PDB Short entry for 5DKW HEADER TRANSFERASE/DNA 04-SEP-15 5DKW TITLE TERNARY CRYSTAL STRUCTURE OF POLYMERASE LAMBDA WITH A GA MISPAIR AT TITLE 2 THE PRIMER TERMINUS WITH CA2+ IN THE ACTIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 249-575; COMPND 5 SYNONYM: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE COMPND 6 KAPPA; COMPND 7 EC: 2.7.7.7; 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, C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3'); COMPND 15 CHAIN: P, E; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 4; COMPND 18 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*GP*GP*TP*AP*CP*TP*G)-3'); COMPND 19 CHAIN: T, F; 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: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630 KEYWDS POLYMERASE LAMBDA, TRANSFERASE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.S.LIU,M.D.TSAI REVDAT 5 20-MAR-24 5DKW 1 SOURCE REVDAT 4 08-NOV-23 5DKW 1 LINK REVDAT 3 19-FEB-20 5DKW 1 REMARK REVDAT 2 09-MAR-16 5DKW 1 JRNL REVDAT 1 24-FEB-16 5DKW 0 JRNL AUTH M.S.LIU,H.Y.TSAI,X.X.LIU,M.C.HO,W.J.WU,M.D.TSAI JRNL TITL STRUCTURAL MECHANISM FOR THE FIDELITY MODULATION OF DNA JRNL TITL 2 POLYMERASE LAMBDA JRNL REF J.AM.CHEM.SOC. V. 138 2389 2016 JRNL REFN ESSN 1520-5126 JRNL PMID 26836966 JRNL DOI 10.1021/JACS.5B13368 REMARK 2 REMARK 2 RESOLUTION. 2.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 35577 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.620 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 29.4739 - 6.4591 0.98 2535 152 0.1777 0.1983 REMARK 3 2 6.4591 - 5.1356 1.00 2477 146 0.1915 0.1984 REMARK 3 3 5.1356 - 4.4890 1.00 2437 146 0.1595 0.2441 REMARK 3 4 4.4890 - 4.0797 1.00 2430 144 0.1475 0.1910 REMARK 3 5 4.0797 - 3.7879 1.00 2400 143 0.1622 0.2400 REMARK 3 6 3.7879 - 3.5650 1.00 2412 143 0.1791 0.1991 REMARK 3 7 3.5650 - 3.3867 1.00 2395 143 0.1750 0.2162 REMARK 3 8 3.3867 - 3.2395 1.00 2380 142 0.1823 0.2491 REMARK 3 9 3.2395 - 3.1149 1.00 2388 142 0.1997 0.2842 REMARK 3 10 3.1149 - 3.0076 1.00 2374 142 0.2103 0.2738 REMARK 3 11 3.0076 - 2.9136 1.00 2392 141 0.2191 0.2760 REMARK 3 12 2.9136 - 2.8304 1.00 2364 141 0.2323 0.2822 REMARK 3 13 2.8304 - 2.7559 1.00 2397 142 0.2468 0.3029 REMARK 3 14 2.7559 - 2.6887 0.94 2198 131 0.2587 0.3347 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.004 6142 REMARK 3 ANGLE : 0.853 8480 REMARK 3 CHIRALITY : 0.076 926 REMARK 3 PLANARITY : 0.004 942 REMARK 3 DIHEDRAL : 18.397 2324 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 5DKW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213366. