HEADER RNA/CYCLOHEXENE-RNA HYBRID 12-NOV-09 3KNC TITLE CRYSTAL STRUCTURE OF THE CENA-RNA HYBRID OCTAMER CE(GCGTAGCG) TITLE 2 :R(CGCUACGC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*(XGR)P*(XCR)P*(XGR)P*(XTR)P*(XAR)P*(XGR)P*(XCR) COMPND 3 P*(XGR)P*(XGR))-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CENA; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: RNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE CENA STRAND WAS SYNTHESIZED.; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: THE RNA STRAND WAS SYNTHESIZED. KEYWDS CYCLOHEXENE, SUGAR MODIFICATION, RNA, RNA-CYCLOHEXENE-RNA HYBRID KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.OVAERE,L.VAN MEERVELT REVDAT 7 21-FEB-24 3KNC 1 REMARK REVDAT 6 13-OCT-21 3KNC 1 REMARK DBREF SEQADV LINK REVDAT 5 01-NOV-17 3KNC 1 REMARK REVDAT 4 01-FEB-12 3KNC 1 SEQADV VERSN REVDAT 3 13-JUL-11 3KNC 1 JRNL REVDAT 2 29-JUN-11 3KNC 1 JRNL REVDAT 1 08-DEC-10 3KNC 0 JRNL AUTH M.OVAERE,P.HERDEWIJN,L.VAN MEERVELT JRNL TITL THE CRYSTAL STRUCTURE OF THE CENA:RNA HYBRID JRNL TITL 2 CE(GCGTAGCG):R(CGCUACGC). JRNL REF CHEMISTRY V. 17 7823 2011 JRNL REFN ISSN 0947-6539 JRNL PMID 21618623 JRNL DOI 10.1002/CHEM.201003594 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 2574 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 114 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 169 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.3790 REMARK 3 BIN FREE R VALUE SET COUNT : 9 REMARK 3 BIN FREE R VALUE : 0.7330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 341 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.49000 REMARK 3 B22 (A**2) : 4.49000 REMARK 3 B33 (A**2) : -6.73000 REMARK 3 B12 (A**2) : 2.24000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.310 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.237 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.190 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.838 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 396 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 617 ; 2.247 ; 2.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 63 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 199 ; 0.010 ; 0.017 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1 ; 0.108 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 392 ; 2.812 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 605 ; 4.317 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FRIEDEL PAIRS WERE USED IN PHASING REMARK 4 REMARK 4 3KNC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056206. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2575 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 36.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER 2.1.