HEADER DNA 19-OCT-16 5M4W TITLE STRUCTURE OF DNA AGCGA-QUADRUPLEX ADOPTED BY 15-MER OLIGONUCLEOTIDE TITLE 2 FOUND IN REGULATORY REGION OF THE PLEKHG3 HUMAN GENE WITH G11 TO I11 TITLE 3 MUTATION, D(GCGAGGGAGCIAGGG),VK34_I11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*IP*AP*GP*GP*G)- COMPND 3 3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS AGCGA-QUADRUPLEX, AGCGA-QUADRUPLEX FAMILY, G-G N1-CARBONIYL SYMMETRIC KEYWDS 2 BASE PAIR, PLEKHG3 GENE, DNA, INOSINE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR V.KOCMAN,J.PLAVEC REVDAT 3 08-MAY-19 5M4W 1 REMARK REVDAT 2 14-FEB-18 5M4W 1 REMARK REVDAT 1 31-MAY-17 5M4W 0 JRNL AUTH V.KOCMAN,J.PLAVEC JRNL TITL TETRAHELICAL STRUCTURAL FAMILY ADOPTED BY AGCGA-RICH JRNL TITL 2 REGULATORY DNA REGIONS. JRNL REF NAT COMMUN V. 8 15355 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 28513602 JRNL DOI 10.1038/NCOMMS15355 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5M4W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001831. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM DNA (5' REMARK 210 -D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*IP*AP*GP*GP*G)-3'), 100 MM REMARK 210 LICL, 90% H2O/10% D2O; 1 MM RESIDUE SPECIFIC 15N LABELED DNA (5'- REMARK 210 D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*IP*AP*GP*GP*G)-3'), 100 MM LICL, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 1D 1H-15N HSQC; REMARK 210 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : UNIFORM NMR SYSTEM REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 B 1 OP2 DC B 2 1.59 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 1 DG A 5 C5' DG A 5 C4' 0.044 REMARK 500 2 DG A 5 C5' DG A 5 C4' 0.044 REMARK 500 4 DG A 5 C5' DG A 5 C4' 0.043 REMARK 500 5 DG A 5 C5' DG A 5 C4' 0.044 REMARK 500 6 DG A 5 C5' DG A 5 C4' 0.044 REMARK 500 9 DG A 5 C5' DG A 5 C4' 0.044 REMARK 500 10 DG A 5 C5' DG A 5 C4' 0.047 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 1 DG A 1 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 2 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 3 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 4 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 6 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG A 6 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA A 8 C4 - C5 - C6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA A 8 C5 - C6 - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DA A 8 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 10 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 10 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DA A 12 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 12 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 12 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 12 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG B 1 O4' - C4' - C3' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG B 1 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 1 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC B 2 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC B 2 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC B 2 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG B 3 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 4 O4' - C1' - N9 ANGL. DEV. = 10.0 DEGREES REMARK 500 1 DA B 4 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA B 4 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA B 4 N1 - C6 - N6 ANGL. DEV. = -6.7 DEGREES REMARK 500 1 DG B 5 O4' - C4' - C3' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 5 C1' - O4' - C4' ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DG B 5 O4' - C1' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG B 5 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG B 5 N1 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DG B 6 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG B 7 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DA B 8 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA B 8 C4 - C5 - C6 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DA B 8 C5 - C6 - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DA B 8 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 582 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DG A 6 0.10 SIDE CHAIN REMARK 500 1 DI A 11 0.16 SIDE CHAIN REMARK 500 1 DC B 2 0.09 SIDE CHAIN REMARK 500 1 DA B 4 0.05 SIDE CHAIN REMARK 500 1 DG B 5 0.11 SIDE CHAIN REMARK 500 1 DG B 6 0.06 SIDE CHAIN REMARK 500 1 DG B 9 0.09 SIDE CHAIN REMARK 500 1 DI B 11 0.06 SIDE CHAIN REMARK 500 1 DG B 14 0.06 SIDE CHAIN REMARK 500 2 DG A 3 0.06 SIDE CHAIN REMARK 500 2 DG A 5 0.04 SIDE CHAIN REMARK 500 2 DG A 6 0.09 SIDE CHAIN REMARK 500 2 DG A 7 0.09 SIDE CHAIN REMARK 500 2 DI A 11 0.14 SIDE CHAIN REMARK 500 2 DG A 14 0.05 SIDE CHAIN REMARK 500 2 DG B 5 0.13 SIDE CHAIN REMARK 500 2 DG B 6 0.06 SIDE CHAIN REMARK 500 2 DI B 11 0.08 SIDE CHAIN REMARK 500 2 DG B 13 0.07 SIDE CHAIN REMARK 500 2 DG B 14 0.07 SIDE CHAIN REMARK 500 2 DG B 15 0.05 SIDE CHAIN REMARK 500 3 DG A 5 0.06 SIDE CHAIN REMARK 500 3 DG A 6 0.09 SIDE CHAIN REMARK 500 3 DG A 7 0.09 SIDE CHAIN REMARK 500 3 DG A 9 0.06 SIDE CHAIN REMARK 500 3 DI A 11 0.08 SIDE CHAIN REMARK 500 3 DG B 3 0.08 SIDE CHAIN REMARK 500 3 DG B 5 0.16 SIDE CHAIN REMARK 500 3 DG B 6 0.09 SIDE CHAIN REMARK 500 3 DG B 9 0.09 SIDE CHAIN REMARK 500 3 DI B 11 0.11 SIDE CHAIN REMARK 500 4 DG A 3 0.05 SIDE CHAIN REMARK 500 4 DG A 6 0.07 SIDE CHAIN REMARK 500 4 DG A 7 0.09 SIDE CHAIN REMARK 500 4 DI A 11 0.16 SIDE CHAIN REMARK 500 4 DG A 13 0.06 SIDE CHAIN REMARK 500 4 DG A 14 0.06 SIDE CHAIN REMARK 500 4 DG A 15 0.07 SIDE CHAIN REMARK 500 4 DA B 4 0.07 SIDE CHAIN REMARK 500 4 DG B 5 0.12 SIDE CHAIN REMARK 500 4 DG B 6 0.07 SIDE CHAIN REMARK 500 4 DG B 9 0.10 SIDE CHAIN REMARK 500 4 DI B 11 0.06 SIDE CHAIN REMARK 500 4 DG B 13 0.06 SIDE CHAIN REMARK 500 5 DG A 3 0.06 SIDE CHAIN REMARK 500 5 DG A 6 0.09 SIDE CHAIN REMARK 500 5 DG A 7 0.09 SIDE CHAIN REMARK 500 5 DI A 11 0.10 SIDE CHAIN REMARK 500 5 DG B 5 0.07 SIDE CHAIN REMARK 500 5 DG B 6 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 107 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34056 RELATED DB: BMRB REMARK 900 STRUCTURE OF DNA AGCGA-QUADRUPLEX ADOPTED BY 15-MER OLIGONUCLEOTIDE REMARK 900 FOUND IN REGULATORY REGION OF THE PLEKHG3 HUMAN GENE WITH G11 TO REMARK 900 I11 MUTATION, D(GCGAGGGAGCIAGGG),VK34_I11 DBREF 5M4W A 1 15 PDB 5M4W 5M4W 1 15 DBREF 5M4W B 1 15 PDB 5M4W 5M4W 1 15 SEQRES 1 A 15 DG DC DG DA DG DG DG DA DG DC DI DA DG SEQRES 2 A 15 DG DG SEQRES 1 B 15 DG DC DG DA DG DG DG DA DG DC DI DA DG SEQRES 2 B 15 DG DG CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1