HEADER TRANSFERASE, LYASE/DNA 20-JUN-12 4FO6 TITLE CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY COMPLEX OF POLYMERASE TITLE 2 LAMBDA WITH A DATP ANALOG OPPOSITE A TEMPLATING T AND AN RCMP AT THE TITLE 3 PRIMER TERMINUS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LOOP MUTANT OF DNA POLYMERASE LAMBDA; 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 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'; COMPND 12 CHAIN: T; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: 5'-D(*CP*AP*GP*TP*AP)-R(P*C)-3'; COMPND 16 CHAIN: P; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 4; COMPND 19 MOLECULE: 5'-D(P*GP*CP*CP*G)-3'; COMPND 20 CHAIN: D; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 5; COMPND 23 MOLECULE: 5'-D(P*TP*AP*CP*TP*G)-3'; COMPND 24 CHAIN: H; COMPND 25 ENGINEERED: YES; COMPND 26 MOL_ID: 6; COMPND 27 MOLECULE: 5'-D(P*CP*AP*GP*TP*A)-3'; COMPND 28 CHAIN: I; COMPND 29 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: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 4; SOURCE 13 SYNTHETIC: YES; SOURCE 14 MOL_ID: 5; SOURCE 15 SYNTHETIC: YES; SOURCE 16 MOL_ID: 6 KEYWDS DNA POLYMERASE, TRANSFERASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.A.GOSAVI,A.F.MOON,T.A.KUNKEL,L.C.PEDERSEN,K.BEBENEK REVDAT 2 13-SEP-23 4FO6 1 REMARK SEQADV LINK REVDAT 1 11-JUL-12 4FO6 0 SPRSDE 11-JUL-12 4FO6 3UQ1 JRNL AUTH R.A.GOSAVI,A.F.MOON,T.A.KUNKEL,L.C.PEDERSEN,K.BEBENEK JRNL TITL THE CATALYTIC CYCLE FOR RIBONUCLEOTIDE INCORPORATION BY JRNL TITL 2 HUMAN DNA POL LAMBDA JRNL REF NUCLEIC ACIDS RES. V. 40 1 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22584622 JRNL DOI 10.1093/NAR/GKS413 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_868) 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 32824 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1603 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 24.0285 - 4.4555 0.98 3107 158 0.1883 0.2011 REMARK 3 2 4.4555 - 3.5401 1.00 3018 153 0.1543 0.1896 REMARK 3 3 3.5401 - 3.0937 1.00 3008 148 0.1816 0.2167 REMARK 3 4 3.0937 - 2.8113 1.00 2971 163 0.2064 0.2854 REMARK 3 5 2.8113 - 2.6100 1.00 2962 156 0.2013 0.2829 REMARK 3 6 2.6100 - 2.4563 0.99 2922 152 0.2034 0.2536 REMARK 3 7 2.4563 - 2.3334 0.99 2915 148 0.2017 0.2509 REMARK 3 8 2.3334 - 2.2319 0.97 2851 147 0.2124 0.2481 REMARK 3 9 2.2319 - 2.1460 0.93 2717 142 0.2313 0.2839 REMARK 3 10 2.1460 - 2.0720 0.84 2465 129 0.2315 0.2760 REMARK 3 11 2.0720 - 2.0073 0.75 2203 107 0.2274 0.2419 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 59.91 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.560 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.50070 REMARK 3 B22 (A**2) : 10.60810 REMARK 3 B33 (A**2) : -3.22100 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 : 0.011 3191 REMARK 3 ANGLE : 1.159 4471 REMARK 3 CHIRALITY : 0.071 501 REMARK 3 PLANARITY : 0.005 453 REMARK 3 DIHEDRAL : 11.139 886 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 4FO6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000073144. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-11 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : 32824 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29700 REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3MGI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM MES PH 6.5, 9%(V/V) PEG400, 100MM REMARK 280 KCL, 10MM MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 27.89000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.73500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.82750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.73500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.89000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.82750 