAL SER SER SEQRES 6 B 421 THR ALA GLY ASN LYS ARG GLU GLY VAL LEU LYS GLU LEU SEQRES 7 B 421 ALA VAL ALA THR LYS VAL LYS LYS HIS LEU GLN ASP ASP SEQRES 8 B 421 MET PHE ILE ILE PRO LEU ALA ILE ASP GLU ASN LEU SER SEQRES 9 B 421 TYR ASP ASP ILE ASN ILE GLU ILE VAL ARG LEU ASN ALA SEQRES 10 B 421 ILE ASP PHE LYS LYS SER TRP ALA LYS GLY LEU GLN ASP SEQRES 11 B 421 LEU LEU ASP ALA PHE GLU LYS GLN ASN VAL PRO LYS LYS SEQRES 12 B 421 PRO PRO ASP HIS SER LYS SER ASN LEU LEU TYR GLN GLN SEQRES 13 B 421 ILE PHE LEU HIS ASP LYS GLN ALA ILE GLU LYS GLU GLU SEQRES 14 B 421 THR TYR ASP SER ASN TRP PHE PRO ILE ILE SER PHE PRO SEQRES 15 B 421 ASN GLU LEU ARG PHE HIS ARG TYR ASP TRP ARG LEU PRO SEQRES 16 B 421 LYS GLN PHE ASP VAL ARG THR LEU ALA PHE PRO ALA ILE SEQRES 17 B 421 ARG TYR LYS GLU TYR LEU CYS THR PHE ALA TRP GLU TYR SEQRES 18 B 421 ASP PHE ILE HIS GLN LEU PRO LYS THR GLU THR TYR ASN SEQRES 19 B 421 GLY GLN GLU SER ILE ARG ILE SER THR SER ASP ILE LEU SEQRES 20 B 421 SER GLY ARG TYR ASP THR ASP PHE ILE ARG ASN TYR GLU SEQRES 21 B 421 CYS GLN ARG LEU ILE VAL GLN LEU ILE ASN LYS ALA PHE SEQRES 22 B 421 GLU LEU ARG MET LYS ASP LYS ASN VAL ARG GLU TYR GLN SEQRES 23 B 421 MET SER LYS THR PHE ALA TYR TRP ILE GLU LYS GLY LYS SEQRES 24 B 421 LEU GLU LYS ASP LYS PHE GLU LYS ILE LYS LEU VAL GLY SEQRES 25 B 421 LYS GLN LYS ASN LYS TYR TRP HIS PHE GLY ILE SER ALA SEQRES 26 B 421 ALA GLY LYS LEU TYR PRO SER PRO VAL LEU MET VAL SER SEQRES 27 B 421 SER HIS ILE ILE PHE THR MET ASP GLY ILE ASN LEU ILE SEQRES 28 B 421 LYS SER LYS SER ILE GLN HIS SER SER ARG ARG LYS GLN SEQRES 29 B 421 GLY LYS ASN TRP TRP ASN ASP LYS TRP ARG GLU LYS LEU SEQRES 30 B 421 LEU ALA PHE ILE ARG PHE LEU SER ASP ASP GLN ASN ALA SEQRES 31 B 421 ILE TYR LEU ASN VAL GLY SER GLU GLU LYS ILE LEU ILE SEQRES 32 B 421 SER ASN LYS PRO LEU LYS PHE PHE GLY LYS MET SER TYR SEQRES 33 B 421 VAL THR PRO SER GLU SEQRES 1 C 21 DT DG DA DG DG DT DA DG DT DA DG DG DT SEQRES 2 C 21 DT DG DT DA DT DA DG DT SEQRES 1 D 20 DT DA DT DA DC DA DA DC DC DT DA DC DT SEQRES 2 D 20 DA DC DC DT DC DA DT HET MG D 101 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG