HEADER HYDROLASE/DNA 06-NOV-10 3PIH TITLE T. MARITIMA UVRA IN COMPLEX WITH FLUORESCEIN-MODIFIED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UVRABC SYSTEM PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UVRA PROTEIN, EXCINUCLEASE ABC SUBUNIT A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (32-MER); COMPND 8 CHAIN: D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: UVRA, TM_0480; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: SYNTHETIC DNA OLIGO KEYWDS HYDROLASE, ABC ATPASE, DNA REPAIR, NUCLEOTIDE EXCISION REPAIR, UVRB, KEYWDS 2 HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.JACIUK,E.NOWAK,M.NOWOTNY REVDAT 4 06-SEP-23 3PIH 1 REMARK LINK REVDAT 3 08-NOV-17 3PIH 1 REMARK REVDAT 2 23-FEB-11 3PIH 1 JRNL REVDAT 1 19-JAN-11 3PIH 0 JRNL AUTH M.JACIUK,E.NOWAK,K.SKOWRONEK,A.TANSKA,M.NOWOTNY JRNL TITL STRUCTURE OF UVRA NUCLEOTIDE EXCISION REPAIR PROTEIN IN JRNL TITL 2 COMPLEX WITH MODIFIED DNA. JRNL REF NAT.STRUCT.MOL.BIOL. V. 18 191 2011 JRNL REFN ISSN 1545-9993 JRNL PMID 21240268 JRNL DOI 10.1038/NSMB.1973 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1275 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 48.0865 - 6.0288 0.99 2936 151 0.2018 0.2081 REMARK 3 2 6.0288 - 4.7867 1.00 2893 154 0.2082 0.2636 REMARK 3 3 4.7867 - 4.1820 1.00 2900 145 0.1608 0.2329 REMARK 3 4 4.1820 - 3.7998 0.99 2866 135 0.1743 0.2547 REMARK 3 5 3.7998 - 3.5275 0.98 2853 140 0.1857 0.3099 REMARK 3 6 3.5275 - 3.3196 0.97 2777 175 0.2133 0.3101 REMARK 3 7 3.3196 - 3.1534 0.94 2716 142 0.2317 0.3550 REMARK 3 8 3.1534 - 3.0162 0.83 2362 140 0.2629 0.3351 REMARK 3 9 3.0162 - 2.9000 0.61 1755 93 0.2523 0.3927 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.06 REMARK 3 K_SOL : 0.27 REMARK 3 B_SOL : 46.75 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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) : -3.95880 REMARK 3 B22 (A**2) : -3.95880 REMARK 3 B33 (A**2) : 7.91760 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 : 0.006 7247 REMARK 3 ANGLE : 1.046 9951 REMARK 3 CHIRALITY : 0.063 1147 REMARK 3 PLANARITY : 0.004 1174 REMARK 3 DIHEDRAL : 18.604 2735 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 3PIH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19081 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 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 (%) : 72.5 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.06100 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) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 2R6F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 49-52% MPD, 0.1-0.2 M AMMONIUM REMARK 280 PHOSPHATE AND 0.1 M TRIS PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 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 -Y,X,Z+1/2 REMARK 290 4555 