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35654 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.689 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.81800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1XSL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 30%(V/V) JEFFAMINE ED REMARK 280 -2100 REAGENT, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 49.73300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 75.65500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.73300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 75.65500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 4730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 4810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, E, F 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 ARG A 538 REMARK 465 ASN A 539 REMARK 465 THR A 540 REMARK 465 HIS A 541 REMARK 465 GLY A 542 REMARK 465 CYS A 543 REMARK 465 LYS A 544 REMARK 465 VAL A 545 REMARK 465 ARG B 538 REMARK 465 ASN B 539 REMARK 465 THR B 540 REMARK 465 HIS B 541 REMARK 465 GLY B 542 REMARK 465 CYS B 543 REMARK 465 LYS B 544 REMARK 465 VAL B 545 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 ASP B 558 NH1 ARG B 561 2.13 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 DG D 1 P DG D 1 OP3 -0.124 REMARK 500 DG C 1 P DG C 1 OP3 -0.123 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 5 O3' - P - OP2 ANGL. DEV. = -22.2 DEGREES REMARK 500 DG T 5 O3' - P - OP1 ANGL. DEV. = -19.6 DEGREES REMARK 500 DG T 5 OP1 - P - OP2 ANGL. DEV. = 10.2 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 CYS A 415 -157.97 -102.40 REMARK 500 CYS B 415 -160.49 -111.41 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 CA A 603 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 O REMARK 620 2 ILE A 302 O 89.4 REMARK 620 3 ILE A 305 O 85.9 79.9 REMARK 620 4 HOH A 786 O 88.3 90.4 168.7 REMARK 620 5 DC D 3 OP1 173.6 89.0 100.0 85.5 REMARK 620 6 HOH D 101 O 87.6 168.1 88.3 101.0 95.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 602 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 427 O REMARK 620 2 ASP A 427 OD1 76.1 REMARK 620 3 DTP A 601 O3G 88.1 67.8 REMARK 620 4 DTP A 601 O1B 133.1 112.4 57.7 REMARK 620 5 DTP A 601 O1A 139.9 67.3 92.5 77.9 REMARK 620 6 HOH A 744 O 94.7 152.0 139.3 93.3 109.9 REMARK 620 7 HOH A 747 O 56.6 120.4 76.1 82.7 160.6 72.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 601 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 300 O REMARK 620 2 ILE B 302 O 80.1 REMARK 620 3 ILE B 305 O 83.1 77.6 REMARK 620 4 DC C 3 OP1 161.0 84.3 104.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 602 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 339 O REMARK 620 2 ILE B 341 O 99.9 REMARK 620 3 ALA B 344 O 89.1 74.0 REMARK 620 4 DA E 5 OP1 168.2 91.4 90.8 REMARK 620 5 HOH E 103 O 73.0 157.6 84.5 95.