HEADER TRANSFERASE/DNA 26-JAN-15 4XUS TITLE CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY COMPLEX OF DNA TITLE 2 POLYMERASE LAMBDA WITH A TEMPLATING A AND AN INCOMING DTTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 251-575; COMPND 5 SYNONYM: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE COMPND 6 KAPPA; COMPND 7 EC: 2.7.7.7,4.2.99.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*A)-3'); COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3'); COMPND 19 CHAIN: T; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 MOL_ID: 4; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE LAMBDA, PROTEIN-DNA COMPLEX, HELIX-HAIRPIN-HELIX, KEYWDS 2 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BURAK,K.E.GUJA,M.GARCIA-DIAZ REVDAT 3 28-FEB-24 4XUS 1 REMARK LINK REVDAT 2 10-FEB-16 4XUS 1 TITLE JRNL REVDAT 1 03-FEB-16 4XUS 0 JRNL AUTH M.J.BURAK,K.E.GUJA,M.GARCIA-DIAZ JRNL TITL NUCLEOTIDE BINDING INTERACTIONS MODULATE DNTP SELECTIVITY JRNL TITL 2 AND FACILITATE 8-OXO-DGTP INCORPORATION BY DNA POLYMERASE JRNL TITL 3 LAMBDA. JRNL REF NUCLEIC ACIDS RES. V. 43 8089 2015 JRNL REFN ESSN 1362-4962 JRNL PMID 26220180 JRNL DOI 10.1093/NAR/GKV760 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.4 REMARK 3 NUMBER OF REFLECTIONS : 17565 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 + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 896 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 9 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.54 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.43 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1591 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2045 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1514 REMARK 3 BIN R VALUE (WORKING SET) : 0.2022 REMARK 3 BIN FREE R VALUE : 0.2460 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.84 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 77 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2473 REMARK 3 NUCLEIC ACID ATOMS : 406 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.84850 REMARK 3 B22 (A**2) : 6.37970 REMARK 3 B33 (A**2) : -1.53110 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) : 0.302 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.446 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.258 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.910 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.869 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5724 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 10307 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1199 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 55 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 882 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5724 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 394 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5919 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.97 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.93 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.61 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -13.8976 10.7447 -15.2951 REMARK 3 T TENSOR REMARK 3 T11: -0.1619 T22: -0.0378 REMARK 3 