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM FORMATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 45.62933 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 22.81467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.81467 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 45.62933 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11444 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 MG MG A 200 LIES ON A SPECIAL POSITION. 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 XGR A 9 N1 C2 N2 N3 C4 C5 C6 REMARK 470 XGR A 9 O6 N7 C8 N9 C1' C2' C3' REMARK 470 XGR A 9 O3' C4' C5' C6' C7' 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 U B 4 C5' U B 4 C4' -0.043 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 100 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 101 O REMARK 620 2 HOH A 102 O 176.6 REMARK 620 3 HOH A 103 O 92.0 86.0 REMARK 620 4 HOH A 104 O 92.6 90.0 90.3 REMARK 620 5 HOH A 105 O 90.9 86.5 90.9 176.2 REMARK 620 6 HOH A 106 O 86.1 96.1 177.4 88.1 90.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 200 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 201 O REMARK 620 2 HOH A 202 O 179.4 REMARK 620 3 HOH A 203 O 89.5 90.0 REMARK 620 4 HOH A 204 O 90.8 88.8 88.5 REMARK 620 5 HOH A 205 O 89.1 91.3 92.6 178.9 REMARK 620 6 HOH A 206 O 93.2 87.2 176.4 89.0 89.9 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 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 200 DBREF 3KNC A 1 9 PDB 3KNC 3KNC 1 9 DBREF 3KNC B 1 8 PDB 3KNC 3KNC 1 8 SEQADV 3KNC XGR A 1 PDB 3KNC C 2 ENGINEERED MUTATION SEQADV 3KNC XCR A 2 PDB 3KNC G 3 ENGINEERED MUTATION SEQADV 3KNC XGR A 3 PDB 3KNC DT 4 ENGINEERED MUTATION SEQADV 3KNC XTR A 4 PDB 3KNC A 5 ENGINEERED MUTATION SEQADV 3KNC XAR A 5 PDB 3KNC G 6 ENGINEERED MUTATION SEQADV 3KNC XGR A 6 PDB 3KNC C 7 ENGINEERED MUTATION SEQADV 3KNC XCR A 7 PDB 3KNC G 8 ENGINEERED MUTATION SEQADV 3KNC XGR A 8 PDB 3KNC G 9 ENGINEERED MUTATION SEQADV 3KNC XGR A 9 PDB 3KNC G 10 ENGINEERED MUTATION SEQRES 1 A 9 XGR XCR XGR XTR XAR XGR XCR XGR XGR SEQRES 1 B 8 C G C U A C G C MODRES 3KNC XGR A 1 DG MODRES 3KNC XCR A 2 DC MODRES 3KNC XGR A 3 DG MODRES 3KNC XTR A 4 DT MODRES 3KNC XGR A 6 DG MODRES 3KNC XCR A 7 DC MODRES 3KNC XGR A 8 DG MODRES 3KNC XGR A 9 DG HET XGR A 1 20 HET XCR A 2 20 HET XGR A 3 23 HET XTR A 4 21 HET XAR A 5 22 HET XGR A 6 23 HET XCR A 7 20 HET XGR A 8 23 HET XGR A 9 4 HET MG A 100 1 HET MG A 200 1 HETNAM XGR [(1R,4S,6S)-4-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9- HETNAM 2 XGR YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN HETNAM 3 XGR PHOSPHATE HETNAM XCR [(1R,4S,6S)-4-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-6- HETNAM 2 XCR HYDROXYCYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE HETNAM XTR [(1R,4S,6S)-6-HYDROXY-4-(5-METHYL-2,4-DIOXO-3,4- HETNAM 