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 604 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 427 OD1 REMARK 620 2 ASP B 429 OD2 93.3 REMARK 620 3 DTP B 603 O1G 75.5 164.4 REMARK 620 4 DTP B 603 O1B 127.0 115.9 65.4 REMARK 620 5 DTP B 603 O1A 75.0 81.8 84.9 67.5 REMARK 620 6 HOH B 745 O 113.6 101.5 93.0 103.0 170.3 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 DTP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTP B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 604 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CB1 RELATED DB: PDB REMARK 900 5CB1 CONTAINS THE SAME PROTEIN- APOENZYME DBREF 5DKW A 249 575 UNP Q9UGP5 DPOLL_HUMAN 249 575 DBREF 5DKW B 249 575 UNP Q9UGP5 DPOLL_HUMAN 249 575 DBREF 5DKW D 1 4 PDB 5DKW 5DKW 1 4 DBREF 5DKW T 1 11 PDB 5DKW 5DKW 1 11 DBREF 5DKW C 1 4 PDB 5DKW 5DKW 1 4 DBREF 5DKW F 1 11 PDB 5DKW 5DKW 1 11 DBREF 5DKW P 1 6 PDB 5DKW 5DKW 1 6 DBREF 5DKW E 1 6 PDB 5DKW 5DKW 1 6 SEQRES 1 A 327 ALA THR ASN HIS ASN LEU HIS ILE THR GLU LYS LEU GLU SEQRES 2 A 327 VAL LEU ALA LYS ALA TYR SER VAL GLN GLY ASP LYS TRP SEQRES 3 A 327 ARG ALA LEU GLY TYR ALA LYS ALA ILE ASN ALA LEU LYS SEQRES 4 A 327 SER PHE HIS LYS PRO VAL THR SER TYR GLN GLU ALA CYS SEQRES 5 A 327 SER ILE PRO GLY ILE GLY LYS ARG MET ALA GLU LYS ILE SEQRES 6 A 327 ILE GLU ILE LEU GLU SER GLY HIS LEU ARG LYS LEU ASP SEQRES 7 A 327 HIS ILE SER GLU SER VAL PRO VAL LEU GLU LEU PHE SER SEQRES 8 A 327 ASN ILE TRP GLY ALA GLY THR LYS THR ALA GLN MET TRP SEQRES 9 A 327 TYR GLN GLN GLY PHE ARG SER LEU GLU ASP ILE ARG SER SEQRES 10 A 327 GLN ALA SER LEU THR THR GLN GLN ALA ILE GLY LEU LYS SEQRES 11 A 327 HIS TYR SER ASP PHE LEU GLU ARG MET PRO ARG GLU GLU SEQRES 12 A 327 ALA THR GLU ILE GLU GLN THR VAL GLN LYS ALA ALA GLN SEQRES 13 A 327 ALA PHE ASN SER GLY LEU LEU CYS VAL ALA CYS GLY SER SEQRES 14 A 327 TYR ARG ARG GLY LYS ALA THR CYS GLY ASP VAL ASP VAL SEQRES 15 A 327 LEU ILE THR HIS PRO ASP GLY ARG SER HIS ARG GLY ILE SEQRES 16 A 327 PHE SER ARG LEU LEU ASP SER LEU ARG GLN GLU GLY PHE SEQRES 17 A 327 LEU THR ASP ASP LEU VAL SER GLN GLU GLU ASN GLY GLN SEQRES 18 A 327 GLN GLN LYS TYR LEU GLY VAL CYS ARG LEU PRO GLY PRO SEQRES 19 A 327 GLY ARG ARG HIS ARG ARG LEU ASP ILE ILE VAL VAL PRO SEQRES 20 A 327 TYR SER GLU PHE ALA CYS ALA LEU LEU TYR PHE THR GLY SEQRES 21 A 327 SER ALA HIS PHE ASN ARG SER MET ARG ALA LEU ALA LYS SEQRES 22 A 327 THR LYS GLY MET SER LEU SER GLU HIS ALA LEU SER THR SEQRES 23 A 327 ALA VAL VAL ARG ASN THR HIS GLY CYS LYS VAL GLY PRO SEQRES 24 A 327 GLY ARG VAL LEU PRO THR PRO THR GLU LYS ASP VAL PHE SEQRES 25 A 327 ARG LEU LEU GLY LEU PRO TYR ARG GLU PRO ALA GLU ARG SEQRES 26 A 327 ASP TRP SEQRES 1 B 327 ALA THR ASN HIS ASN LEU HIS ILE THR GLU LYS LEU GLU SEQRES 2 B 327 VAL LEU ALA LYS ALA TYR SER VAL GLN GLY ASP LYS TRP SEQRES 3 B 327 ARG ALA LEU GLY TYR ALA LYS ALA ILE ASN ALA LEU LYS SEQRES 4 B 327 SER PHE HIS LYS PRO VAL THR SER TYR GLN GLU ALA CYS SEQRES 5 B 327 SER ILE PRO GLY ILE GLY LYS ARG MET ALA GLU LYS ILE SEQRES 6 B 327 ILE GLU ILE LEU GLU SER GLY HIS LEU ARG LYS LEU ASP SEQRES 7 B 327 HIS ILE SER GLU SER VAL PRO VAL LEU GLU LEU PHE SER SEQRES 8 B 327 ASN ILE TRP GLY ALA GLY THR LYS THR ALA GLN MET TRP SEQRES 9 B 327 TYR GLN GLN GLY PHE ARG SER LEU