T33: -0.1314 T12: -0.0331 REMARK 3 T13: 0.0403 T23: -0.0445 REMARK 3 L TENSOR REMARK 3 L11: 1.2995 L22: 1.2410 REMARK 3 L33: 0.9880 L12: -0.1098 REMARK 3 L13: 0.4529 L23: 0.4466 REMARK 3 S TENSOR REMARK 3 S11: 0.0186 S12: 0.2510 S13: -0.1173 REMARK 3 S21: -0.1163 S22: 0.1017 S23: -0.1282 REMARK 3 S31: -0.0169 S32: 0.1076 S33: -0.1203 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { P|* } REMARK 3 ORIGIN FOR THE GROUP (A): -25.4205 14.8346 -8.7894 REMARK 3 T TENSOR REMARK 3 T11: -0.3960 T22: 0.1174 REMARK 3 T33: -0.1866 T12: -0.0127 REMARK 3 T13: 0.2835 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 0.9814 L22: 5.4959 REMARK 3 L33: 1.9821 L12: 0.3407 REMARK 3 L13: 0.3880 L23: 2.1488 REMARK 3 S TENSOR REMARK 3 S11: -0.0340 S12: 0.0745 S13: -0.0188 REMARK 3 S21: -0.0319 S22: -0.1003 S23: -0.1323 REMARK 3 S31: -0.1209 S32: -0.0526 S33: 0.1342 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { D|* } REMARK 3 ORIGIN FOR THE GROUP (A): -20.1420 28.3461 -29.8440 REMARK 3 T TENSOR REMARK 3 T11: 0.1635 T22: 0.1336 REMARK 3 T33: -0.2325 T12: -0.0759 REMARK 3 T13: -0.1302 T23: 0.1120 REMARK 3 L TENSOR REMARK 3 L11: 3.7335 L22: 1.4884 REMARK 3 L33: 1.7475 L12: -1.9509 REMARK 3 L13: -1.5314 L23: -0.5417 REMARK 3 S TENSOR REMARK 3 S11: 0.0127 S12: 0.1169 S13: -0.0049 REMARK 3 S21: -0.0279 S22: 0.0478 S23: -0.0797 REMARK 3 S31: -0.1092 S32: -0.0115 S33: -0.0605 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { T|* } REMARK 3 ORIGIN FOR THE GROUP (A): -27.1195 15.4803 -17.3203 REMARK 3 T TENSOR REMARK 3 T11: -0.1230 T22: 0.1114 REMARK 3 T33: -0.1144 T12: 0.0361 REMARK 3 T13: 0.0218 T23: 0.0710 REMARK 3 L TENSOR REMARK 3 L11: 2.3015 L22: 2.1799 REMARK 3 L33: 5.0810 L12: -0.3414 REMARK 3 L13: 1.3805 L23: -1.2017 REMARK 3 S TENSOR REMARK 3 S11: -0.1353 S12: 0.4986 S13: -0.0440 REMARK 3 S21: -0.2968 S22: -0.1464 S23: 0.5114 REMARK 3 S31: -0.1935 S32: -0.3506 S33: 0.2817 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4XUS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17565 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 42.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 44.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.71700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE TRIHYDRATE 2.0 M REMARK 280 SODIUM FORMATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 28.02500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.53000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.64000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.53000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.02500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.64000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 5790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, P, T 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 ASN A 251 REMARK 465 THR A 540 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 ASN A 253 CG OD1 ND2 REMARK 470 HIS A 255 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 256 CG1 CG2 CD1 REMARK 470 LYS A 259 CG CD CE NZ REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 VAL A 293 CG1 CG2 REMARK 470 SER A 295 OG REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 GLU A 298 