2 XTR DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOHEX-2-EN-1-YL]METHYL HETNAM 3 XTR DIHYDROGEN PHOSPHATE HETNAM XAR [(1R,4S,6S)-4-(6-AMINO-9H-PURIN-9-YL)-6- HETNAM 2 XAR HYDROXYCYCLOHEX-2-EN-1-YL]METHYL DIHYDROGEN PHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 XGR 5(C12 H16 N5 O6 P) FORMUL 1 XCR 2(C11 H16 N3 O6 P) FORMUL 1 XTR C12 H17 N2 O7 P FORMUL 1 XAR C12 H16 N5 O5 P FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *47(H2 O) LINK O3' XTR A 4 P XAR A 5 1555 1555 1.57 LINK MG MG A 100 O HOH A 101 1555 1555 2.14 LINK MG MG A 100 O HOH A 102 1555 1555 2.13 LINK MG MG A 100 O HOH A 103 1555 1555 2.13 LINK MG MG A 100 O HOH A 104 1555 1555 2.15 LINK MG MG A 100 O HOH A 105 1555 1555 2.14 LINK MG MG A 100 O HOH A 106 1555 1555 2.14 LINK MG MG A 200 O HOH A 201 1555 1555 2.16 LINK MG MG A 200 O HOH A 202 1555 1555 2.17 LINK MG MG A 200 O HOH A 203 1555 1555 2.18 LINK MG MG A 200 O HOH A 204 1555 1555 2.16 LINK MG MG A 200 O HOH A 205 1555 1555 2.16 LINK MG MG A 200 O HOH A 206 1555 1555 2.16 SITE 1 AC1 6 HOH A 101 HOH A 102 HOH A 103 HOH A 104 SITE 2 AC1 6 HOH A 105 HOH A 106 SITE 1 AC2 6 HOH A 201 HOH A 202 HOH A 203 HOH A 204 SITE 2 AC2 6 HOH A 205 HOH A 206 CRYST1 41.919 41.919 68.444 90.00 90.00 120.00 P 32 2 1 6 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 0.023856 0.013773 0.000000 0.00000 SCALE2 0.000000 0.027546 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014610 0.00000 HETATM 1 N1 XGR A 1 15.217 -13.830 -2.098 1.00 49.22 N HETATM 2 C2 XGR A 1 14.996 -14.919 -1.316 1.00 48.32 C HETATM 3 N2 XGR A 1 15.852 -15.950 -1.453 1.00 49.38 N HETATM 4 N3 XGR A 1 13.983 -14.984 -0.471 1.00 50.70 N HETATM 5 C4 XGR A 1 13.211 -13.874 -0.438 1.00 52.42 C HETATM 6 C5 XGR A 1 13.374 -12.752 -1.182 1.00 51.19 C HETATM 7 C6 XGR A 1 14.433 -12.686 -2.087 1.00 50.38 C HETATM 8 O6 XGR A 1 14.719 -11.745 -2.823 1.00 54.08 O HETATM 9 N7 XGR A 1 12.394 -11.816 -0.902 1.00 53.93 N HETATM 10 C8 XGR A 1 11.641 -12.400 -0.008 1.00 54.29 C HETATM 11 N9 XGR A 1 12.078 -13.643 0.342 1.00 55.93 N HETATM 12 C1' XGR A 1 11.445 -14.513 1.332 1.00 58.70 C HETATM 13 C2' XGR A 1 11.997 -14.342 2.753 1.00 60.71 C HETATM 14 C3' XGR A 1 11.470 -13.073 3.433 1.00 63.73 C HETATM 15 O3' XGR A 1 11.949 -12.968 4.744 1.00 62.65 O HETATM 16 C4' XGR A 1 9.965 -13.072 3.555 1.00 68.56 C HETATM 17 C5' XGR A 1 9.471 -11.645 3.819 1.00 73.28 C HETATM 18 O5' XGR A 1 8.857 -11.065 2.659 1.00 76.22 O HETATM 19 C6' XGR A 1 9.321 -13.612 2.306 1.00 66.78 C HETATM 20 C7' XGR A 1 9.976 -14.226 1.337 1.00 62.16 C HETATM 21 P XCR A 2 13.493 -12.749 5.018 1.00 63.70 P HETATM 22 N1 XCR A 2 17.201 -14.312 1.160 1.00 58.19 N HETATM 23 C2 XCR A 2 18.156 -13.936 0.190 1.00 57.53 C HETATM 24 O2 XCR A 2 19.105 -14.698 -0.102 1.00 61.35 O HETATM 25 N3 XCR A 