HEADER HYDROLASE 23-JUL-08 2VYF TITLE CRYSTAL STRUCTURE OF THE DNAC COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATIVE DNA HELICASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DNAC; COMPND 5 EC: 3.6.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS KAUSTOPHILUS HTA426; SOURCE 3 ORGANISM_TAXID: 235909; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET21B KEYWDS HYDROLASE, DNA REPLICATION, NUCLEOTIDE-BINDING, DNAC, HELICASE, ATP- KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.LO,K.L.TSAI,Y.J.SUN,C.D.HSIAO REVDAT 3 08-MAY-24 2VYF 1 REMARK REVDAT 2 10-MAR-09 2VYF 1 JRNL REVDAT 1 30-DEC-08 2VYF 0 JRNL AUTH Y.H.LO,K.L.TSAI,Y.J.SUN,W.T.CHEN,C.Y.HUANG,C.D.HSIAO JRNL TITL THE CRYSTAL STRUCTURE OF A REPLICATIVE HEXAMERIC HELICASE JRNL TITL 2 DNAC AND ITS COMPLEX WITH SINGLE-STRANDED DNA. JRNL REF NUCLEIC ACIDS RES. V. 37 804 2009 JRNL REFN ISSN 0305-1048 JRNL PMID 19074952 JRNL DOI 10.1093/NAR/GKN999 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.87 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 18500 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.293 REMARK 3 FREE R VALUE : 0.324 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1447 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 52.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4310 REMARK 3 BIN FREE R VALUE : 0.4500 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5942 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 167.6 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -27.14000 REMARK 3 B22 (A**2) : -27.14000 REMARK 3 B33 (A**2) : 54.28000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.67 REMARK 3 ESD FROM SIGMAA (A) : 0.78 REMARK 3 LOW RESOLUTION CUTOFF (A) : 6.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.77 REMARK 3 ESD FROM C-V SIGMAA (A) : 1.04 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.230 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 104.7 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE RESIDUES IN CHAIN A INCLUDING 1- 7, REMARK 3 258-264, 365-381, 400-409,AND 436-454 WERE MISSING. THE RESIDUES REMARK 3 IN CHAIN B INCLUDING 1-6, 155-157, 179-182, 322-331, 365-381, REMARK 3 397-410 AND 426-454 WERE MISSING. REMARK 4 REMARK 4 2VYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1290037005. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18502 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.68000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 79.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.41200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 54.41200 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 54.41200 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 31170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 135870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -219.