HEADER HYDROLASE/DNA 23-JUL-08 2VYE TITLE CRYSTAL STRUCTURE OF THE DNAC-SSDNA COMPLEX CAVEAT 2VYE ILE B 1415 HAS WRONG CHIRALITY FOR AN L-AMINO ACID DT C 2008 CAVEAT 2 2VYE HAS WRONG CHIRALITY FOR A D-NUCLEIC ACID 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; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'; COMPND 9 CHAIN: C; COMPND 10 SYNONYM: SSDT15; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS KAUSTOPHILUS HTA426; SOURCE 3 ORGANISM_TAXID: 235909; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_VECTOR: PET21B; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 562 KEYWDS HYDROLASE, DNA REPLICATION, NUCLEOTIDE-BINDING, DNAC, HELICASE, ATP- KEYWDS 2 BINDING, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.LO,K.L.TSAI,Y.J.SUN,C.D.HSIAO REVDAT 5 13-DEC-23 2VYE 1 REMARK REVDAT 4 24-JAN-18 2VYE 1 SOURCE REVDAT 3 16-MAY-12 2VYE 1 HEADER CAVEAT KEYWDS REMARK REVDAT 3 2 1 VERSN DBREF MASTER REVDAT 2 10-MAR-09 2VYE 1 JRNL REVDAT 1 30-DEC-08 2VYE 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. 4.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 4.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 157515.120 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 76.4 REMARK 3 NUMBER OF REFLECTIONS : 11729 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) : 0.302 REMARK 3 FREE R VALUE : 0.374 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1213 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 4.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 4.36 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 52.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1205 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE : 0.4100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 126 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6262 REMARK 3 NUCLEIC ACID ATOMS : 177 REMARK 3 HETEROGEN ATOMS : 0 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) : 186.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -42.10000 REMARK 3 B22 (A**2) : -42.10000 REMARK 3 B33 (A**2) : 84.19000 REMARK 3 B12 (A**2) : 60.23000 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) : 0.50 REMARK 3 ESD FROM SIGMAA (A) : 1.01 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.75 REMARK 3 ESD FROM C-V SIGMAA (A) : 1.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 2.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.740 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 : 0.43 REMARK 3 BSOL : 230.5 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 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2VYE 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_1290036984. 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 : 6.5 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 : 14077 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.100 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 (%) : 91.1 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2VYF REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 77.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 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 52.05600 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 52.05600 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 52.05600 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: NONAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: NONAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 35350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 155010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -177.