Y,-X,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.12800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.12800 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: 9370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 81370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 107.51000 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 A 1 REMARK 465 ALA A 61 REMARK 465 ARG A 62 REMARK 465 GLN A 63 REMARK 465 PHE A 64 REMARK 465 LEU A 65 REMARK 465 GLY A 66 REMARK 465 ASN A 67 REMARK 465 LEU A 68 REMARK 465 VAL A 90 REMARK 465 VAL A 155 REMARK 465 ALA A 156 REMARK 465 THR A 157 REMARK 465 GLU A 158 REMARK 465 LYS A 159 REMARK 465 LYS A 160 REMARK 465 GLY A 161 REMARK 465 THR A 162 REMARK 465 PHE A 163 REMARK 465 LYS A 164 REMARK 465 LYS A 165 REMARK 465 GLU A 166 REMARK 465 ILE A 167 REMARK 465 GLU A 168 REMARK 465 GLU A 169 REMARK 465 PHE A 170 REMARK 465 ILE A 171 REMARK 465 SER A 172 REMARK 465 LYS A 173 REMARK 465 GLY A 174 REMARK 465 PHE A 175 REMARK 465 ALA A 176 REMARK 465 ARG A 177 REMARK 465 ILE A 178 REMARK 465 GLU A 179 REMARK 465 ILE A 180 REMARK 465 ASP A 181 REMARK 465 GLY A 182 REMARK 465 GLU A 183 REMARK 465 ILE A 184 REMARK 465 TYR A 185 REMARK 465 ARG A 186 REMARK 465 LEU A 187 REMARK 465 GLU A 188 REMARK 465 GLU A 189 REMARK 465 VAL A 190 REMARK 465 PRO A 191 REMARK 465 GLU A 192 REMARK 465 LEU A 193 REMARK 465 ASP A 194 REMARK 465 LYS A 195 REMARK 465 ASN A 196 REMARK 465 LYS A 197 REMARK 465 ARG A 198 REMARK 465 HIS A 199 REMARK 465 THR A 200 REMARK 465 VAL A 201 REMARK 465 LYS A 202 REMARK 465 ILE A 294 REMARK 465 ASP A 295 REMARK 465 GLU A 296 REMARK 465 GLU A 297 REMARK 465 LYS A 298 REMARK 465 SER A 299 REMARK 465 VAL A 300 REMARK 465 LEU A 301 REMARK 465 GLU A 302 REMARK 465 GLY A 303 REMARK 465 HIS A 330 REMARK 465 LEU A 331 REMARK 465 PRO A 332 REMARK 465 PHE A 333 REMARK 465 LYS A 334 REMARK 465 ASP A 335 REMARK 465 LEU A 336 REMARK 465 ASP A 349 REMARK 465 ARG A 350 REMARK 465 GLU A 366 REMARK 465 SER A 367 REMARK 465 PRO A 368 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 TYR A 60 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 ILE A 115 CG1 CG2 CD1 REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 ARG A 125 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 130 CG CD CE NZ REMARK 470 LEU A 203 CG CD1 CD2 REMARK 470 VAL A 204 CG1 CG2 REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 MET A 251 CG SD CE REMARK 470 VAL A 254 CG1 CG2 REMARK 470 PHE A 259 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 265 CG CD CE NZ REMARK 470 LEU A 292 CG CD1 CD2 REMARK 470 VAL A 293 CG1 CG2 REMARK 470 ILE A 306 CG1 CG2 CD1 REMARK 470 ARG A 312 NE CZ NH1 NH2 REMARK 470 ARG A 313 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 323 CG CD OE1 OE2 REMARK 470 LYS A 