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 -0.500000 -0.866025 0.000000 176.96800 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 88.48400 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 153.25878 REMARK 350 BIOMT3 3 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 SER A 2 REMARK 465 GLU A 3 REMARK 465 LEU A 4 REMARK 465 PHE A 5 REMARK 465 SER A 6 REMARK 465 GLU A 7 REMARK 465 ASN A 259 REMARK 465 ALA A 260 REMARK 465 GLN A 261 REMARK 465 ASN A 262 REMARK 465 LEU A 263 REMARK 465 ARG A 264 REMARK 465 SER A 366 REMARK 465 VAL A 367 REMARK 465 GLU A 368 REMARK 465 GLN A 369 REMARK 465 ARG A 370 REMARK 465 GLN A 371 REMARK 465 ASP A 372 REMARK 465 LYS A 373 REMARK 465 ARG A 374 REMARK 465 PRO A 375 REMARK 465 MET A 376 REMARK 465 MET A 377 REMARK 465 SER A 378 REMARK 465 ASP A 379 REMARK 465 LEU A 380 REMARK 465 ARG A 381 REMARK 465 TYR A 401 REMARK 465 TYR A 402 REMARK 465 ASN A 403 REMARK 465 LYS A 404 REMARK 465 ASP A 405 REMARK 465 SER A 406 REMARK 465 GLU A 407 REMARK 465 ASN A 408 REMARK 465 LYS A 409 REMARK 465 LYS A 437 REMARK 465 PHE A 438 REMARK 465 VAL A 439 REMARK 465 ASN A 440 REMARK 465 LEU A 441 REMARK 465 GLU A 442 REMARK 465 ARG A 443 REMARK 465 ARG A 444 REMARK 465 PHE A 445 REMARK 465 ASP A 446 REMARK 465 GLU A 447 REMARK 465 ALA A 448 REMARK 465 GLN A 449 REMARK 465 ILE A 450 REMARK 465 PRO A 451 REMARK 465 PRO A 452 REMARK 465 GLY A 453 REMARK 465 ALA A 454 REMARK 465 MET B 1001 REMARK 465 SER B 1002 REMARK 465 GLU B 1003 REMARK 465 LEU B 1004 REMARK 465 PHE B 1005 REMARK 465 SER B 1006 REMARK 465 SER B 1156 REMARK 465 GLY B 1157 REMARK 465 ASN B 1180 REMARK 465 GLY B 1181 REMARK 465 ASP B 1182 REMARK 465 GLN B 1323 REMARK 465 LEU B 1324 REMARK 465 ILE B 1325 REMARK 465 GLN B 1326 REMARK 465 GLY B 1327 REMARK 465 SER B 1328 REMARK 465 GLY B 1329 REMARK 465 ARG B 1330 REMARK 465 ASN B 1331 REMARK 465 SER B 1366 REMARK 465 VAL B 1367 REMARK 465 GLU B 1368 REMARK 465 GLN B 1369 REMARK 465 ARG B 1370 REMARK 465 GLN B 1371 REMARK 465 ASP B 1372 REMARK 465 LYS B 1373 REMARK 465 ARG B 1374 REMARK 465 PRO B 1375 REMARK 465 MET B 1376 REMARK 465 MET B 1377 REMARK 465 SER B 1378 REMARK 465 ASP B 1379 REMARK 465 LEU B 1380 REMARK 465 ARG B 1381 REMARK 465 ARG B 1398 REMARK 465 ASP B 1399 REMARK 465 ASP B 1400 REMARK 465 TYR B 1401 REMARK 465 TYR B 1402 REMARK 465 ASN B 1403 REMARK 465 LYS B 1404 REMARK 465 ASP B 1405 REMARK 465 SER B 1406 REMARK 465 GLU B 1407 REMARK 465 ASN B 1408 REMARK 465 LYS B 1409 REMARK 465 ASN B 1410 REMARK 465 VAL B 1427 REMARK 465 GLN B 1428 REMARK 465 LEU B 1429 REMARK 465 ALA B 1430 REMARK 465 PHE B 1431 REMARK 465 ILE B 1432 REMARK 465 LYS B 1433 REMARK 465 GLU B 1434 REMARK 465 TYR B 1435 REMARK 465 ASN B 1436 REMARK 465 LYS B 1437 REMARK 465 PHE B 1438 REMARK 465 VAL B 1439 REMARK 465 ASN B 1440 REMARK 465 LEU B 1441 REMARK 465 GLU B 1442 REMARK 465 ARG B 1443 REMARK 465 ARG B 1444 REMARK 