HEADER DNA 27-NOV-01 1KGK TITLE DIRECT OBSERVATION OF A CYTOSINE ANALOG THAT FORMS FIVE HYDROGEN BONDS TITLE 2 TO GUANOSINE; GUANYL G-CLAMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*(GCK)P*GP*TP*AP*TP*AP*CP*GP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID PHASE CHEMICAL SYNTHESIS. KEYWDS A-FORM DOUBLE HELIX, CYTOSINE ANALOGUE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR C.J.WILDS,M.A.MAIER,V.TERESHKO,M.MANOHARAN,M.EGLI REVDAT 4 14-FEB-24 1KGK 1 REMARK LINK REVDAT 3 24-FEB-09 1KGK 1 VERSN REVDAT 2 04-JAN-02 1KGK 1 JRNL REVDAT 1 21-DEC-01 1KGK 0 JRNL AUTH C.J.WILDS,M.A.MAIER,V.TERESHKO,M.MANOHARAN,M.EGLI JRNL TITL DIRECT OBSERVATION OF A CYTOSINE ANALOGUE THAT FORMS FIVE JRNL TITL 2 HYDROGEN BONDS TO GUANOSINE: GUANIDINO G-CLAMP JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 41 115 2002 JRNL REFN ESSN 0570-0833 JRNL PMID 12491456 JRNL DOI 10.1002/1521-3773(20020104)41:1<115::AID-ANIE115>3.0.CO;2-R REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.128 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 27320 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.126 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 26023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 432 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 155 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 608.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 283.50 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 5528 REMARK 3 NUMBER OF RESTRAINTS : 26595 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.021 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.222 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.055 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KGK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000014933. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-00 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27320 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04700 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) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 MM DNA, 5% MPD, 20 MM SODIUM REMARK 280 CACODYLATE, 40 MM SODIUM CHLORIDE, 6 MM POTASSIUM CHLORIDE, 10 REMARK 280 MM MAGNESIUM CHLORIDE; EQUILIBRATED AGAINST 35% MPD, PH 6.0, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 12.26000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.34000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.34000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.26000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.51000 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: DIMERIC 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 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 HO5' DG A 1 O HOH A 1317 1.53 REMARK 500 O HOH B 1241 O HOH B 1375 1.66 REMARK 500 O HOH A 1310 O HOH A 1352 1.73 REMARK 500 O HOH B 1314 O HOH B 1315 1.82 REMARK 500 O5' DG A 1 O HOH A 1317 2.10 REMARK 500 N1 SPK A 221 O HOH A 1354 2.11 REMARK 500 O HOH B 1288 O HOH B 1307 2.15 REMARK 500 O HOH B 1313 O HOH B 1335 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 H1C SPK A 221 O HOH A 1329 1455 1.60 REMARK 500 O HOH A 1316 O HOH B 1255 3545 2.11 REMARK 500 O HOH A 1333 O HOH B 1276 3555 2.17 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 A 1 C3' DG A 1 C2' -0.049 REMARK 500 DG A 1 C2' DG A 1 C1' -0.099 REMARK 500 DG A 3 C2' DG A 3 C1' -0.109 REMARK 500 DT A 4 C2' DT A 4 C1' -0.104 REMARK 500 DT A 4 O4' DT A 4 C1' 0.085 REMARK 500 DA A 7 O3' DC A 8 P -0.085 REMARK 500 DG A 9 C2' DG A 9 C1' -0.065 REMARK 500 DG B 111 C3' DG B 111 C2' -0.049 REMARK 500 DG B 111 C2' DG B 111 C1' -0.109 REMARK 500 DG B 111 O4' DG B 111 C1' 0.101 REMARK 500 DA B 115 C2' DA B 115 C1' -0.092 REMARK 500 DT B 116 C2' DT B 116 C1' -0.066 REMARK 500 DG B 119 C2' DG B 119 C1' -0.084 REMARK 500 DC B 120 C3' DC B 120 C2' -0.049 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 A 1 O4' - C1' - C2' ANGL. DEV. = 3.5 DEGREES REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = -6.6 DEGREES REMARK 500 DG A 3 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DG A 3 O4' - C1' - C2' ANGL. DEV. = 5.4 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = -7.1 DEGREES REMARK 500 DT A 4 O4' - C1' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT A 6 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DC A 8 O5' - P - OP2 ANGL. DEV. = -8.6 DEGREES REMARK 500 DG B 111 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 DG B 111 O4' - C1' - C2' ANGL. DEV. = 4.2 DEGREES REMARK 500 DG B 111 O4' - C1' - N9 ANGL. DEV. = -8.3 DEGREES REMARK 500 DG B 113 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DA B 117 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DG B 119 O4' - C1' - C2' ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MOE A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MOE B 316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPK A 221 DBREF 1KGK A 1 10 PDB 1KGK 1KGK 1 10 DBREF 1KGK B 111 120 PDB 1KGK 1KGK 111 120 SEQRES 1 A 10 DG GCK DG DT DA DT DA DC DG DC SEQRES 1 B 10 DG GCK DG DT DA DT DA DC DG DC MODRES 1KGK GCK A 2 DC MODRES 1KGK GCK B 112 DC HET GCK A 2 54 HET GCK B 112 54 HET MOE A 306 12 HET SPK A 221 44 HET MOE B 316 12 HETNAM GCK PHOSPHORIC ACID 9-(2-GUANIDINOETHOXY-3-(2-DEOXY-BETA-D- HETNAM 2 GCK ERYTHROPENTOFURANOSYL))-3H-PYRIMIDO-[5,4-B][1,4]- HETNAM 3 GCK BENZOOXAZIN-2-ONE]-5'-ESTER HETNAM MOE METHOXY-ETHOXYL HETNAM SPK SPERMINE (FULLY PROTONATED FORM) FORMUL 1 GCK 2(C18 H24 N6 O9 P 1+) FORMUL 3 MOE 2(C3 H7 O2 1-) FORMUL 4 SPK C10 H30 N4 4+ FORMUL 6 HOH *155(H2 O) LINK O3' DG A 1 P GCK A 2 1555 1555 1.56 LINK O3' GCK A 2 P DG A 3 1555 1555 1.58 LINK C2' DT A 6 O2' MOE A 306 1555 1555 1.41 LINK O3' DG B 111 P GCK B 112 1555 1555 1.54 LINK O3' GCK B 112 P DG B 113 1555 1555 1.59 LINK C2' DT B 116 O2' MOE B 316 1555 1555 1.45 SITE 1 AC1 3 DG A 1 DT A 6 DA A 7 SITE 1 AC2 4 GCK A 2 DT B 116 DA B 117 HOH B1255 SITE 1 AC3 12 GCK A 2 HOH A1204 HOH A1206 HOH A1230 SITE 2 AC3 12 HOH A1262 HOH A1329 HOH A1354 DA B 115 SITE 3 AC3 12 DT B 116 HOH B1215 HOH B1299 HOH B1373 CRYST1 24.520 43.020 46.680 90.00 90.00 90.00 P 21 21 21 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 0.040783 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023245 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021422 0.00000