GLU ASP ILE ARG SER SEQRES 10 B 327 GLN ALA SER LEU THR THR GLN GLN ALA ILE GLY LEU LYS SEQRES 11 B 327 HIS TYR SER ASP PHE LEU GLU ARG MET PRO ARG GLU GLU SEQRES 12 B 327 ALA THR GLU ILE GLU GLN THR VAL GLN LYS ALA ALA GLN SEQRES 13 B 327 ALA PHE ASN SER GLY LEU LEU CYS VAL ALA CYS GLY SER SEQRES 14 B 327 TYR ARG ARG GLY LYS ALA THR CYS GLY ASP VAL ASP VAL SEQRES 15 B 327 LEU ILE THR HIS PRO ASP GLY ARG SER HIS ARG GLY ILE SEQRES 16 B 327 PHE SER ARG LEU LEU ASP SER LEU ARG GLN GLU GLY PHE SEQRES 17 B 327 LEU THR ASP ASP LEU VAL SER GLN GLU GLU ASN GLY GLN SEQRES 18 B 327 GLN GLN LYS TYR LEU GLY VAL CYS ARG LEU PRO GLY PRO SEQRES 19 B 327 GLY ARG ARG HIS ARG ARG LEU ASP ILE ILE VAL VAL PRO SEQRES 20 B 327 TYR SER GLU PHE ALA CYS ALA LEU LEU TYR PHE THR GLY SEQRES 21 B 327 SER ALA HIS PHE ASN ARG SER MET ARG ALA LEU ALA LYS SEQRES 22 B 327 THR LYS GLY MET SER LEU SER GLU HIS ALA LEU SER THR SEQRES 23 B 327 ALA VAL VAL ARG ASN THR HIS GLY CYS LYS VAL GLY PRO SEQRES 24 B 327 GLY ARG VAL LEU PRO THR PRO THR GLU LYS ASP VAL PHE SEQRES 25 B 327 ARG LEU LEU GLY LEU PRO TYR ARG GLU PRO ALA GLU ARG SEQRES 26 B 327 ASP TRP SEQRES 1 D 4 DG DC DC DG SEQRES 1 P 6 DC DA DG DT DA DC SEQRES 1 T 11 DC DG DG DC DG DG DT DA DC DT DG SEQRES 1 C 4 DG DC DC DG SEQRES 1 E 6 DC DA DG DT DA DC SEQRES 1 F 11 DC DG DG DC DG DG DT DA DC DT DG HET DTP A 601 30 HET CA A 602 1 HET CA A 603 1 HET CA B 601 1 HET CA B 602 1 HET DTP B 603 30 HET CA B 604 1 HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETNAM CA CALCIUM ION FORMUL 9 DTP 2(C10 H16 N5 O12 P3) FORMUL 10 CA 5(CA 2+) FORMUL 16 HOH *205(H2 O) HELIX 1 AA1 ASN A 253 GLN A 270 1 18 HELIX 2 AA2 ASP A 272 SER A 288 1 17 HELIX 3 AA3 SER A 295 ILE A 302 1 8 HELIX 4 AA4 GLY A 306 GLY A 320 1 15 HELIX 5 AA5 LEU A 322 HIS A 327 5 6 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 GLN A 404 1 16 HELIX 12 AB3 GLY A 416 ARG A 419 5 4 HELIX 13 AB4 ILE A 443 GLU A 454 1 12 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 HELIX 19 AC1 ASN B 253 GLN B 270 1 18 HELIX 20 AC2 ASP B 272 SER B 288 1 17 HELIX 21 AC3 SER B 295 SER B 301 1 7 HELIX 22 AC4 GLY B 306 SER B 319 1 14 HELIX 23 AC5 LEU B 322 HIS B 327 5 6 HELIX 24 AC6 SER B 331 SER B 339 1 9 HELIX 25 AC7 GLY B 345 GLN B 355 1 11 HELIX 26 AC8 SER B 359 ALA B 367 1 9 HELIX 27 AC9 THR B 370 HIS B 379 1 10 HELIX 28 AD1 HIS B 379 GLU B 385 1 7 HELIX 29 AD2 ARG B 389 ALA B 405 1 17 HELIX 30 AD3 GLY B 416 ARG B 419 5 4 HELIX 31 AD4 ILE B 443 GLU B 454 1 12 HELIX 32 AD5 PRO B 495 SER B 497 5 3 HELIX 33 AD6 GLU B 498 GLY B 508 1 11 HELIX 34 AD7 SER B 509 LYS B 523 1 15 HELIX 35 AD8 THR B 555 LEU B 562 1 8 HELIX 36 AD9 GLU B 569 ARG B 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 ASP A 490 N VAL A 430 SHEET 4 AA2 5 GLN A 470 CYS A 477 -1 N GLN A 471 O VAL A 493 SHEET 5 AA2 5 LEU A 457 ASN A 467 -1 N THR A 458 O VAL A 476 SHEET 1 AA3 3 MET A 525 