2 18.025 -12.727 -0.422 1.00 53.53 N HETATM 26 C4 XCR A 2 17.009 -11.903 -0.135 1.00 54.60 C HETATM 27 N4 XCR A 2 16.920 -10.725 -0.793 1.00 54.32 N HETATM 28 C5 XCR A 2 16.027 -12.255 0.831 1.00 55.40 C HETATM 29 C6 XCR A 2 16.171 -13.443 1.432 1.00 58.02 C HETATM 30 C1' XCR A 2 17.280 -15.646 1.905 1.00 61.13 C HETATM 31 C2' XCR A 2 18.148 -15.604 3.177 1.00 62.98 C HETATM 32 C3' XCR A 2 17.508 -14.784 4.324 1.00 62.18 C HETATM 33 O3' XCR A 2 18.344 -14.793 5.478 1.00 63.44 O HETATM 34 C4' XCR A 2 16.187 -15.361 4.753 1.00 59.37 C HETATM 35 C5' XCR A 2 15.384 -14.292 5.401 1.00 55.89 C HETATM 36 O5' XCR A 2 14.211 -14.101 4.665 1.00 58.85 O HETATM 37 C6' XCR A 2 15.435 -15.961 3.593 1.00 61.20 C HETATM 38 C7' XCR A 2 15.909 -16.103 2.355 1.00 60.48 C HETATM 39 OP1 XCR A 2 13.677 -12.567 6.468 1.00 69.13 O HETATM 40 OP2 XCR A 2 13.888 -11.727 4.033 1.00 66.16 O HETATM 41 P XGR A 3 19.180 -13.509 5.869 1.00 62.48 P HETATM 42 N1 XGR A 3 22.005 -9.662 -1.190 1.00 46.91 N HETATM 43 C2 XGR A 3 23.031 -10.553 -1.265 1.00 51.10 C HETATM 44 N2 XGR A 3 23.992 -10.289 -2.182 1.00 54.36 N HETATM 45 N3 XGR A 3 23.126 -11.625 -0.502 1.00 49.00 N HETATM 46 C4 XGR A 3 22.105 -11.735 0.353 1.00 48.98 C HETATM 47 C5 XGR A 3 21.039 -10.901 0.482 1.00 45.34 C HETATM 48 C6 XGR A 3 20.952 -9.773 -0.335 1.00 46.72 C HETATM 49 O6 XGR A 3 20.075 -8.904 -0.373 1.00 52.70 O HETATM 50 N7 XGR A 3 20.174 -11.359 1.469 1.00 48.54 N HETATM 51 C8 XGR A 3 20.747 -12.460 1.910 1.00 51.98 C HETATM 52 N9 XGR A 3 21.937 -12.764 1.285 1.00 55.07 N HETATM 53 C1' XGR A 3 22.849 -13.925 1.523 1.00 60.04 C HETATM 54 C2' XGR A 3 23.781 -13.706 2.714 1.00 62.30 C HETATM 55 C3' XGR A 3 23.048 -13.700 4.058 1.00 61.95 C HETATM 56 O3' XGR A 3 24.050 -13.573 5.040 1.00 64.66 O HETATM 57 C4' XGR A 3 22.376 -15.051 4.302 1.00 63.44 C HETATM 58 C5' XGR A 3 21.202 -14.989 5.274 1.00 59.34 C HETATM 59 O5' XGR A 3 20.564 -13.745 5.131 1.00 58.56 O HETATM 60 C6' XGR A 3 21.905 -15.695 3.010 1.00 66.22 C HETATM 61 C7' XGR A 3 22.106 -15.206 1.786 1.00 63.29 C HETATM 62 OP1 XGR A 3 19.555 -13.613 7.289 1.00 69.68 O HETATM 63 OP2 XGR A 3 18.496 -12.322 5.300 1.00 62.47 O HETATM 64 C4' XTR A 4 27.668 -11.206 3.220 1.00 63.14 C HETATM 65 C7' XTR A 4 26.476 -11.073 0.982 1.00 59.27 C HETATM 66 C6' XTR A 4 26.947 -11.776 2.013 1.00 64.09 C HETATM 67 C1' XTR A 4 26.584 -9.584 0.802 1.00 57.16 C HETATM 68 O4 XTR A 4 21.735 -7.231 1.679 1.00 54.71 O HETATM 69 C4 XTR A 4 22.819 -7.767 1.496 1.00 48.66 C HETATM 70 C5 XTR A 4 23.265 -8.856 2.284 1.00 44.25 C HETATM 71 C5M XTR A 4 22.412 -9.385 3.380 1.00 43.01 C HETATM 72 C6 XTR A 4 24.441 -9.395 2.033 1.00 46.58 C HETATM 73 N3 XTR A 4 23.681 -7.355 0.526 1.00 50.34 N HETATM 74 C2 XTR A 4 24.892 -7.894 0.253 1.00 49.42 C HETATM 75 O2 XTR A 4 25.580 -7.456 -0.641 1.00 53.50 O HETATM 76 N1 XTR A 4 25.265 -8.941 1.036 1.00 50.50 N HETATM 77 C2' XTR A 4 27.651 -9.087 1.767 1.00 60.89 C HETATM 78 C3' XTR A 4 27.544 -9.691 3.174 1.00 63.14 C HETATM 79 P XTR A 4 24.684 -12.199 5.550 1.00 65.66 P HETATM 80 OP1 XTR A 4 25.573 -12.582 6.652 1.00 69.90 O HETATM 81 OP2 XTR A 4 23.631 -11.184 5.731 1.00 62.83 O HETATM 82 O5' XTR A 4 25.654 -11.678 4.412 1.00 63.45 O HETATM 83 C5' XTR A 4 27.061 -11.798 4.482 1.00 61.48 C HETATM 84 O3' XTR A 4 28.534 -9.109 3.989 1.00 64.70 O HETATM 85 O1P XAR A 5 26.741 -7.837 5.186 1.00 64.19 O HETATM 86 P XAR A 5 28.185 -7.962 5.006 1.00 62.43 P HETATM 87 O2P XAR A 5 29.136 -8.196 6.092 1.00 63.69 O HETATM 88 O5' XAR A 5 28.569 -6.677 4.167 1.00 60.21 O HETATM 89 C5' XAR A 5 29.915 -6.421 3.827 1.00 59.46 C HETATM 90 C4' XAR A 5 29.977 -5.353 2.763 1.00 58.51 C HETATM 91 C3' XAR A 5 29.102 -4.190 3.169 1.00 57.68 C HETATM 92 O3' XAR A 5 29.868 -3.430 4.071 1.00 60.15 O HETATM 93 C2' XAR A 5 28.692 -3.325 1.979 1.00 56.39 C HETATM 94 C1' XAR A 5 27.822 -4.127 1.001 1.00 55.19 C HETATM 95 C7' XAR A 5 28.506 -5.450 0.764 1.00 58.64 C HETATM 96 C6' XAR A 5 29.462 -5.984 1.514 1.00 59.26 C HETATM 97 N9 XAR A 5 26.439 -4.327 1.491 1.00 53.08 N HETATM 98 C8 XAR A 5 25.998 -5.188 2.462 1.00 50.20 C HETATM 99 N7 XAR A 5 24.711 -5.097 2.684 1.00 49.76 N HETATM 100 C5 XAR A 5 24.272 -4.134 1.797 1.00 47.85 C HETATM 101 C4 XAR A 5 25.311 -3.654 1.062 1.00 49.70 C HETATM 102 N3 XAR A 5 25.245 -2.712 0.108 1.00 52.67 N HETATM 103 C6 XAR A 5 23.009 -3.588 1.524 1.00 49.73 C HETATM 104 N6 XAR A 5 21.893 -3.947 2.143 1.00 51.52 N HETATM 105 N1 XAR A 5 22.900 -2.643 0.586 1.00 50.81 N HETATM 106 C2 XAR A 5 24.001 -2.268 -0.058 1.00 50.50 C HETATM 107 P XGR A 6 29.207 -2.611 5.254 1.00 57.89 P HETATM 108 N1 XGR A 6 20.986 0.095 2.821 1.00 45.96 N HETATM 109 C2 XGR A 6 21.622 1.125 2.203 1.00 43.12 C HETATM 110 N2 XGR A 6 20.849 2.049 1.660 1.00 44.61 N HETATM 111 N3 XGR A 6 22.914 1.241 2.151 1.00 42.73 N HETATM 112 C4 XGR A 6 23.528 0.208 2.757 1.00 45.71 C HETATM 113 C5 XGR A 6 22.990 -0.871 3.359 1.00 43.83 C HETATM 114 C6 XGR A 6 21.615 -0.977 3.417 1.00 46.16 C HETATM 115 O6 XGR A 6 20.950 -1.877 3.934 1.00 50.05 O HETATM 116 N7 XGR A 6 23.965 -1.714 3.870 1.00 48.12 N HETATM 117 C8 XGR A 6 25.088 -1.148 3.551 1.00 49.05 C HETATM 118 N9 XGR A 6 24.896 0.032 2.870 1.00 52.05 N HETATM 119 C1' XGR A 6 25.921 0.946 2.370 1.00 54.85 C HETATM 120 C2' XGR A 6 26.304 1.903 3.513 1.00 55.95 C HETATM 121 C3' XGR A 6 27.231 1.252 4.542 1.00 55.21 C HETATM 122 O3' XGR A 6 27.619 2.179 5.527 1.00 56.40 O HETATM 123 C4' XGR A 6 28.511 0.872 3.891 1.00 54.22 C HETATM 124 C5' XGR A 6 29.182 -0.089 4.816 1.00 53.84 C HETATM 125 O5' XGR A 6 28.695 -1.349 4.471 1.00 52.70 O HETATM 126 C6' XGR