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D, H, I 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 ALA A 242 REMARK 465 GLN A 243 REMARK 465 PRO A 244 REMARK 465 SER A 245 REMARK 465 SER A 246 REMARK 465 GLN A 247 REMARK 465 LYS A 248 REMARK 465 ALA A 249 REMARK 465 THR A 250 REMARK 465 ASN A 251 REMARK 465 ARG A 438 REMARK 465 SER A 439 REMARK 465 HIS A 440 REMARK 465 ARG A 441 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 HIS A 252 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 256 CD1 REMARK 470 GLU A 258 CG CD OE1 OE2 REMARK 470 LYS A 259 NZ REMARK 470 GLU A 261 CD OE1 OE2 REMARK 470 LYS A 265 CE NZ REMARK 470 LYS A 281 CE NZ REMARK 470 ASN A 284 OD1 ND2 REMARK 470 LYS A 291 CD CE NZ REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 SER A 301 OG REMARK 470 ILE A 302 CD1 REMARK 470 ILE A 314 CG1 CG2 CD1 REMARK 470 GLU A 318 CG CD OE1 OE2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 324 CD CE NZ REMARK 470 HIS A 327 ND1 CD2 CE1 NE2 REMARK 470 GLU A 330 CD OE1 OE2 REMARK 470 LYS A 378 CE NZ REMARK 470 GLU A 385 OE1 OE2 REMARK 470 GLU A 396 OE1 OE2 REMARK 470 LYS A 401 CD CE NZ REMARK 470 GLN A 404 CD OE1 NE2 REMARK 470 SER A 408 OG REMARK 470 ILE A 443 CG1 CG2 CD1 REMARK 470 ARG A 446 CZ NH1 NH2 REMARK 470 ASP A 449 OD1 OD2 REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 GLU A 470 CD OE1 OE2 REMARK 470 VAL A 545 CG1 CG2 REMARK 470 ARG A 568 NH1 NH2 REMARK 470 GLU A 569 OE1 OE2 REMARK 470 GLU A 572 OE1 OE2 REMARK 470 DC I 1 O5' C5' 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 DG D 1 P DG D 1 OP3 -0.125 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 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DG T 2 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG T 3 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT T 5 N3 - C4 - O4 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT T 5 C5 - C4 - O4 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG T 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT T 7 O4' - C4' - C3' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT T 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT T 10 O4' - C1' - N1 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG T 11 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG D 1 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DG D 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC H 9 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG H 11 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC I 1 O4' - C1' - N1 ANGL. DEV. = 2.6 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 255 42.60 -85.92 REMARK 500 CYS A 415 -143.93 -111.23 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 NA A 602 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 O REMARK 620 2 ILE A 302 O 101.2 REMARK 620 3 ILE A 305 O 91.6 82.8 REMARK 620 4 DC D 3 OP1 169.3 88.4 94.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 605 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 101.0 REMARK 620 3 ALA A 344 O 89.7 87.9 REMARK 620 4 HOH A 704 O 88.9 89.3 176.5 REMARK 620 5 HOH A 728 O 69.9 167.8 84.0 98.5 REMARK 620 6 DA P 5 OP1 160.2 98.7 91.4 91.0 90.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD1 REMARK 620 2 ASP A 429 OD1 92.6 REMARK 620 3 F2A A 606 O2B 168.7 92.8 REMARK 620 4 F2A A 606 O1A 102.1 87.3 88.0 REMARK 620 5 F2A A 606 O3G 90.3 177.1 84.4 91.6 REMARK 620 6 HOH A 701 O 82.7 91.3 87.3 175.0 89.