MG 2+ HELIX 1 AA1 ALA A 15 GLY A 17 5 3 HELIX 2 AA2 ASP A 22 GLY A 31 1 10 HELIX 3 AA3 THR A 46 LYS A 62 1 17 HELIX 4 AA4 GLY A 77 GLY A 83 1 7 HELIX 5 AA5 THR A 97 PHE A 106 1 10 HELIX 6 AA6 SER A 109 ASP A 132 1 24 HELIX 7 AA7 PRO A 144 CYS A 151 1 8 HELIX 8 AA8 GLN A 205 LEU A 214 1 10 HELIX 9 AA9 GLU A 226 ALA A 230 1 5 HELIX 10 AB1 TRP A 231 PHE A 234 5 4 HELIX 11 AB2 ILE A 248 GLY A 265 1 18 HELIX 12 AB3 LYS A 331 LYS A 351 1 21 HELIX 13 AB4 ASN A 366 THR A 377 1 12 HELIX 14 AB5 GLU A 451 THR A 463 1 13 HELIX 15 AB6 LYS A 464 ASN A 466 5 3 HELIX 16 AB7 PRO A 477 PHE A 482 1 6 HELIX 17 AB8 PHE A 482 SER A 493 1 12 HELIX 18 AB9 PHE A 503 ILE A 507 1 5 HELIX 19 AC1 ASP B 14 GLY B 29 1 16 HELIX 20 AC2 VAL B 43 GLU B 55 1 13 HELIX 21 AC3 SER B 65 LYS B 70 1 6 HELIX 22 AC4 ARG B 71 GLN B 89 1 19 HELIX 23 AC5 ASP B 90 MET B 92 5 3 HELIX 24 AC6 ASN B 109 ARG B 114 1 6 HELIX 25 AC7 SER B 123 GLN B 138 1 16 HELIX 26 AC8 ASP B 146 ILE B 157 1 12 HELIX 27 AC9 PHE B 158 ASP B 161 5 4 HELIX 28 AD1 TYR B 190 LEU B 194 5 5 HELIX 29 AD2 TRP B 219 PHE B 223 5 5 HELIX 30 AD3 THR B 243 LEU B 247 1 5 HELIX 31 AD4 ARG B 257 MET B 277 1 21 HELIX 32 AD5 LYS B 278 LYS B 280 5 3 HELIX 33 AD6 LEU B 300 LYS B 304 5 5 HELIX 34 AD7 SER B 353 LYS B 366 1 14 HELIX 35 AD8 TRP B 369 SER B 385 1 17 SHEET 1 AA1 4 LYS A 2 GLU A 3 0 SHEET 2 AA1 4 LYS B 409 SER B 415 1 O PHE B 411 N LYS A 2 SHEET 3 AA1 4 ILE B 165 ASP B 172 -1 N LYS B 167 O MET B 414 SHEET 4 AA1 4 TYR A 397 LYS A 398 -1 N TYR A 397 O ASP B 172 SHEET 1 AA210 ILE A 5 TYR A 6 0 SHEET 2 AA210 ASN A 409 ILE A 412 -1 O ALA A 410 N ILE A 5 SHEET 3 AA210 LYS A 417 LEU A 420 -1 O PHE A 419 N TYR A 411 SHEET 4 AA210 ILE A 441 GLU A 444 -1 O ILE A 441 N LEU A 420 SHEET 5 AA210 ASN A 382 THR A 389 -1 N THR A 387 O GLU A 444 SHEET 6 AA210 GLU A 356 ALA A 361 1 N ILE A 359 O VAL A 384 SHEET 7 AA210 VAL A 278 LYS A 287 1 N LEU A 281 O HIS A 360 SHEET 8 AA210 ASN A 296 PHE A 304 -1 O GLN A 302 N GLY A 282 SHEET 9 AA210 THR A 311 PRO A 319 -1 O PHE A 313 N ALA A 301 SHEET 10 AA210 LEU A 501 ALA A 502 -1 O LEU A 501 N VAL A 312 SHEET 1 AA3 