465 PHE B 1445 REMARK 465 ASP B 1446 REMARK 465 GLU B 1447 REMARK 465 ALA B 1448 REMARK 465 GLN B 1449 REMARK 465 ILE B 1450 REMARK 465 PRO B 1451 REMARK 465 PRO B 1452 REMARK 465 GLY B 1453 REMARK 465 ALA B 1454 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 ILE A 258 CA C O CB CG1 CG2 CD1 REMARK 470 ARG A 365 CA C O CB CG CD NE REMARK 470 ARG A 365 CZ NH1 NH2 REMARK 470 ASP A 400 CA C O CB CG OD1 OD2 REMARK 470 ASN A 436 CA C O CB CG OD1 ND2 REMARK 470 HIS B1155 CA C O CB CG ND1 CD2 REMARK 470 HIS B1155 CE1 NE2 REMARK 470 ARG B1179 CA C O CB CG CD NE REMARK 470 ARG B1179 CZ NH1 NH2 REMARK 470 LEU B1322 CA C O CB CG CD1 CD2 REMARK 470 ARG B1365 CA C O CB CG CD NE REMARK 470 ARG B1365 CZ NH1 NH2 REMARK 470 TYR B1397 CA C O CB CG CD1 CD2 REMARK 470 TYR B1397 CE1 CE2 CZ OH REMARK 470 THR B1426 CA C O CB OG1 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 NH2 ARG A 297 N LYS B 1154 1.94 REMARK 500 O VAL B 1227 CG2 THR B 1231 1.98 REMARK 500 O ASN B 1161 N LYS B 1163 2.01 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 O LYS A 154 NH1 ARG B 1307 2655 1.77 REMARK 500 OG SER A 87 NZ LYS B 1163 4665 1.89 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 ILE A 162 CG1 - CB - CG2 ANGL. DEV. = -18.2 DEGREES REMARK 500 PRO A 294 C - N - CA ANGL. DEV. = 12.4 DEGREES REMARK 500 LEU B1139 CA - CB - CG ANGL. DEV. = 14.9 DEGREES REMARK 500 ARG B1202 N - CA - C ANGL. DEV. = 18.8 DEGREES REMARK 500 ALA B1260 N - CA - C ANGL. DEV. = 24.8 DEGREES REMARK 500 ASN B1262 N - CA - C ANGL. DEV. = -17.6 DEGREES REMARK 500 ARG B1297 N - CA - C ANGL. DEV. = 25.1 DEGREES REMARK 500 MET B1316 N - CA - C ANGL. DEV. = -16.8 DEGREES REMARK 500 ASP B1391 C - N - CA ANGL. DEV. = 17.0 DEGREES REMARK 500 ILE B1411 N - CA - C ANGL. DEV. = 22.4 DEGREES REMARK 500 ALA B1417 C - N - CA ANGL. DEV. = 15.2 DEGREES REMARK 500 GLN B1419 N - CA - C ANGL. DEV. = 20.7 DEGREES REMARK 500 PRO B1423 C - N - CA ANGL. DEV. = 11.4 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 PRO A 11 107.74 -57.93 REMARK 500 PRO A 40 -71.08 -9.30 REMARK 500 THR A 98 99.58 -176.51 REMARK 500 ASN A 101 40.44 77.55 REMARK 500 ASN A 161 -159.26 -15.89 REMARK 500 THR A 184 114.41 -173.51 REMARK 500 ILE A 186 79.98 49.55 REMARK 500 PRO A 187 -133.09 -90.87 REMARK 500 THR A 188 -166.19 -70.72 REMARK 500 PHE A 190 -61.69 -8.70 REMARK 500 THR A 191 -39.00 -39.06 REMARK 500 GLU A 192 -133.36 -70.85 REMARK 500 THR A 197 45.48 -149.38 REMARK 500 PHE A 200 98.34 46.59 REMARK 500 SER A 203 -7.21 66.07 REMARK 500 ARG A 211 -152.89 -165.28 REMARK 500 SER A 213 76.35 58.53 REMARK 500 VAL A 214 101.22 -57.02 REMARK 500 ASN A 232 30.93 -99.00 REMARK 500 GLU A 255 68.31 -105.90 REMARK 500 ALA A 286 -133.64 60.94 REMARK 500 GLU A 311 -66.27 -97.30 REMARK 500 LEU A 314 -134.55 -84.57 REMARK 500 TYR A 321 109.06 89.80 REMARK 500 GLN A 326 71.03 41.97 REMARK 500 ARG A 330 -167.48 -74.16 REMARK 500 ASN A 334 97.09 34.83 REMARK 500 ARG A 335 83.56 8.68 REMARK 500 GLN A 336 -66.18 -174.02 REMARK 500 GLN A 337 -70.19 -53.43 REMARK 500 ARG A 398 128.40 151.32 REMARK 500 ASP A 399 -155.31 54.89 REMARK 500 ALA A 417 -60.47 -99.41 REMARK 500 GLN A 419 61.34 -168.72 REMARK 500 ARG A 420 119.70 -38.33 REMARK 500 ASN A 421 -0.96 84.81 REMARK 500 PRO A 423 -168.15 -74.19 REMARK 500 VAL A 424 -165.56 -105.45 REMARK 500 ILE A 432 -132.92 45.39 REMARK 500 TYR A 435 -60.70 -96.66 REMARK 500 ILE B1014 -36.17 -36.72 REMARK 500 LEU B1067 -2.85 34.06 REMARK 500 LEU B1077 23.81 43.67 REMARK 500 GLU B1078 89.14 19.35 REMARK 500 PRO B1097 -83.24 -69.82 REMARK 500 ASN B1101 25.18 -78.54 REMARK 500 GLU B1135 103.11 65.52 REMARK 500 ASN B1161 9.58 -44.69 REMARK 500 ILE B1162 -20.61 -14.63 REMARK 500 THR B1184 -13.76 -159.56 REMARK 500 REMARK 500 THIS ENTRY HAS 81 RAMACHANDRAN OUTLIERS. 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 AU A1436 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU A1437 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU B2426 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU B2427 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VYE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DNAC-SSDNA COMPLEX DBREF 2VYF A 1 454 UNP Q5KU75 Q5KU75_GEOKA 1 454 DBREF 2VYF B 1001 1454 UNP Q5KU75 Q5KU75_GEOKA 1 454 SEQRES 1 A 454 MET SER GLU LEU PHE SER GLU ARG ILE PRO PRO GLN SER SEQRES 2 A 454 ILE GLU ALA GLU GLN ALA VAL LEU GLY ALA VAL PHE LEU SEQRES 3 A 454 ASP PRO THR ALA LEU THR LEU ALA SER GLU ARG LEU ILE SEQRES 4 A 454 PRO GLU ASP PHE TYR ARG ALA ALA HIS GLN LYS ILE PHE SEQRES 5 A 454 HIS ALA MET LEU ARG VAL ALA ASP LYS GLY GLU PRO VAL SEQRES 6 A 454 ASP LEU VAL THR VAL THR ALA GLU LEU ALA ALA LEU GLU SEQRES 7 A 454 GLN LEU GLU GLU VAL GLY GLY VAL SER TYR LEU SER GLU SEQRES 8 A 454 LEU ALA ASP SER VAL PRO THR ALA ALA ASN VAL GLU TYR SEQRES 9 A 454 TYR ALA ARG ILE VAL GLU GLU LYS SER LEU LEU ARG ARG SEQRES 10 A 454 LEU ILE ARG THR ALA THR SER ILE ALA GLN ASP GLY TYR SEQRES 11 A 454 THR ARG GLU ASP GLU ILE ASP VAL LEU LEU ASP GLU ALA SEQRES 12 A 454 GLU ARG LYS ILE MET GLU VAL SER GLN ARG LYS HIS SER SEQRES 13 A 454 GLY ALA PHE LYS ASN ILE LYS ASP VAL LEU VAL GLN THR SEQRES 14 A 454 TYR ASP ASN ILE GLU MET LEU HIS ASN ARG ASN GLY ASP SEQRES 15 A 454 ILE THR GLY ILE PRO THR GLY PHE THR GLU LEU ASP ARG SEQRES 16 A 454 MET THR SER GLY PHE GLN ARG SER ASP LEU ILE ILE VAL SEQRES 17 A 454 ALA ALA ARG PRO SER VAL GLY LYS THR ALA PHE ALA LEU SEQRES 18 A 454 ASN ILE ALA GLN ASN VAL ALA THR LYS THR ASN GLU ASN SEQRES 19 A 454 VAL ALA ILE PHE SER LEU GLU MET SER ALA GLN GLN LEU SEQRES 20 A 454 VAL MET ARG MET LEU CYS ALA GLU GLY ASN ILE ASN ALA SEQRES 21 A 454 GLN ASN LEU ARG THR GLY LYS LEU THR PRO GLU ASP TRP SEQRES 22 A 454 GLY LYS LEU THR MET ALA MET GLY SER LEU SER ASN ALA SEQRES 23 A 454 