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 BIOMT1 2 -0.500000 -0.866025 0.000000 180.83000 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 90.41500 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 156.60337 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 ARG A 8 REMARK 465 LYS A 373 REMARK 465 ARG A 374 REMARK 465 TYR A 401 REMARK 465 TYR A 402 REMARK 465 PRO A 423 REMARK 465 VAL A 424 REMARK 465 GLY A 425 REMARK 465 THR A 426 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 ASN B 1161 REMARK 465 ILE B 1162 REMARK 465 LYS B 1163 REMARK 465 ILE B 1258 REMARK 465 ASN B 1259 REMARK 465 ALA B 1260 REMARK 465 GLN B 1261 REMARK 465 ASN B 1262 REMARK 465 LEU B 1263 REMARK 465 ARG B 1264 REMARK 465 THR B 1265 REMARK 465 GLY B 1266 REMARK 465 LYS B 1267 REMARK 465 PRO B 1375 REMARK 465 MET B 1376 REMARK 465 MET B 1377 REMARK 465 SER B 1378 REMARK 465 LEU B 1396 REMARK 465 TYR B 1397 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 ILE B 1411 REMARK 465 ILE B 1412 REMARK 465 GLU B 1413 REMARK 465 ILE B 1414 REMARK 465 ASN B 1421 REMARK 465 GLY B 1422 REMARK 465 PRO B 1423 REMARK 465 VAL B 1424 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 LYS A 409 CG CD CE NZ REMARK 470 LEU A 441 CA C O CB CG CD1 CD2 REMARK 470 GLN B1336 CG CD OE1 NE2 REMARK 470 VAL B1427 CA C O CB CG1 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 OD1 ASN A 257 NZ LYS A 437 2.07 REMARK 500 ND2 ASN A 403 OD2 ASP A 405 2.10 REMARK 500 O GLU B 1368 OD2 ASP B 1372 2.11 REMARK 500 NE2 GLN B 1079 OP2 DT C 2004 2.12 REMARK 500 NH1 ARG A 302 OE2 GLU A 352 2.14 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 CYS A 253 CB CYS A 253 SG 0.311 REMARK 500 GLU B1333 CB GLU B1333 CG 0.121 REMARK 500 DT C2005 C5' DT C2005 C4' 0.042 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 CYS A 253 CA - CB - SG ANGL. DEV. = 8.8 DEGREES REMARK 500 LEU A 283 CA - CB - CG ANGL. DEV. = -15.5 DEGREES REMARK 500 ARG A 302 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 TYR A 321 CA - CB - CG ANGL. DEV. = 11.6 DEGREES REMARK 500 LEU A 324 CB - CG - CD1 ANGL. DEV. = -11.3 DEGREES REMARK 500 GLY A 384 N - CA - C ANGL. DEV. = 17.6 DEGREES REMARK 500 ARG B1008 N - CA - C ANGL. DEV. = -18.9 DEGREES REMARK 500 ILE B1009 N - CA - C ANGL. DEV. = 17.5 DEGREES REMARK 500 LEU B1176 CA - CB - CG ANGL. DEV. = 16.2 DEGREES REMARK 500 GLU B1333 N - CA - C ANGL. DEV. = 16.9 DEGREES REMARK 500 ASP B1379 CB - CA - C ANGL. DEV. = 12.1 DEGREES REMARK 500 ASP B1379 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 PHE B1395 CA - C - O ANGL. DEV. = 25.6 DEGREES REMARK 500 DT C2001 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT C2003 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DT C2005 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DT C2005 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT C2008 O4' - C1' - C2' ANGL. DEV. = 4.1 DEGREES REMARK 500 DT C2008 N1 - C1' - C2' ANGL. DEV. = 11.0 DEGREES REMARK 500 DT C2008 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT C2009 O4' - C4' - C3' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT C2009 O4' - C1' - N1 ANGL. DEV. = 5.5 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 SER A 13 84.90 -155.31 REMARK 500 GLU A 15 -37.33 -33.95 REMARK 500 GLU A 17 -70.68 -41.51 REMARK 500 ASP A 27 116.07 -178.16 REMARK 500 PRO A 40 -38.93 -31.79 REMARK 500 MET A 55 -73.19 -45.31 REMARK 500 LYS A 61 3.44 -59.92 REMARK 500 GLU A 78 30.04 87.45 REMARK 500 VAL A 83 27.07 -73.07 REMARK 500 SER A 95 -8.26 -52.25 REMARK 500 THR A 98 117.23 -177.89 REMARK 500 ALA A 100 -12.51 -46.06 REMARK 500 THR A 131 -75.37 -73.49 REMARK 500 GLU A 135 89.24 -178.94 REMARK 500 ARG A 153 -41.52 -142.45 REMARK 500 HIS A 155 75.42 -52.61 REMARK 500 SER A 156 -146.46 -85.44 REMARK 500 ALA A 158 63.85 -101.63 REMARK 500 ARG A 179 44.78 -73.88 REMARK 500 PHE A 200 102.60 -57.12 REMARK 500 SER A 203 10.85 90.82 REMARK 500 ALA A 210 -173.58 -179.08 REMARK 500 PRO A 212 -161.18 -56.37 REMARK 500 VAL A 214 7.30 