3 GLN A 18 CYS A 20 0 SHEET 2 AA3 3 ILE A 12 PHE A 14 -1 N PHE A 14 O GLN A 18 SHEET 3 AA3 3 LYS A 270 LEU A 271 -1 O LYS A 270 N LEU A 13 SHEET 1 AA4 4 ILE A 91 PHE A 93 0 SHEET 2 AA4 4 SER A 41 VAL A 43 1 N SER A 41 O VAL A 92 SHEET 3 AA4 4 VAL A 138 VAL A 143 1 O PHE A 140 N GLY A 42 SHEET 4 AA4 4 THR A 221 ARG A 225 1 O GLN A 222 N TRP A 139 SHEET 1 AA5 2 TYR A 321 ASN A 322 0 SHEET 2 AA5 2 GLU A 327 TYR A 328 -1 O GLU A 327 N ASN A 322 SHEET 1 AA6 2 PHE A 425 VAL A 426 0 SHEET 2 AA6 2 SER A 431 THR A 432 -1 O SER A 431 N VAL A 426 SHEET 1 AA7 5 VAL B 32 TRP B 33 0 SHEET 2 AA7 5 LYS B 4 SER B 8 1 N ILE B 7 O TRP B 33 SHEET 3 AA7 5 THR B 57 VAL B 63 1 O LEU B 61 N SER B 8 SHEET 4 AA7 5 ILE B 94 ALA B 98 1 O LEU B 97 N ILE B 62 SHEET 5 AA7 5 ILE B 118 ASP B 119 1 O ILE B 118 N ALA B 98 SHEET 1 AA8 5 ALA B 326 LYS B 328 0 SHEET 2 AA8 5 VAL B 334 MET B 336 -1 O MET B 336 N ALA B 326 SHEET 3 AA8 5 TRP B 175 SER B 180 -1 N PHE B 176 O LEU B 335 SHEET 4 AA8 5 LYS B 400 SER B 404 -1 O LEU B 402 N ILE B 179 SHEET 5 AA8 5 ALA B 390 ASN B 394 -1 N ILE B 391 O ILE B 403 SHEET 1 AA9 4 ILE B 208 TYR B 210 0 SHEET 2 AA9 4 TYR B 213 THR B 216 -1 O CYS B 215 N ILE B 208 SHEET 3 AA9 4 GLU B 184 HIS B 188 -1 N HIS B 188 O LEU B 214 SHEET 4 AA9 4 ILE B 239 SER B 242 -1 O ILE B 241 N LEU B 185 SHEET 1 AB1 4 ARG B 283 GLN B 286 0 SHEET 2 AB1 4 PHE B 291 TRP B 294 -1 O ALA B 292 N TYR B 285 SHEET 3 AB1 4 LYS B 317 ILE B 323 -1 O ILE B 323 N TYR B 293 SHEET 4 AB1 4 VAL B 311 GLN B 314 -1 N GLN B 314 O LYS B 317 SHEET 1 AB2 5 ARG B 283 GLN B 286 0 SHEET 2 AB2 5 PHE B 291 TRP B 294 -1 O ALA B 292 N TYR B 285 SHEET 3 AB2 5 LYS B 317 ILE B 323 -1 O ILE B 323 N TYR B 293 SHEET 4 AB2 5 SER B 339 ASP B 346 -1 O THR B 344 N TYR B 318 SHEET 5 AB2 5 ASN B 349 LEU B 350 -1 O ASN B 349 N ASP B 346 CISPEP 1 THR B 11 PRO B 12 0 3.61 CISPEP 2 TYR B 330 PRO B 331 0 1.47 CRYST1 136.189 136.189 174.919 90.00 90.00 120.00 P 32 2 1 6 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 0.007343 0.004239 0.000000 0.00000 SCALE2 0.000000 0.008479 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005717 0.00000