A 6 28.239 0.143 2.610 1.00 56.74 C HETATM 127 C7' XGR A 6 27.109 0.161 1.929 1.00 54.52 C HETATM 128 OP1 XGR A 6 30.251 -2.106 6.151 1.00 62.02 O HETATM 129 OP2 XGR A 6 28.068 -3.373 5.765 1.00 58.36 O HETATM 130 P XCR A 7 27.031 2.071 6.977 1.00 52.44 P HETATM 131 N1 XCR A 7 21.657 2.552 5.695 1.00 54.05 N HETATM 132 C2 XCR A 7 20.309 2.218 5.756 1.00 54.89 C HETATM 133 O2 XCR A 7 19.471 3.031 5.349 1.00 57.26 O HETATM 134 N3 XCR A 7 19.971 1.019 6.270 1.00 53.86 N HETATM 135 C4 XCR A 7 20.924 0.193 6.714 1.00 54.66 C HETATM 136 N4 XCR A 7 20.601 -0.999 7.229 1.00 57.50 N HETATM 137 C5 XCR A 7 22.275 0.521 6.668 1.00 51.51 C HETATM 138 C6 XCR A 7 22.582 1.691 6.161 1.00 52.77 C HETATM 139 C1' XCR A 7 22.094 3.870 5.152 1.00 54.29 C HETATM 140 C2' XCR A 7 22.201 4.887 6.303 1.00 56.58 C HETATM 141 C3' XCR A 7 23.453 4.729 7.163 1.00 54.42 C HETATM 142 O3' XCR A 7 23.451 5.707 8.190 1.00 56.81 O HETATM 143 C4' XCR A 7 24.692 4.944 6.305 1.00 54.18 C HETATM 144 C5' XCR A 7 25.899 4.356 7.003 1.00 52.44 C HETATM 145 O5' XCR A 7 25.773 2.964 6.937 1.00 52.07 O HETATM 146 C6' XCR A 7 24.571 4.248 4.970 1.00 55.85 C HETATM 147 C7' XCR A 7 23.438 3.762 4.462 1.00 56.00 C HETATM 148 OP1 XCR A 7 27.954 2.735 7.871 1.00 58.40 O HETATM 149 OP2 XCR A 7 26.539 0.707 7.130 1.00 52.60 O HETATM 150 P XGR A 8 22.631 5.525 9.531 1.00 55.58 P HETATM 151 N1 XGR A 8 15.761 0.258 9.690 1.00 63.24 N HETATM 152 C2 XGR A 8 14.955 1.335 9.393 1.00 62.35 C HETATM 153 N2 XGR A 8 13.654 1.103 9.455 1.00 64.20 N HETATM 154 N3 XGR A 8 15.398 2.547 9.076 1.00 60.34 N HETATM 155 C4 XGR A 8 16.755 2.586 9.053 1.00 57.26 C HETATM 156 C5 XGR A 8 17.641 1.566 9.320 1.00 57.38 C HETATM 157 C6 XGR A 8 17.168 0.284 9.681 1.00 61.96 C HETATM 158 O6 XGR A 8 17.854 -0.739 9.964 1.00 61.70 O HETATM 159 N7 XGR A 8 18.942 1.997 9.184 1.00 55.20 N HETATM 160 C8 XGR A 8 18.828 3.241 8.845 1.00 53.66 C HETATM 161 N9 XGR A 8 17.547 3.672 8.754 1.00 54.33 N HETATM 162 C1' XGR A 8 17.148 5.001 8.346 1.00 56.79 C HETATM 163 C2' XGR A 8 16.975 5.975 9.510 1.00 58.81 C HETATM 164 C3' XGR A 8 18.307 6.450 10.080 1.00 58.49 C HETATM 165 O3' XGR A 8 18.043 7.361 11.122 1.00 61.33 O HETATM 166 C4' XGR A 8 19.176 7.144 9.043 1.00 54.84 C HETATM 167 C5' XGR A 8 20.615 7.174 9.515 1.00 53.16 C HETATM 168 O5' XGR A 8 21.182 5.953 9.122 1.00 54.32 O HETATM 169 C6' XGR A 8 19.103 6.414 7.732 1.00 55.32 C HETATM 170 C7' XGR A 8 18.220 5.479 7.409 1.00 54.86 C HETATM 171 OP1 XGR A 8 23.021 6.551 10.483 1.00 55.87 O HETATM 172 OP2 XGR A 8 22.556 4.085 9.781 1.00 55.96 O HETATM 173 P XGR A 9 18.449 6.941 12.593 1.00 61.45 P HETATM 174 O5' XGR A 9 17.934 8.242 13.377 1.00 63.46 O HETATM 175 OP1 XGR A 9 19.913 6.876 12.749 1.00 58.41 O HETATM 176 OP2 XGR A 9 17.513 5.881 12.958 1.00 62.25 O TER 177 XGR A 9