324 CG CD CE NZ REMARK 470 GLU A 338 CG CD OE1 OE2 REMARK 470 ASP A 339 CG OD1 OD2 REMARK 470 ILE A 344 CG1 CG2 CD1 REMARK 470 LEU A 345 CG CD1 CD2 REMARK 470 ASP A 348 CG OD1 OD2 REMARK 470 PHE A 351 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 364 CG CD OE1 OE2 REMARK 470 GLU A 369 CG CD OE1 OE2 REMARK 470 GLU A 372 CG CD OE1 OE2 REMARK 470 LYS A 376 CG CD CE NZ REMARK 470 LEU A 426 CG CD1 CD2 REMARK 470 GLU A 430 CG CD OE1 OE2 REMARK 470 ARG A 431 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 434 CG1 CG2 REMARK 470 GLU A 436 CG CD OE1 OE2 REMARK 470 LYS A 439 CG CD CE NZ REMARK 470 ARG A 474 CZ NH1 NH2 REMARK 470 LEU A 559 CG CD1 CD2 REMARK 470 LYS A 560 CG CD CE NZ REMARK 470 ASN A 561 CG OD1 ND2 REMARK 470 ASP A 563 CG OD1 OD2 REMARK 470 LYS A 576 CG CD CE NZ REMARK 470 LYS A 581 CG CD CE NZ REMARK 470 LYS A 641 CG CD CE NZ REMARK 470 LYS A 660 CG CD CE NZ REMARK 470 LYS A 712 CG CD CE NZ REMARK 470 LYS A 783 CG CD CE NZ REMARK 470 ARG A 823 CG CD NE CZ NH1 NH2 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 DG D 4 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA D 5 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DT D 6 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT D 14 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC D 15 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 DG D 18 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC D 22 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT D 25 O4' - C1' - N1 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG D 26 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG D 26 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG D 26 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA D 27 O4' - C4' - C3' ANGL. DEV. = -3.9 DEGREES REMARK 500 DT D 28 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA D 30 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC D 31 O4' - C1' - N1 ANGL. DEV. = 1.8 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 HIS A 12 -125.53 41.68 REMARK 500 LYS A 15 53.14 -93.78 REMARK 500 TYR A 53 -70.10 -70.02 REMARK 500 LEU A 57 -154.22 -84.93 REMARK 500 ASP A 72 88.31 -63.15 REMARK 500 PRO A 81 127.53 -39.12 REMARK 500 ASP A 86 -167.46 -168.50 REMARK 500 GLU A 103 -9.12 73.59 REMARK 500 PRO A 121 13.54 -62.62 REMARK 500 GLU A 122 -43.14 -154.95 REMARK 500 GLU A 145 106.34 -57.97 REMARK 500 CYS A 255 -16.73 -159.47 REMARK 500 CYS A 279 -7.22 -150.55 REMARK 500 PRO A 290 38.96 -56.09 REMARK 500 ASP A 311 100.10 -165.64 REMARK 500 VAL A 340 18.63 97.57 REMARK 500 TYR A 346 -43.61 -140.35 REMARK 500 GLU A 364 20.24 -77.02 REMARK 500 ARG A 391 -36.15 77.95 REMARK 500 ARG A 431 -1.60 -59.08 REMARK 500 ILE A 433 -72.79 -85.86 REMARK 500 SER A 466 174.45 -58.85 REMARK 500 PHE A 551 145.70 -178.54 