PDB Short entry for 1QYL HEADER DNA 11-SEP-03 1QYL TITLE GCATGCT + VANADIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*AP*TP*GP*CP*T)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS QUADRUPLEX DNA, DNA EXPDTA X-RAY DIFFRACTION AUTHOR C.J.CARDIN,Y.GAN,J.H.THORPE,S.C.M.TEIXEIRA,B.C.GALE,M.I.A.MORAES REVDAT 4 03-APR-24 1QYL 1 REMARK REVDAT 3 14-FEB-24 1QYL 1 REMARK LINK REVDAT 2 24-FEB-09 1QYL 1 VERSN REVDAT 1 21-OCT-03 1QYL 0 JRNL AUTH C.J.CARDIN,Y.GAN,J.H.THORPE,S.C.M.TEIXEIRA,B.C.GALE, JRNL AUTH 2 M.I.A.MORAES JRNL TITL METAL ION DISTRIBUTION AND STABILISATION OF THE DNA JRNL TITL 2 QUADRUPLEX STRUCTURE FORMED BY D(GCATGCT) JRNL REF TO BE PUBLISHED JRNL REFN 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) : 5.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.149 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.149 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 3.700 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 311 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.149 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 266 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 8224 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 140 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 180.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1655 REMARK 3 NUMBER OF RESTRAINTS : 1425 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.023 REMARK 3 ANGLE DISTANCES (A) : 0.042 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.004 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.013 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.033 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) REMARK 4 REMARK 4 1QYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000020227. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8416 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8848 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 5.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.1000 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) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.14700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 12.63 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: XTALVIEW REMARK 200 STARTING MODEL: NDB ENTRY UDG028 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NACACODYLATE, VANADIUM CHLORIDE, REMARK 280 SODIUM CHLORIDE, MPD, PH 5.7, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 11.26600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.23450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 11.26600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.23450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 11.26600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 29.23450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 11.26600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 29.23450 REMARK 290 SMTRY3 8 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 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 -1.000000 0.000000 0.000000 22.53200 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 22.53200 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 V V A 8 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 100 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 103 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 119 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 124 LIES ON A SPECIAL POSITION. 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 O4' DG A 1 C1' 0.084 REMARK 500 DT A 4 C2 DT A 4 N3 -0.057 REMARK 500 DT A 4 N3 DT A 4 C4 -0.048 REMARK 500 DG A 5 O4' DG A 5 C1' 0.081 REMARK 500 DG A 5 N7 DG A 5 C8 -0.038 REMARK 500 DC A 6 N1 DC A 6 C6 -0.039 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 O5' - C5' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC A 2 N3 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT A 4 C6 - N1 - C2 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG A 5 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC A 6 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DC A 6 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 DT A 7 N1 - C2 - N3 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT A 7 C2 - N3 - C4 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT A 7 N1 - C2 - O2 ANGL. DEV. = -7.0 DEGREES REMARK 500 DT A 7 N3 - C4 - O4 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT A 7 C4 - C5 - C7 ANGL. DEV. = 12.0 DEGREES REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -13.8 DEGREES 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 V A 8 V REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 103 O REMARK 620 2 HOH A 103 O 180.0 REMARK 620 3 HOH A 103 O 180.0 0.0 REMARK 620 4 HOH A 103 O 0.0 180.0 180.0 REMARK 620 5 HOH A 108 O 75.5 104.5 104.5 75.5 REMARK 620 6 HOH A 108 O 104.5 75.5 75.5 104.5 29.5 REMARK 620 7 HOH A 108 O 104.5 75.5 75.5 104.5 174.3 151.1 REMARK 620 8 HOH A 108 O 75.5 104.5 104.5 75.5 151.1 174.3 29.5 REMARK 620 9 HOH A 124 O 90.0 90.0 90.0 90.0 87.1 92.9 87.1 92.9 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE V A 8 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QYK RELATED DB: PDB REMARK 900 GCATGCT + BARIUM REMARK 900 RELATED ID: 1QZL RELATED DB: PDB REMARK 900 GCATGCT + COBALT REMARK 900 RELATED ID: 1R2O RELATED DB: PDB REMARK 900 GCATGCT + NI2+ DBREF 1QYL A 1 7 PDB 1QYL 1QYL 1 7 SEQRES 1 A 7 DG DC DA DT DG DC DT HET V A 8 1 HETNAM V VANADIUM ION FORMUL 2 V V 3+ FORMUL 3 HOH *45(H2 O) LINK V V A 8 O HOH A 103 1555 1555 2.23 LINK V V A 8 O HOH A 103 1555 3555 2.23 LINK V V A 8 O HOH A 103 1555 4555 2.23 LINK V V A 8 O HOH A 103 1555 2555 2.23 LINK V V A 8 O HOH A 108 1555 1555 2.10 LINK V V A 8 O HOH A 108 1555 3555 2.10 LINK V V A 8 O HOH A 108 1555 4555 2.10 LINK V V A 8 O HOH A 108 1555 2555 2.10 LINK V V A 8 O HOH A 124 1555 1555 2.12 LINK V V A 8 O HOH A 124 1555 2555 2.12 LINK V V A 8 O HOH A 124 1555 3555 2.12 LINK V V A 8 O HOH A 124 1555 4555 2.12 SITE 1 AC1 3 HOH A 103 HOH A 108 HOH A 124 CRYST1 22.532 58.469 24.148 90.00 90.00 90.00 C 2 2 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 0.044381 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017103 0.000000 0.00000 SCALE3 0.000000 0.000000 0.041411 0.00000