GLY ILE TYR ILE ASP ASP THR PRO SER ILE ARG VAL SER SEQRES 24 A 454 ASP ILE ARG ALA LYS CYS ARG ARG LEU LYS GLN GLU SER SEQRES 25 A 454 GLY LEU GLY MET VAL VAL ILE ASP TYR LEU GLN LEU ILE SEQRES 26 A 454 GLN GLY SER GLY ARG ASN ARG GLU ASN ARG GLN GLN GLU SEQRES 27 A 454 VAL SER GLU ILE SER ARG SER LEU LYS ALA LEU ALA ARG SEQRES 28 A 454 GLU LEU GLU VAL PRO VAL ILE ALA LEU SER GLN LEU SER SEQRES 29 A 454 ARG SER VAL GLU GLN ARG GLN ASP LYS ARG PRO MET MET SEQRES 30 A 454 SER ASP LEU ARG GLU SER GLY SER ILE GLU GLN ASP ALA SEQRES 31 A 454 ASP ILE VAL ALA PHE LEU TYR ARG ASP ASP TYR TYR ASN SEQRES 32 A 454 LYS ASP SER GLU ASN LYS ASN ILE ILE GLU ILE ILE ILE SEQRES 33 A 454 ALA LYS GLN ARG ASN GLY PRO VAL GLY THR VAL GLN LEU SEQRES 34 A 454 ALA PHE ILE LYS GLU TYR ASN LYS PHE VAL ASN LEU GLU SEQRES 35 A 454 ARG ARG PHE ASP GLU ALA GLN ILE PRO PRO GLY ALA SEQRES 1 B 454 MET SER GLU LEU PHE SER GLU ARG ILE PRO PRO GLN SER SEQRES 2 B 454 ILE GLU ALA GLU GLN ALA VAL LEU GLY ALA VAL PHE LEU SEQRES 3 B 454 ASP PRO THR ALA LEU THR LEU ALA SER GLU ARG LEU ILE SEQRES 4 B 454 PRO GLU ASP PHE TYR ARG ALA ALA HIS GLN LYS ILE PHE SEQRES 5 B 454 HIS ALA MET LEU ARG VAL ALA ASP LYS GLY GLU PRO VAL SEQRES 6 B 454 ASP LEU VAL THR VAL THR ALA GLU LEU ALA ALA LEU GLU SEQRES 7 B 454 GLN LEU GLU GLU VAL GLY GLY VAL SER TYR LEU SER GLU SEQRES 8 B 454 LEU ALA ASP SER VAL PRO THR ALA ALA ASN VAL GLU TYR SEQRES 9 B 454 TYR ALA ARG ILE VAL GLU GLU LYS SER LEU LEU ARG ARG SEQRES 10 B 454 LEU ILE ARG THR ALA THR SER ILE ALA GLN ASP GLY TYR SEQRES 11 B 454 THR ARG GLU ASP GLU ILE ASP VAL LEU LEU ASP GLU ALA SEQRES 12 B 454 GLU ARG LYS ILE MET GLU VAL SER GLN ARG LYS HIS SER SEQRES 13 B 454 GLY ALA PHE LYS ASN ILE LYS ASP VAL LEU VAL GLN THR SEQRES 14 B 454 TYR ASP ASN ILE GLU MET LEU HIS ASN ARG ASN GLY ASP SEQRES 15 B 454 ILE THR GLY ILE PRO THR GLY PHE THR GLU LEU ASP ARG SEQRES 16 B 454 MET THR SER GLY PHE GLN ARG SER ASP LEU ILE ILE VAL SEQRES 17 B 454 ALA ALA ARG PRO SER VAL GLY LYS THR ALA PHE ALA LEU SEQRES 18 B 454 ASN ILE ALA GLN ASN VAL ALA THR LYS THR ASN GLU ASN SEQRES 19 B 454 VAL ALA ILE PHE SER LEU GLU MET SER ALA GLN GLN LEU SEQRES 20 B 454 VAL MET ARG MET LEU CYS ALA GLU GLY ASN ILE ASN ALA SEQRES 21 B 454 GLN ASN LEU ARG THR GLY LYS LEU THR PRO GLU ASP TRP SEQRES 22 B 454 GLY LYS LEU THR MET ALA MET GLY SER LEU SER ASN ALA SEQRES 23 B 454 GLY ILE TYR ILE ASP ASP THR PRO SER ILE ARG VAL SER SEQRES 24 B 454 ASP ILE ARG ALA LYS CYS ARG ARG LEU LYS GLN GLU SER SEQRES 25 B 454 GLY LEU GLY MET VAL VAL ILE ASP TYR LEU GLN LEU ILE SEQRES 26 B 454 GLN GLY SER GLY ARG ASN ARG GLU ASN ARG GLN GLN GLU SEQRES 27 B 454 VAL SER GLU ILE SER ARG SER LEU LYS ALA LEU ALA ARG SEQRES 28 B 454 GLU LEU GLU VAL PRO VAL ILE ALA LEU SER GLN LEU SER SEQRES 29 B 454 ARG SER VAL GLU GLN ARG GLN ASP LYS ARG PRO MET MET SEQRES 30 B 454 SER ASP LEU ARG GLU SER GLY