REMARK 500 ASP A 563 -3.62 -53.47 REMARK 500 ASN A 580 125.46 -38.66 REMARK 500 ASN A 598 -129.02 52.45 REMARK 500 ASN A 602 62.70 35.78 REMARK 500 THR A 630 -71.99 -132.46 REMARK 500 LYS A 643 65.51 -114.12 REMARK 500 LYS A 682 -6.57 69.82 REMARK 500 TYR A 702 133.70 -35.73 REMARK 500 ASN A 703 -167.86 -122.82 REMARK 500 GLN A 720 19.12 53.39 REMARK 500 LYS A 757 30.39 38.67 REMARK 500 GLU A 774 -72.02 -68.22 REMARK 500 PHE A 775 -33.51 -29.42 REMARK 500 GLN A 801 107.24 -46.71 REMARK 500 THR A 805 1.27 -63.06 REMARK 500 ARG A 827 42.71 -152.47 REMARK 500 GLU A 834 74.98 23.23 REMARK 500 GLU A 883 -169.24 -125.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 919 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 120 SG REMARK 620 2 CYS A 123 SG 88.5 REMARK 620 3 CYS A 252 SG 76.5 79.7 REMARK 620 4 CYS A 255 SG 89.8 153.8 74.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 918 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 276 SG REMARK 620 2 CYS A 279 SG 111.4 REMARK 620 3 CYS A 384 SG 113.4 117.3 REMARK 620 4 CYS A 387 SG 113.4 101.1 99.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 917 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 716 SG REMARK 620 2 CYS A 719 SG 128.1 REMARK 620 3 CYS A 739 SG 110.8 95.7 REMARK 620 4 CYS A 742 SG 111.3 104.7 102.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PPV A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PPV A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 917 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 918 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 919 DBREF 3PIH A 1 916 UNP Q9WYV0 UVRA_THEMA 1 916 DBREF 3PIH D 1 32 PDB 3PIH 3PIH 1 32 SEQRES 1 A 916 MET ASN GLU ILE VAL VAL LYS GLY ALA ARG VAL HIS ASN SEQRES 2 A 916 LEU LYS ASN ILE THR VAL ARG ILE PRO LYS ASN ARG LEU SEQRES 3 A 916 VAL VAL ILE THR GLY VAL SER GLY SER GLY LYS SER SER SEQRES 4 A 916 LEU ALA MET ASP THR ILE TYR ALA GLU GLY GLN ARG ARG SEQRES 5 A 916 TYR LEU GLU SER LEU SER THR TYR ALA ARG GLN PHE LEU SEQRES 6 A 916 GLY ASN LEU LYS LYS PRO ASP VAL ASP GLU ILE GLU GLY SEQRES 7 A 916 LEU SER PRO ALA ILE ALA ILE ASP GLN LYS THR VAL SER SEQRES 8 A 916 HIS ASN PRO ARG SER THR VAL GLY THR VAL THR GLU ILE SEQRES 9 A 916 TYR ASP TYR LEU ARG VAL LEU TYR ALA ARG ILE GLY LYS SEQRES 10 A 916 ALA HIS CYS PRO GLU CYS GLY ARG PRO LEU GLU LYS LYS SEQRES 11 A 916 SER ILE ASP GLU ILE LEU GLN ASP LEU PHE ASN SER PHE SEQRES 12 A 916 LYS GLU GLY SER ARG ILE TYR ILE LEU ALA PRO VAL ALA SEQRES 13 A 916 THR GLU LYS LYS GLY THR PHE LYS LYS GLU ILE GLU GLU SEQRES 14 A 916 PHE ILE SER LYS GLY PHE ALA ARG ILE GLU ILE ASP GLY SEQRES 15 A 916 GLU ILE TYR ARG LEU GLU GLU VAL PRO GLU LEU ASP LYS SEQRES 16 A 916 ASN LYS ARG HIS THR VAL LYS LEU VAL VAL ASP ARG LEU SEQRES 17 A 916 ILE LEU GLU