CG CD OE1 OE2 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 ILE A 314 CG1 CG2 CD1 REMARK 470 LEU A 317 CG CD1 CD2 REMARK 470 SER A 319 OG REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 441 CG CD NE CZ NH1 NH2 REMARK 470 SER A 445 OG REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 VAL A 537 CG1 CG2 REMARK 470 CYS A 543 SG REMARK 470 VAL A 545 CG1 CG2 REMARK 470 GLU A 572 CG CD OE1 OE2 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 DC D 3 O3' DC D 3 C3' -0.045 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 DG T 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG T 6 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT T 7 O4' - C1' - N1 ANGL. DEV. = 2.0 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 290 -75.01 -73.00 REMARK 500 CYS A 415 -142.92 -112.95 REMARK 500 ARG A 438 -26.35 -140.77 REMARK 500 SER A 463 85.25 -158.19 REMARK 500 SER A 509 170.99 -58.32 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 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 91.5 REMARK 620 3 ALA A 344 O 88.7 85.3 REMARK 620 4 HOH A 753 O 90.4 86.7 172.0 REMARK 620 5 DA P 5 OP1 174.4 93.8 89.9 91.7 REMARK 620 6 HOH P 221 O 85.6 175.8 97.7 90.2 89.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD2 105.1 REMARK 620 3 TTP A 601 O2A 93.8 92.8 REMARK 620 4 TTP A 601 O2B 167.8 86.9 83.0 REMARK 620 5 TTP A 601 O2G 82.6 169.9 80.0 85.2 REMARK 620 6 HOH A 761 O 92.2 101.7 162.3 87.6 84.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TTP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DOC P 101 DBREF 4XUS A 251 575 UNP Q9UGP5 DPOLL_HUMAN 251 575 DBREF 4XUS D 1 4 PDB 4XUS 4XUS 1 4 DBREF 4XUS P 1 5 PDB 4XUS 4XUS 1 5 DBREF 4XUS T 1 11 PDB 4XUS 4XUS 1 11 SEQRES 1 A 325 ASN HIS ASN LEU HIS ILE THR GLU LYS LEU GLU VAL LEU SEQRES 2 A 325 ALA LYS ALA TYR SER VAL GLN GLY ASP LYS TRP ARG ALA SEQRES 3 A 325 LEU GLY TYR ALA LYS ALA ILE ASN ALA LEU LYS SER PHE SEQRES 4 A 325 HIS LYS PRO VAL THR SER TYR GLN GLU ALA CYS SER ILE SEQRES 5 A 325 PRO GLY ILE GLY LYS ARG MET ALA GLU LYS ILE ILE GLU SEQRES 6 A 325 ILE LEU GLU SER GLY HIS LEU ARG LYS LEU ASP HIS ILE SEQRES 7 A 325 SER GLU SER VAL PRO VAL LEU GLU LEU PHE SER ASN ILE SEQRES 8 A 325 TRP GLY ALA GLY THR LYS THR ALA GLN MET TRP TYR GLN SEQRES 9 A 325 GLN GLY PHE ARG SER LEU GLU ASP ILE ARG SER GLN ALA SEQRES 10 A 325 SER LEU THR THR GLN GLN ALA ILE GLY LEU LYS HIS TYR SEQRES 11 A 325 SER ASP PHE LEU GLU ARG MET PRO ARG GLU GLU ALA THR SEQRES 12 A 325 GLU ILE GLU GLN THR VAL GLN LYS ALA ALA GLN ALA PHE SEQRES 13 A 325 ASN SER GLY LEU LEU CYS VAL ALA CYS GLY SER TYR ARG SEQRES 14 A 325 ARG GLY LYS ALA THR CYS GLY ASP VAL ASP VAL LEU ILE SEQRES 15 A 325 THR HIS PRO ASP GLY ARG SER HIS ARG GLY ILE PHE SER SEQRES 16 A 325 ARG LEU LEU ASP SER LEU ARG GLN GLU GLY PHE LEU THR SEQRES 17 A 325 ASP ASP LEU VAL SER GLN GLU GLU ASN GLY GLN GLN GLN SEQRES 18 A 325 LYS TYR LEU GLY VAL CYS ARG LEU PRO GLY PRO GLY ARG SEQRES 19 A 325 ARG HIS ARG ARG LEU ASP ILE ILE VAL VAL PRO TYR SER SEQRES 20 A 325 GLU PHE ALA CYS ALA LEU LEU TYR PHE THR GLY SER ALA SEQRES 21 A 325 HIS PHE ASN ARG SER MET ARG ALA LEU ALA LYS THR LYS SEQRES 22 A 325 GLY MET SER LEU SER GLU HIS ALA LEU SER THR ALA VAL