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 VAL A 550 LEU A 551 -1 O LEU A 551 N LEU A 532 SHEET 1 AA4 2 MET B 387 PRO B 388 0 SHEET 2 AA4 2 THR B 424 CYS B 425 -1 O CYS B 425 N MET B 387 SHEET 1 AA5 5 LEU B 411 CYS B 415 0 SHEET 2 AA5 5 VAL B 428 THR B 433 -1 O LEU B 431 N VAL B 413 SHEET 3 AA5 5 ARG B 487 VAL B 493 1 O ILE B 492 N ILE B 432 SHEET 4 AA5 5 GLN B 470 CYS B 477 -1 N CYS B 477 O ARG B 487 SHEET 5 AA5 5 LEU B 457 ASN B 467 -1 N THR B 458 O VAL B 476 SHEET 1 AA6 3 MET B 525 LEU B 527 0 SHEET 2 AA6 3 LEU B 532 THR B 534 -1 O SER B 533 N SER B 526 SHEET 3 AA6 3 VAL B 550 LEU B 551 -1 O LEU B 551 N LEU B 532 LINK O CYS A 300 CA CA A 603 1555 1555 2.53 LINK O ILE A 302 CA CA A 603 1555 1555 2.72 LINK O ILE A 305 CA CA A 603 1555 1555 2.53 LINK O ASP A 427 CA CA A 602 1555 1555 3.03 LINK OD1 ASP A 427 CA CA A 602 1555 1555 2.45 LINK O3G DTP A 601 CA CA A 602 1555 1555 3.06 LINK O1B DTP A 601 CA CA A 602 1555 1555 2.32 LINK O1A DTP A 601 CA CA A 602 1555 1555 2.65 LINK CA CA A 602 O HOH A 744 1555 1555 2.35 LINK CA CA A 602 O HOH A 747 1555 1555 2.79 LINK CA CA A 603 O HOH A 786 1555 1555 2.82 LINK CA CA A 603 OP1 DC D 3 1555 1555 2.88 LINK CA CA A 603 O HOH D 101 1555 1555 2.83 LINK O CYS B 300 CA CA B 601 1555 1555 2.43 LINK O ILE B 302 CA CA B 601 1555 1555 2.80 LINK O ILE B 305 CA CA B 601 1555 1555 2.66 LINK O SER B 339 CA CA B 602 1555 1555 2.63 LINK O ILE B 341 CA CA B 602 1555 1555 2.67 LINK O ALA B 344 CA CA B 602 1555 1555 2.64 LINK OD1 ASP B 427 CA CA B 604 1555 1555 2.35 LINK OD2 ASP B 429 CA CA B 604 1555 1555 2.70 LINK CA CA B 601 OP1 DC C 3 1555 1555 3.20 LINK CA CA B 602 OP1 DA E 5 1555 1555 2.54 LINK CA CA B 602 O HOH E 103 1555 1555 2.93 LINK O1G DTP B 603 CA CA B 604 1555 1555 2.59 LINK O1B DTP B 603 CA CA B 604 1555 1555 2.87 LINK O1A DTP B 603 CA CA B 604 1555 1555 2.42 LINK CA CA B 604 O HOH B 745 1555 1555 2.54 CISPEP 1 GLY A 508 SER A 509 0 5.02 CISPEP 2 GLY B 508 SER B 509 0 2.43 SITE 1 AC1 15 ARG A 386 GLY A 416 SER A 417 ARG A 420 SITE 2 AC1 15 GLY A 426 ASP A 427 ASP A 429 TYR A 505 SITE 3 AC1 15 PHE A 506 GLY A 508 ASN A 513 CA A 602 SITE 4 AC1 15 HOH A 710 DC P 6 DG T 5 SITE 1 AC2 4 ASP A 427 DTP A 601 HOH A 744 HOH A 747 SITE 1 AC3 6 CYS A 300 ILE A 302 ILE A 305 HOH A 786 SITE 2 AC3 6 DC D 3 HOH D 101 SITE 1 AC4 4 CYS B 300 ILE B 302 ILE B 305 DC C 3 SITE 1 AC5 5 SER B 339 ILE B 341 ALA B 344 DA E 5 SITE 2 AC5 5 HOH E 103 SITE 1 AC6 15 ARG B 386 GLY B 416 SER B 417 ARG B 420 SITE 2 AC6 15 GLY B 426 ASP B 427 ASP B 429 TYR B 505 SITE 3 AC6 15 PHE B 506 GLY B 508 ASN B 513 CA B 604 SITE 4 AC6 15 HOH B 702 DC E 6 DG F 5 SITE 1 AC7 4 ASP B 427 ASP B 429 DTP B 603 HOH B 745 CRYST1 99.466 151.310 83.606 90.00 90.00 90.00 P 21 21 2 8 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 0.010054 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006609 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011961 0.00000