THR ARG ASN GLU HIS ARG ILE LEU ASP SER SEQRES 18 A 916 LEU GLU LEU ALA MET ARG GLU GLY LYS GLY PHE VAL GLU SEQRES 19 A 916 ILE ARG ASN VAL ASP THR GLY GLU SER LYS ILE PHE SER SEQRES 20 A 916 GLU ASN LEU MET CYS PRO VAL CYS GLY ILE GLY PHE PRO SEQRES 21 A 916 GLU ILE THR PRO LYS LEU PHE SER PHE ASN SER PRO TYR SEQRES 22 A 916 GLY ALA CYS PRO ASN CYS HIS GLY LEU GLY PHE THR PHE SEQRES 23 A 916 GLU VAL ASP PRO SER LEU VAL ILE ASP GLU GLU LYS SER SEQRES 24 A 916 VAL LEU GLU GLY ALA ILE ILE PRO TYR ARG TRP ASP ARG SEQRES 25 A 916 ARG LEU SER ARG TRP VAL ALA ARG GLU ILE GLU LYS ARG SEQRES 26 A 916 GLY VAL SER PRO HIS LEU PRO PHE LYS ASP LEU PRO GLU SEQRES 27 A 916 ASP VAL LYS GLU PHE ILE LEU TYR GLY ASP ASP ARG PHE SEQRES 28 A 916 GLU GLY VAL VAL PRO LYS VAL GLN ARG TRP HIS ARG GLU SEQRES 29 A 916 THR GLU SER PRO GLU MET LYS GLU TRP LEU GLU LYS ASN SEQRES 30 A 916 PHE ILE VAL GLN ARG THR CYS SER VAL CYS GLY GLY ARG SEQRES 31 A 916 ARG LEU ASN ARG GLU ALA LEU SER VAL LYS ILE ASN GLY SEQRES 32 A 916 LEU ASN ILE HIS GLU PHE THR GLU LEU SER ILE SER GLU SEQRES 33 A 916 GLU LEU GLU PHE LEU LYS ASN LEU ASN LEU THR GLU ARG SEQRES 34 A 916 GLU ARG GLU ILE VAL GLY GLU LEU LEU LYS GLU ILE GLU SEQRES 35 A 916 LYS ARG LEU GLU PHE LEU VAL ASP VAL GLY LEU GLU TYR SEQRES 36 A 916 LEU THR LEU SER ARG SER ALA THR THR LEU SER GLY GLY SEQRES 37 A 916 GLU SER GLN ARG ILE ARG LEU ALA THR GLN ILE GLY SER SEQRES 38 A 916 GLY LEU THR GLY VAL ILE TYR VAL LEU ASP GLU PRO THR SEQRES 39 A 916 ILE GLY LEU HIS PRO ARG ASP THR GLU ARG LEU ILE LYS SEQRES 40 A 916 THR LEU LYS LYS LEU ARG ASP LEU GLY ASN THR VAL ILE SEQRES 41 A 916 VAL VAL GLU HIS ASP GLU GLU VAL ILE ARG ASN ALA ASP SEQRES 42 A 916 HIS ILE ILE ASP ILE GLY PRO GLY GLY GLY THR ASN GLY SEQRES 43 A 916 GLY ARG VAL VAL PHE GLN GLY THR VAL ASP GLU LEU LEU SEQRES 44 A 916 LYS ASN PRO ASP SER SER LEU THR GLY GLU TYR LEU SER SEQRES 45 A 916 GLY LYS ARG LYS ILE THR VAL ASN LYS THR ARG ARG LEU SEQRES 46 A 916 PRO TYR ALA SER LEU LYS ILE LYS GLY VAL ARG HIS ASN SEQRES 47 A 916 ASN LEU LYS ASN ILE ASP VAL GLU ILE PRO LEU GLY VAL SEQRES 48 A 916 PHE VAL CYS VAL THR GLY VAL SER GLY SER GLY LYS SER SEQRES 49 A 916 SER LEU VAL MET GLU THR LEU TYR PRO ALA LEU MET ASN SEQRES 50 A 916 LEU LEU HIS LYS THR LYS LEU PRO ALA GLY GLU PHE ASP SEQRES 51 A 916 SER ILE GLU GLY HIS GLU ASN ILE ASP LYS MET ILE ALA SEQRES 52 A 916 ILE ASP GLN SER PRO ILE GLY ARG THR PRO ARG SER ASN SEQRES 53 A 916 PRO ALA THR TYR THR LYS VAL PHE ASP GLU ILE ARG SER SEQRES 54 A 916 LEU PHE ALA MET THR PRO ALA ALA LYS ALA ARG GLY TYR SEQRES 55 A 916 ASN LYS SER ARG PHE SER PHE ASN LEU LYS GLY GLY ARG SEQRES 56 A 916 CYS GLU ALA CYS GLN GLY GLN GLY TYR VAL LYS ILE GLU SEQRES 57 A 916 MET LEU PHE LEU PRO ASP VAL TYR VAL GLU CYS ASP VAL SEQRES 58 A 916 CYS LYS