SER ILE GLU GLN ASP ALA SEQRES 31 B 454 ASP ILE VAL ALA PHE LEU TYR ARG ASP ASP TYR TYR ASN SEQRES 32 B 454 LYS ASP SER GLU ASN LYS ASN ILE ILE GLU ILE ILE ILE SEQRES 33 B 454 ALA LYS GLN ARG ASN GLY PRO VAL GLY THR VAL GLN LEU SEQRES 34 B 454 ALA PHE ILE LYS GLU TYR ASN LYS PHE VAL ASN LEU GLU SEQRES 35 B 454 ARG ARG PHE ASP GLU ALA GLN ILE PRO PRO GLY ALA HET AU A1436 1 HET AU A1437 1 HET AU B2426 1 HET AU B2427 1 HETNAM AU GOLD ION FORMUL 3 AU 4(AU 1+) HELIX 1 1 SER A 13 ASP A 27 1 15 HELIX 2 2 ASP A 27 LEU A 38 1 12 HELIX 3 3 ILE A 39 PHE A 43 5 5 HELIX 4 4 ARG A 45 ALA A 59 1 15 HELIX 5 5 VAL A 68 LEU A 77 1 10 HELIX 6 6 GLY A 85 SER A 95 1 11 HELIX 7 7 ASN A 101 THR A 131 1 31 HELIX 8 8 GLU A 135 SER A 151 1 17 HELIX 9 9 LYS A 163 GLU A 174 1 12 HELIX 10 10 GLU A 192 THR A 197 1 6 HELIX 11 11 GLY A 215 LYS A 230 1 16 HELIX 12 12 SER A 243 CYS A 253 1 11 HELIX 13 13 ASP A 272 LEU A 283 1 12 HELIX 14 14 ARG A 297 SER A 312 1 16 HELIX 15 15 GLN A 336 GLU A 352 1 17 HELIX 16 16 SER A 385 ALA A 390 1 6 HELIX 17 17 SER B 1013 ASP B 1027 1 15 HELIX 18 18 ASP B 1027 GLU B 1036 1 10 HELIX 19 19 ILE B 1039 PHE B 1043 5 5 HELIX 20 20 ARG B 1045 GLY B 1062 1 18 HELIX 21 21 VAL B 1068 LEU B 1074 1 7 HELIX 22 22 GLN B 1079 GLY B 1084 1 6 HELIX 23 23 GLY B 1084 SER B 1095 1 12 HELIX 24 24 ASN B 1101 ARG B 1132 1 32 HELIX 25 25 GLU B 1135 GLN B 1152 1 18 HELIX 26 26 ILE B 1162 ASN B 1178 1 17 HELIX 27 27 THR B 1191 THR B 1197 1 7 HELIX 28 28 LYS B 1216 THR B 1229 1 14 HELIX 29 29 SER B 1243 GLY B 1256 1 14 HELIX 30 30 ASP B 1272 ASN B 1285 1 14 HELIX 31 31 VAL B 1298 GLN B 1310 1 13 HELIX 32 32 ARG B 1335 LEU B 1353 1 19 HELIX 33 33 SER B 1385 ALA B 1390 1 6 SHEET 1 AA 8 ILE A 288 ASP A 291 0 SHEET 2 AA 8 ASN A 234 SER A 239 1 O VAL A 235 N TYR A 289 SHEET 3 AA 8 GLY A 315 ASP A 320 1 O MET A 316 N ALA A 236 SHEET 4 AA 8 VAL A 357 GLN A 362 1 O ILE A 358 N ILE A 319 SHEET 5 AA 8 LEU A 205 ALA A 210 1 O ILE A 206 N ALA A 359 SHEET 6 AA 8 ILE A 392 TYR A 397 1 O ILE A 392 N ILE A 207 SHEET 7 AA 8 ILE A 411 GLN A 419 -1 O GLU A 413 N TYR A 397 SHEET 8 AA 8 GLY A 425 ALA A 430 -1 O GLY A 425 N ILE A 416 SHEET 1 BA 7 GLY B1287 ASP B1291 0 SHEET 2 BA 7 ASN B1234 SER B1239 1 O VAL B1235 N TYR B1289 SHEET 3 BA 7 MET B1316 ASP B1320 1 O MET B1316 N ALA B1236 SHEET 4 BA 7 VAL B1357 GLN B1362 1 O ILE B1358 N ILE B1319 SHEET 5 BA 7 LEU B1205 ALA B1210 1 O ILE B1206 N ALA B1359 SHEET 6 BA 7 ALA B1394 PHE B1395 1 O ALA B1394 N ALA B1209 SHEET 7 BA 7 ILE B1415 ILE B1416 -1 O ILE B1415 N PHE B1395 SITE 1 AC1 2 LEU A 221 ASN A 222 SITE 1 AC2 3 MET A 249 ARG A 250 CYS A 253 SITE 1 AC3 1 LEU B1221 SITE 1 AC4 1 MET B1249 CRYST1 176.968 176.968 108.824 90.00 90.00 120.00 P 63 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 0.005651 0.003262 0.000000 0.00000 SCALE2 0.000000 0.006525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009189 0.00000