SEQRES 23 A 325 VAL ARG ASN THR HIS GLY CYS LYS VAL GLY PRO GLY ARG SEQRES 24 A 325 VAL LEU PRO THR PRO THR GLU LYS ASP VAL PHE ARG LEU SEQRES 25 A 325 LEU GLY LEU PRO TYR ARG GLU PRO ALA GLU ARG ASP TRP SEQRES 1 D 4 DG DC DC DG SEQRES 1 P 5 DC DA DG DT DA SEQRES 1 T 11 DC DG DG DC DA DG DT DA DC DT DG HET TTP A 601 29 HET MG A 602 1 HET MG A 603 1 HET DOC P 101 18 HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE FORMUL 5 TTP C10 H17 N2 O14 P3 FORMUL 6 MG 2(MG 2+) FORMUL 8 DOC C9 H14 N3 O6 P FORMUL 9 HOH *255(H2 O) HELIX 1 AA1 HIS A 255 GLY A 271 1 17 HELIX 2 AA2 ASP A 272 SER A 288 1 17 HELIX 3 AA3 SER A 295 SER A 301 1 7 HELIX 4 AA4 GLY A 306 GLY A 320 1 15 HELIX 5 AA5 LEU A 322 ILE A 328 5 7 HELIX 6 AA6 SER A 331 ASN A 340 1 10 HELIX 7 AA7 GLY A 345 GLN A 355 1 11 HELIX 8 AA8 SER A 359 ALA A 367 1 9 HELIX 9 AA9 THR A 370 HIS A 379 1 10 HELIX 10 AB1 HIS A 379 GLU A 385 1 7 HELIX 11 AB2 ARG A 389 ASN A 407 1 19 HELIX 12 AB3 CYS A 415 ARG A 420 1 6 HELIX 13 AB4 GLY A 442 GLU A 454 1 13 HELIX 14 AB5 PRO A 495 SER A 497 5 3 HELIX 15 AB6 GLU A 498 GLY A 508 1 11 HELIX 16 AB7 SER A 509 LYS A 523 1 15 HELIX 17 AB8 THR A 555 LEU A 563 1 9 HELIX 18 AB9 GLU A 569 ARG A 573 5 5 SHEET 1 AA1 2 MET A 387 PRO A 388 0 SHEET 2 AA1 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 AA2 5 LEU A 411 ALA A 414 0 SHEET 2 AA2 5 VAL A 428 THR A 433 -1 O LEU A 431 N VAL A 413 SHEET 3 AA2 5 ARG A 487 VAL A 493 1 O ILE A 492 N ILE A 432 SHEET 4 AA2 5 LYS A 472 CYS A 477 -1 N GLY A 475 O LEU A 489 SHEET 5 AA2 5 LEU A 457 VAL A 462 -1 N LEU A 461 O LEU A 474 SHEET 1 AA3 3 SER A 526 LEU A 527 0 SHEET 2 AA3 3 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 SHEET 3 AA3 3 ARG A 549 VAL A 550 -1 O ARG A 549 N THR A 534 LINK O3' DA P 5 P DOC P 101 1555 1555 1.59 LINK O SER A 339 MG MG A 602 1555 1555 2.13 LINK O ILE A 341 MG MG A 602 1555 1555 2.52 LINK O ALA A 344 MG MG A 602 1555 1555 2.29 LINK OD1 ASP A 427 MG MG A 603 1555 1555 2.09 LINK OD2 ASP A 429 MG MG A 603 1555 1555 1.94 LINK O2A TTP A 601 MG MG A 603 1555 1555 2.24 LINK O2B TTP A 601 MG MG A 603 1555 1555 2.36 LINK O2G TTP A 601 MG MG A 603 1555 1555 2.43 LINK MG MG A 602 O HOH A 753 1555 1555 2.44 LINK MG MG A 602 OP1 DA P 5 1555 1555 2.65 LINK MG MG A 602 O HOH P 221 1555 1555 2.68 LINK MG MG A 603 O HOH A 761 1555 1555 2.08 CISPEP 1 HIS A 252 ASN A 253 0 -3.34 CISPEP 2 GLY A 508 SER A 509 0 -2.51 SITE 1 AC1 21 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 2 AC1 21 GLY A 426 ASP A 427 ASP A 429 TYR A 505 SITE 3 AC1 21 PHE A 506 THR A 507 GLY A 508 ALA A 510 SITE 4 AC1 21 ASN A 513 MG A 603 HOH A 740 HOH A 761 SITE 5 AC1 21 HOH A 765 HOH A 766 DOC P 101 HOH P 216 SITE 6 AC1 21 DA T 5 SITE 1 AC2 6 SER A 339 ILE A 341 ALA A 344 HOH A 753 SITE 2 AC2 6 DA P 5 HOH P 221 SITE 1 AC3 4 ASP A 427 ASP A 429 TTP A 601 HOH A 761 SITE 1 AC4 11 ASP A 490 TYR A 505 TTP A 601 HOH A 739 SITE 2 AC4 11 DA P 5 HOH P 209 HOH P 215 HOH P 216 SITE 3 AC4 11 DA T 5 DG T 6 HOH T 113 CRYST1 56.050 63.280 141.060 90.00 90.00 90.00 P 21 21 21 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 0.017841 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015803 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007089 0.00000