GLY LYS ARG TYR ASN ARG GLU THR LEU GLU ILE SEQRES 59 A 916 THR TYR LYS GLY LYS ASN ILE SER ASP ILE LEU ASP MET SEQRES 60 A 916 THR VAL ASP GLU ALA LEU GLU PHE PHE LYS ASN ILE PRO SEQRES 61 A 916 SER ILE LYS ARG THR LEU GLN VAL LEU HIS ASP VAL GLY SEQRES 62 A 916 LEU GLY TYR VAL LYS LEU GLY GLN PRO ALA THR THR LEU SEQRES 63 A 916 SER GLY GLY GLU ALA GLN ARG ILE LYS LEU ALA SER GLU SEQRES 64 A 916 LEU ARG LYS ARG ASP THR GLY ARG THR LEU TYR ILE LEU SEQRES 65 A 916 ASP GLU PRO THR VAL GLY LEU HIS PHE GLU ASP VAL ARG SEQRES 66 A 916 LYS LEU VAL GLU VAL LEU HIS ARG LEU VAL ASP ARG GLY SEQRES 67 A 916 ASN THR VAL ILE VAL ILE GLU HIS ASN LEU ASP VAL ILE SEQRES 68 A 916 LYS ASN ALA ASP HIS ILE ILE ASP LEU GLY PRO GLU GLY SEQRES 69 A 916 GLY LYS GLU GLY GLY TYR ILE VAL ALA THR GLY THR PRO SEQRES 70 A 916 GLU GLU ILE ALA LYS ASN PRO HIS SER TYR THR GLY ARG SEQRES 71 A 916 PHE LEU LYS ASN VAL LEU SEQRES 1 D 32 DA DG DT DG DA DT DC DA DG DT DG DG DT SEQRES 2 D 32 DT DC DC DG DG DA DA DC DC DA DC DT DG SEQRES 3 D 32 DA DT DC DA DC DT HET PPV A1001 9 HET PPV A1002 9 HET ZN A 917 1 HET ZN A 918 1 HET ZN A 919 1 HETNAM PPV PYROPHOSPHATE HETNAM ZN ZINC ION FORMUL 3 PPV 2(H4 O7 P2) FORMUL 5 ZN 3(ZN 2+) FORMUL 8 HOH *24(H2 O) HELIX 1 1 LYS A 37 MET A 42 1 6 HELIX 2 2 THR A 44 GLU A 55 1 12 HELIX 3 3 THR A 97 THR A 102 1 6 HELIX 4 4 GLU A 103 ILE A 115 1 13 HELIX 5 5 SER A 131 PHE A 143 1 13 HELIX 6 6 GLU A 211 ARG A 213 5 3 HELIX 7 7 ASN A 214 LYS A 230 1 17 HELIX 8 8 THR A 263 SER A 268 5 6 HELIX 9 9 ILE A 305 ARG A 309 5 5 HELIX 10 10 ASP A 311 GLU A 323 1 13 HELIX 11 11 LYS A 341 GLY A 347 1 7 HELIX 12 12 GLY A 353 GLU A 364 1 12 HELIX 13 13 MET A 370 ASN A 377 1 8 HELIX 14 14 GLU A 395 LEU A 397 5 3 HELIX 15 15 ILE A 406 LEU A 412 1 7 HELIX 16 16 SER A 413 ASN A 423 1 11 HELIX 17 17 ILE A 433 ASP A 450 1 18 HELIX 18 18 SER A 461 LEU A 465 5 5 HELIX 19 19 SER A 466 SER A 481 1 16 HELIX 20 20 HIS A 498 ARG A 500 5 3 HELIX 21 21 ASP A 501 LEU A 512 1 12 HELIX 22 22 ASP A 525 ASN A 531 1 7 HELIX 23 23 GLY A 542 GLY A 546 5 5 HELIX 24 24 THR A 554 ASN A 561 1 8 HELIX 25 25 SER A 565 GLY A 573 1 9 HELIX 26 26 GLY A 622 THR A 630 1 9 HELIX 27 27 THR A 630 LYS A 641 1 12 HELIX 28 28 GLY A 654 ILE A 658 5 5 HELIX 29 29 ASN A 676 THR A 681 1 6 HELIX 30 30 LYS A 682 ALA A 692 1 11 HELIX 31 31 THR A 694 ARG A 700 1 7 HELIX 32 32 ASN A 703 SER A 708 5 6 HELIX 33 33 GLU A 750 ILE A 754 5 5 HELIX 34 34 ASN A 760 ASP A 766 1 7 HELIX 35 35 THR A 768 PHE A 776 1 9 HELIX 36 36 ILE A 779 VAL A 792 1 14 HELIX 37 37 GLY A 793 VAL A 797 5 5 HELIX 38 38 SER A 807 ARG A 821 1 15 HELIX 39 39 HIS A 840 ARG A 857 1 18 HELIX 40 40 ASN A 867 LYS A 872 1 6 HELIX 41 41 GLY A 884 GLY A 888 5 5 HELIX 42 42 THR A 896 LYS A 902 1 7 HELIX 43 43 SER A 906 LYS A 913 1 8 SHEET 1 A 3 ARG