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 604 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 OD2 REMARK 620 2 ASP A 429 OD2 95.0 REMARK 620 3 ASP A 490 OD2 90.4 92.5 REMARK 620 4 F2A A 606 O1A 98.3 91.5 170.0 REMARK 620 5 HOH A 823 O 85.8 173.2 94.3 81.7 REMARK 620 6 C P 6 O3' 168.6 93.3 81.3 89.3 86.9 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 MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F2A A 606 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UPQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY COMPLEX OF REMARK 900 POLYMERASE LAMBDA WITH AN RATP ANALOG OPPOSITE A TEMPLATING T. REMARK 900 RELATED ID: 3UQ0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE POST-CATALYTIC PRODUCT COMPLEX OF REMARK 900 POLYMERASE LAMBDA WITH AN RAMP AT THE PRIMER TERMINUS. REMARK 900 RELATED ID: 3UQ2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE POST-CATALYTIC PRODUCT COMPLEX OF REMARK 900 POLYMERASE LAMBDA WITH AN RAMP INSERTED OPPOSITE A TEMPLATING G AND REMARK 900 DAMP INSERTED OPPOSITE A TEMPLATING T AT THE PRIMER TERMINUS. REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THIS IS A DELETION-SUBSTITUTION MUTANT, WITH REMARK 999 RESIDUES SQEENGQQQ IN THE WILDTYPE SUBSTITUTED BY RESIDUES KGET. REMARK 999 HOWEVER, THE RESIDUE NUMBERING WAS KEPT CONSISTENT WITH THE WT REMARK 999 PROTEIN. DBREF 4FO6 A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 4FO6 T 1 11 PDB 4FO6 4FO6 1 11 DBREF 4FO6 P 1 6 PDB 4FO6 4FO6 1 6 DBREF 4FO6 D 1 4 PDB 4FO6 4FO6 1 4 DBREF 4FO6 H 7 11 PDB 4FO6 4FO6 7 11 DBREF 4FO6 I 1 5 PDB 4FO6 4FO6 1 5 SEQADV 4FO6 LYS A 463 UNP Q9UGP5 SER 463 SEE REMARK 999 SEQADV 4FO6 GLY A 464 UNP Q9UGP5 GLN 464 SEE REMARK 999 SEQADV 4FO6 GLU A 470 UNP Q9UGP5 GLN 470 SEE REMARK 999 SEQADV 4FO6 THR A 471 UNP Q9UGP5 GLN 471 SEE REMARK 999 SEQADV 4FO6 ALA A 543 UNP Q9UGP5 CYS 543 ENGINEERED MUTATION SEQRES 1 A 329 ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU SEQRES 2 A 329 HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR SEQRES 3 A 329 SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA SEQRES 4 A 329 LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL SEQRES 5 A 329 THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY SEQRES 6 A 329 LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER SEQRES 7 A 329 GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL SEQRES 8 A 329 PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY SEQRES 9 A 329 THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG SEQRES 10 A 329 SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR SEQRES 11 A 329 GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU SEQRES 12 A 329 GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN SEQRES 13 A 329 THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU SEQRES 14 A 329 LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA SEQRES 15 A 329 THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP SEQRES 16 A 329 GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP SEQRES 17 A 329 SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL SEQRES 18 A 329 LYS GLY GLU THR LYS TYR LEU GLY VAL CYS ARG LEU PRO SEQRES 19 A 329 GLY PRO GLY ARG ARG HIS ARG ARG LEU ASP ILE ILE VAL SEQRES 20 A 329 VAL PRO TYR SER GLU PHE ALA CYS ALA LEU LEU TYR PHE SEQRES 21 A 329 THR GLY SER ALA HIS PHE ASN ARG SER MET ARG ALA LEU SEQRES 22 A 329 ALA LYS THR LYS GLY MET SER LEU SER GLU HIS ALA LEU SEQRES 23 A 329 SER THR ALA VAL VAL ARG ASN THR HIS GLY ALA LYS VAL SEQRES 24 A 329 GLY PRO GLY ARG VAL LEU PRO THR PRO THR GLU LYS ASP SEQRES 25 A 329 VAL PHE ARG LEU LEU GLY LEU PRO TYR ARG GLU PRO ALA SEQRES 26 A 329 GLU ARG ASP TRP SEQRES 1 T 11 DC DG DG DC DT DG DT DA