49.40 REMARK 500 PHE A 238 75.73 -104.91 REMARK 500 ALA A 244 -76.00 -34.14 REMARK 500 ALA A 260 -39.81 -35.77 REMARK 500 ASP A 291 112.82 -166.47 REMARK 500 SER A 295 123.78 -171.98 REMARK 500 TYR A 321 107.55 44.19 REMARK 500 ASN A 331 -168.07 -73.49 REMARK 500 GLU A 333 49.33 77.13 REMARK 500 GLN A 362 -168.45 -116.27 REMARK 500 SER A 364 -72.74 -137.39 REMARK 500 ARG A 365 -74.37 -53.42 REMARK 500 SER A 406 -157.91 -66.03 REMARK 500 ASN A 408 107.21 -52.05 REMARK 500 ASN A 410 115.15 -162.36 REMARK 500 GLN A 419 120.80 -176.34 REMARK 500 PRO B1010 175.57 -52.25 REMARK 500 GLN B1012 130.57 -178.90 REMARK 500 SER B1013 70.10 -119.89 REMARK 500 LEU B1031 -75.77 -48.03 REMARK 500 PRO B1040 -57.60 -27.34 REMARK 500 MET B1055 -78.19 -46.66 REMARK 500 LEU B1056 -37.17 -39.66 REMARK 500 ALA B1059 -80.11 -57.37 REMARK 500 LEU B1067 -30.54 -34.92 REMARK 500 VAL B1068 -79.46 -80.08 REMARK 500 THR B1069 -25.92 -35.70 REMARK 500 REMARK 500 THIS ENTRY HAS 89 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 B1321 0.08 SIDE CHAIN REMARK 500 DT C2009 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VYF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DNAC DBREF 2VYE A 1 454 UNP Q5KU75 Q5KU75_GEOKA 1 454 DBREF 2VYE B 1001 1454 UNP Q5KU75 Q5KU75_GEOKA 1 454 DBREF 2VYE C 2001 2009 PDB 2VYE 2VYE 2001 2009 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 SEQRES 1 C 9 DT DT DT DT DT DT DT DT DT HELIX 1 1 SER A 13 ASP A 27 1 15 HELIX 2 2 PRO A 28 LEU A 38 1 11 HELIX 3 3 ILE A 39 PHE A 43 5 5 HELIX 4 4 ARG A 45 LYS A 61 1 17 HELIX 5 5 ASP A 66 GLU A 78 1 13 HELIX 6 6 GLY A 84 SER A 95 1 12 HELIX 7 7 THR A 98 ALA A 100 5 3 HELIX 8 8 ASN A 101 ARG A 132 1 32 HELIX 9 9 GLU A 135 GLN A 152 1 18 HELIX 10 10 ASN A 161 ARG A 179 1 19 HELIX 11 11 PHE A 190 SER A 198 1 9 HELIX 12 12 VAL A 214 LYS A 230 1 17 HELIX 13 13 SER A 243 ASN A 257 1 15 HELIX 14 14 ASN A 259 THR A 265 1 7 HELIX 15 15 THR A 269 ASN A 285 1 17 HELIX 16 16 ARG A 297 SER A 312 1 16 HELIX 17 17 TYR A 321 ILE A 325 5 5 HELIX 18 18 ASN A 334 LEU A 353 1 20 HELIX 19 19 SER A 364 ARG A 370 1 7 HELIX 20 20 MET A 376 GLY A 384 1 9 HELIX 21 21 SER A 385 ALA A 390 1 6 HELIX 22 22 SER B 1013 ASP B 1027 1 15 HELIX 23 23 PRO B 1028 SER B 1035 1 8 HELIX 24 24 ILE B 1039 PHE B 1043 5 5 HELIX 25 25 ARG B 1045 GLY B 1062 1 18 HELIX 26 26 ASP B 1066 LEU B 1077 1 12 HELIX 27 27 GLY B 1084 VAL B 1096 1 13 HELIX 28 28 VAL B 1102 ARG B 1132 1 31 HELIX 29 29 GLU B 1135 GLN B 1152 1 18 HELIX 30 30 ASP B 1164 ASN B 1178 1 15 HELIX 31 31 PHE B 1190 MET B 1196 1 7 HELIX 32 32 GLY B 1215 THR B 1231 1 17 HELIX 33 33 SER B 1243 ASN B 1257 1 15 HELIX 34 34 THR B 1269 ASN B 1285 1 17 HELIX 35 35 ARG B 1297 SER B 1312 1 16 HELIX 36 36 TYR B 1321 ILE B 1325 5 5 HELIX 37 37 GLN B 1336 GLU B 1354 1 19 HELIX 38 38 SER B 1364 ARG B 1374 1 11 HELIX 39 39 SER B 1383 ALA B 1390 1 8 SHEET 1 AA 9 ILE A 288 ILE A 290 0 SHEET 2 AA 9 ASN A 234 SER A 239 1 O VAL A 235 N TYR A 289 SHEET 3 AA 9 LEU A 314 ASP A 320 1 N GLY A 315 O ASN A 234 SHEET 4 AA 9 VAL A 357 SER A 361 1 O ILE A 358 N ILE A 319 SHEET 5 AA 9 LEU A 205 ALA A 209 1 O ILE A 206 N ALA A 359 SHEET 6 AA 9 ILE A 392 TYR A 397 1 O ILE A 392 N ILE A 207 SHEET 7 AA 9 ASN A 410 GLN A 419 -1 O GLU A 413 N TYR A 397 SHEET 8 AA 9 GLN A 428 ILE A 432 -1 O LEU A 429 N ILE A 412 SHEET 9 AA 9 LYS A 437 VAL A 439 -1 O LYS A 437 N ILE A 432 SHEET 1 BA 7 ILE B1288 ASP B1292 0 SHEET 2 BA 7 VAL B1235 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 ILE B1392 ALA B1394 1 O ILE B1392 N ILE B1207 SHEET 7 BA 7 ILE B1416 GLN B1419 -1 N ALA B1417 O VAL B1393 CRYST1 180.830 180.830 104.112 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 0.005530 0.003193 0.000000 0.00000 SCALE2 0.000000 0.006386 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009605 0.00000