A 20 PRO A 22 0 SHEET 2 A 3 GLU A 3 LYS A 7 -1 N ILE A 4 O ILE A 21 SHEET 3 A 3 GLU A 75 GLU A 77 -1 O GLU A 77 N VAL A 5 SHEET 1 B 6 ALA A 82 ILE A 85 0 SHEET 2 B 6 ILE A 487 ASP A 491 1 O VAL A 489 N ILE A 83 SHEET 3 B 6 THR A 518 VAL A 522 1 O ILE A 520 N TYR A 488 SHEET 4 B 6 LEU A 26 GLY A 31 1 N VAL A 27 O VAL A 521 SHEET 5 B 6 HIS A 534 GLY A 539 1 O ILE A 538 N THR A 30 SHEET 6 B 6 ARG A 548 GLY A 553 -1 O GLY A 553 N ILE A 535 SHEET 1 C 3 LYS A 117 ALA A 118 0 SHEET 2 C 3 VAL A 399 ILE A 401 -1 O LYS A 400 N LYS A 117 SHEET 3 C 3 LEU A 404 ASN A 405 -1 O LEU A 404 N ILE A 401 SHEET 1 D 4 ASP A 206 ILE A 209 0 SHEET 2 D 4 ARG A 148 LEU A 152 -1 N ILE A 149 O LEU A 208 SHEET 3 D 4 PHE A 232 ASN A 237 -1 O GLU A 234 N LEU A 152 SHEET 4 D 4 SER A 243 SER A 247 -1 O PHE A 246 N VAL A 233 SHEET 1 E 2 PHE A 284 VAL A 288 0 SHEET 2 E 2 ILE A 379 THR A 383 -1 O ARG A 382 N THR A 285 SHEET 1 F 3 ILE A 603 PRO A 608 0 SHEET 2 F 3 SER A 589 VAL A 595 -1 N LEU A 590 O ILE A 607 SHEET 3 F 3 SER A 651 GLU A 653 -1 O SER A 651 N LYS A 593 SHEET 1 G 6 LYS A 660 ILE A 664 0 SHEET 2 G 6 THR A 828 ASP A 833 1 O LEU A 829 N LYS A 660 SHEET 3 G 6 THR A 860 ILE A 864 1 O ILE A 862 N TYR A 830 SHEET 4 G 6 PHE A 612 THR A 616 1 N VAL A 615 O VAL A 863 SHEET 5 G 6 HIS A 876 GLY A 881 1 O ILE A 878 N CYS A 614 SHEET 6 G 6 TYR A 890 GLY A 895 -1 O ALA A 893 N ASP A 879 SHEET 1 H 2 TYR A 724 ILE A 727 0 SHEET 2 H 2 VAL A 735 GLU A 738 -1 O VAL A 735 N ILE A 727 LINK SG CYS A 120 ZN ZN A 919 1555 1555 2.64 LINK SG CYS A 123 ZN ZN A 919 1555 1555 2.32 LINK SG CYS A 252 ZN ZN A 919 1555 1555 2.89 LINK SG CYS A 255 ZN ZN A 919 1555 1555 2.36 LINK SG CYS A 276 ZN ZN A 918 1555 1555 2.62 LINK SG CYS A 279 ZN ZN A 918 1555 1555 2.58 LINK SG CYS A 384 ZN ZN A 918 1555 1555 2.38 LINK SG CYS A 387 ZN ZN A 918 1555 1555 2.46 LINK SG CYS A 716 ZN ZN A 917 1555 1555 2.36 LINK SG CYS A 719 ZN ZN A 917 1555 1555 2.22 LINK SG CYS A 739 ZN ZN A 917 1555 1555 2.49 LINK SG CYS A 742 ZN ZN A 917 1555 1555 2.44 CISPEP 1 SER A 328 PRO A 329 0 -2.42 CISPEP 2 GLU A 369 MET A 370 0 1.49 CISPEP 3 GLY A 539 PRO A 540 0 0.91 CISPEP 4 GLY A 881 PRO A 882 0 1.17 SITE 1 AC1 7 GLU A 469 SER A 619 GLY A 620 SER A 621 SITE 2 AC1 7 GLY A 622 LYS A 623 SER A 624 SITE 1 AC2 10 SER A 33 GLY A 34 SER A 35 GLY A 36 SITE 2 AC2 10 LYS A 37 SER A 38 HIS A 524 SER A 807 SITE 3 AC2 10 GLY A 809 GLY A 838 SITE 1 AC3 4 CYS A 716 CYS A 719 CYS A 739 CYS A 742 SITE 1 AC4 4 CYS A 276 CYS A 279 CYS A 384 CYS A 387 SITE 1 AC5 4 CYS A 120 CYS A 123 CYS A 252 CYS A 255 CRYST1 107.510 107.510 108.256 90.00 90.00 90.00 P 42 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 0.009301 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009301 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009237 0.00000