DC DT DG SEQRES 1 P 6 DC DA DG DT DA C SEQRES 1 D 4 DG DC DC DG SEQRES 1 H 5 DT DA DC DT DG SEQRES 1 I 5 DC DA DG DT DA HET MG A 601 1 HET NA A 602 1 HET CL A 603 1 HET MN A 604 1 HET NA A 605 1 HET F2A A 606 30 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM MN MANGANESE (II) ION HETNAM F2A 2'-DEOXY-5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 F2A PHOSPHORYL]METHYL}PHOSPHORYL]ADENOSINE FORMUL 7 MG MG 2+ FORMUL 8 NA 2(NA 1+) FORMUL 9 CL CL 1- FORMUL 10 MN MN 2+ FORMUL 12 F2A C11 H18 N5 O11 P3 FORMUL 13 HOH *212(H2 O) HELIX 1 1 ILE A 256 GLN A 270 1 15 HELIX 2 2 ASP A 272 SER A 288 1 17 HELIX 3 3 SER A 295 CYS A 300 1 6 HELIX 4 4 GLY A 306 GLY A 320 1 15 HELIX 5 5 LEU A 322 HIS A 327 1 6 HELIX 6 6 SER A 331 ASN A 340 1 10 HELIX 7 7 GLY A 345 GLN A 355 1 11 HELIX 8 8 SER A 359 ALA A 367 1 9 HELIX 9 9 THR A 370 HIS A 379 1 10 HELIX 10 10 SER A 381 GLU A 385 5 5 HELIX 11 11 ARG A 389 ALA A 405 1 17 HELIX 12 12 CYS A 415 ARG A 420 1 6 HELIX 13 13 ILE A 443 GLU A 454 1 12 HELIX 14 14 GLU A 498 GLY A 508 1 11 HELIX 15 15 SER A 509 LYS A 523 1 15 HELIX 16 16 THR A 555 LEU A 563 1 9 HELIX 17 17 GLU A 569 ASP A 574 5 6 SHEET 1 A 2 MET A 387 PRO A 388 0 SHEET 2 A 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387 SHEET 1 B 5 LEU A 411 ALA A 414 0 SHEET 2 B 5 VAL A 428 HIS A 434 -1 O LEU A 431 N VAL A 413 SHEET 3 B 5 ARG A 487 PRO A 495 1 O ASP A 490 N VAL A 430 SHEET 4 B 5 LYS A 472 CYS A 477 -1 N CYS A 477 O ARG A 487 SHEET 5 B 5 LEU A 457 LYS A 463 -1 N LEU A 461 O LEU A 474 SHEET 1 C 3 SER A 526 LEU A 527 0 SHEET 2 C 3 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526 SHEET 3 C 3 ARG A 549 VAL A 550 -1 O ARG A 549 N THR A 534 SHEET 1 D 2 VAL A 537 ARG A 538 0 SHEET 2 D 2 LYS A 544 GLY A 546 -1 O VAL A 545 N VAL A 537 LINK O CYS A 300 NA NA A 602 1555 1555 2.94 LINK O ILE A 302 NA NA A 602 1555 1555 2.40 LINK O ILE A 305 NA NA A 602 1555 1555 2.84 LINK O SER A 339 NA NA A 605 1555 1555 2.39 LINK O ILE A 341 NA NA A 605 1555 1555 2.41 LINK O ALA A 344 NA NA A 605 1555 1555 2.36 LINK OD1 ASP A 427 MG MG A 601 1555 1555 1.99 LINK OD2 ASP A 427 MN MN A 604 1555 1555 2.03 LINK OD1 ASP A 429 MG MG A 601 1555 1555 1.96 LINK OD2 ASP A 429 MN MN A 604 1555 1555 2.15 LINK OD2 ASP A 490 MN MN A 604 1555 1555 2.16 LINK MG MG A 601 O2B F2A A 606 1555 1555 2.05 LINK MG MG A 601 O1A F2A A 606 1555 1555 2.14 LINK MG MG A 601 O3G F2A A 606 1555 1555 2.19 LINK MG MG A 601 O HOH A 701 1555 1555 2.08 LINK NA NA A 602 OP1 DC D 3 1555 1555 3.17 LINK MN MN A 604 O1A F2A A 606 1555 1555 2.29 LINK MN MN A 604 O HOH A 823 1555 1555 2.21 LINK MN MN A 604 O3' C P 6 1555 1555 2.19 LINK NA NA A 605 O HOH A 704 1555 1555 2.42 LINK NA NA A 605 O HOH A 728 1555 1555 2.43 LINK NA NA A 605 OP1 DA P 5 1555 1555 2.49 CISPEP 1 GLY A 508 SER A 509 0 7.79 SITE 1 AC1 5 ASP A 427 ASP A 429 MN A 604 F2A A 606 SITE 2 AC1 5 HOH A 701 SITE 1 AC2 4 CYS A 300 ILE A 302 ILE A 305 DC D 3 SITE 1 AC3 3 ARG A 517 GLU A 529 DG T 6 SITE 1 AC4 7 ASP A 427 ASP A 429 ASP A 490 MG A 601 SITE 2 AC4 7 F2A A 606 HOH A 823 C P 6 SITE 1 AC5 6 SER A 339 ILE A 341 ALA A 344 HOH A 704 SITE 2 AC5 6 HOH A 728 DA P 5 SITE 1 AC6 25 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 2 AC6 25 CYS A 425 GLY A 426 ASP A 427 ASP A 429 SITE 3 AC6 25 TYR A 505 PHE A 506 THR A 507 GLY A 508 SITE 4 AC6 25 ALA A 510 ASN A 513 MG A 601 MN A 604 SITE 5 AC6 25 HOH A 701 HOH A 703 HOH A 735 HOH A 737 SITE 6 AC6 25 HOH A 782 HOH A 823 C P 6 DT T 5 SITE 7 AC6 25 DG T 6 CRYST1 55.780 63.655 141.470 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 0.017928 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007069 0.00000