HEADER DNA 26-AUG-12 4B8D TITLE TENSEGRITY TRIANGLE FROM ENZYMATICALLY MANUFACTURED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*DGP COMPND 3 *GP*AP*CP*AP*TP*CP*A)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*CP*GP*TP*AP*CP*AP)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*GP*GP*CP*TP*GP*CP)-3'; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP)-3'; COMPND 16 CHAIN: D; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 OTHER_DETAILS: SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE - SOURCE 7 ENZYMATICALLY PRODUCED; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 OTHER_DETAILS: SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE - SOURCE 14 ENZYMATICALLY PRODUCED; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 20 OTHER_DETAILS: SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE - SOURCE 21 ENZYMATICALLY PRODUCED; SOURCE 22 MOL_ID: 4; SOURCE 23 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 24 ORGANISM_TAXID: 32630; SOURCE 25 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 26 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 27 OTHER_DETAILS: SINGLE STRANDED MONOCLONAL DNA OLIGONUCLEOTIDE - SOURCE 28 ENZYMATICALLY PRODUCED KEYWDS DNA, ROLLING CIRCLE AMPLIFICATION, DNA ORIGAMI EXPDTA X-RAY DIFFRACTION AUTHOR C.DUCANI,C.D.KAUL,M.MOCHE,W.M.SHIH,B.HOGBERG REVDAT 5 20-DEC-23 4B8D 1 REMARK REVDAT 4 30-OCT-19 4B8D 1 REMARK LINK REVDAT 3 10-JUL-13 4B8D 1 JRNL REVDAT 2 12-JUN-13 4B8D 1 JRNL REVDAT 1 05-JUN-13 4B8D 0 JRNL AUTH C.DUCANI,C.D.KAUL,M.MOCHE,W.M.SHIH,B.HOGBERG JRNL TITL ENZYMATIC PRODUCTION OF 'MONOCLONAL STOICHIOMETRIC' JRNL TITL 2 SINGLE-STRANDED DNA OLIGONUCLEOTIDES JRNL REF NAT.METHODS V. 10 647 2013 JRNL REFN ISSN 1548-7091 JRNL PMID 23727986 JRNL DOI 10.1038/NMETH.2503 REMARK 2 REMARK 2 RESOLUTION. 4.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 1980 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) : 0.185 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.340 REMARK 3 FREE R VALUE TEST SET COUNT : 185 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 4.79 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 5.36 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 558 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2475 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 509 REMARK 3 BIN R VALUE (WORKING SET) : 0.2433 REMARK 3 BIN FREE R VALUE : 0.2933 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.78 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 49 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 863 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 273.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 65.61980 REMARK 3 B22 (A**2) : 65.61980 REMARK 3 B33 (A**2) : -131.23960 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.672 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.644 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.871 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.874 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 988 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1517 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 514 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 42 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 988 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 130 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1014 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 2.46 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL REMARK 3 OTHER TORSION ANGLES (DEGREES) : 29.75 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IDEAL-DIST CONTACT TERM CONTACT SETUP. REMARK 3 RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=0. NUMBER OF REMARK 3 ATOMS WITH PROPER CCP4 ATOM TYPE=861. NUMBER WITH APPROX DEFAULT REMARK 3 CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2. REMARK 4 REMARK 4 4B8D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1290053887. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-12 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1980 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.790 REMARK 200 RESOLUTION RANGE LOW (A) : 42.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 5.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3GBI REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 85.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 8.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 53.21850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.72572 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.71800 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 53.21850 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 30.72572 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 31.71800 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 53.21850 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 30.72572 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.71800 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.45143 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 63.43600 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 61.45143 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 63.43600 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 61.45143 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 63.43600 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 THE STRUCTURE UNIT IS GENERATED FROM 7 DNA STRANDS WHICH FORM REMARK 400 A NETWORK UNIT WITH INTERNAL 3-FOLD SYMMETRY. EXTENDING OF THE REMARK 400 STRUCTURE UNIT IN 3-D SPACE RESULTS THE CRYSTAL AT R3 SPACE REMARK 400 GROUP (REPRESENTED AS H3). THE DNA SEQUENCES OF THE 7 STRANDS REMARK 400 ARE: REMARK 400 (#1) 3 STRANDS REMARK 400 5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP REMARK 400 *CP*A)-3' REMARK 400 REMARK 400 (#2) 1 STRAND REMARK 400 5'-D(*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP* REMARK 400 CP*G)-3' REMARK 400 REMARK 400 (#3) 3 STRANDS REMARK 400 5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3' REMARK 400 REMARK 400 THE ASYMMETRIC UNIT IS COMPRISED OF ONE FULL #1 STRAND (CHAIN A), REMARK 400 7-RESIDUE REPEATING UNIT OF #2 STRAND (CHAIN B) AND TWO FRAGMENTS REMARK 400 OF #3 STRAND (CHAINS C AND D). REMARK 400 REMARK 400 THE #2 STRAND SELF-ASSOICATES TO FORM A CIRCULAR DNA MOLECULE REMARK 400 WITH INTERNAL 3-FOLD SYMMETRY. IT HAS 3 SYMMETRIC AND SEQUENTIAL REMARK 400 REPEATING UNITS. CHAIN B IN THE ASYMMETRIC UNIT REPRESENTS ONE REMARK 400 OF THESE REPEATING UNITS. REMARK 400 REMARK 400 CHAINS D (FIRST 8 RESIDUES OF STRAND #3) AND C (NEXT 6 RESIDUES REMARK 400 OF STRAND #3) TOGETHER FORM THE THIRD DNA STRAND (#3) OF THE REMARK 400 EXPERIMENT. THIS DNA STRAND SPANS TWO ASYMMETRIC UNITS - HENCE IT REMARK 400 WAS DIVIDED INTO THE CURRENT CHAINS C AND D FOR CONVENIENT REMARK 400 REPRESENTATION. CHAIN C (1_555) IS COVALENTLY LINKED TO REMARK 400 CHAIN D OF ANOTHER ASYMMETRIC UNIT (3_555); AND CHAIN D (1_555) REMARK 400 IS COVALENTLY LINKED TO CHAIN C OF ANOTHER ASYMMETRIC UNIT REMARK 400 (2_555). REMARK 400 REMARK 400 THE SELECTION OF RESIDUES FROM THE DNA #2 AND #3 REMARK 400 ARE DICTATED BY THEIR PROXIMITY (BASE PAIRING) TO CHAIN A. 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 P DC B 119 O3' DA B 125 2555 1.59 REMARK 500 P DG C 209 O3' DT D 108 3555 1.60 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 101 P DG A 101 OP3 -0.124 REMARK 500 DT D 101 P DT D 101 OP3 -0.117 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 101 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 DG A 101 O4' - C4' - C3' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG A 101 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG A 101 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 102 O4' - C1' - N9 ANGL. DEV. = 9.4 DEGREES REMARK 500 DG A 103 O4' - C1' - N9 ANGL. DEV. = 8.0 DEGREES REMARK 500 DG A 103 C3' - O3' - P ANGL. DEV. = 10.2 DEGREES REMARK 500 DC A 104 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DC A 104 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DA A 105 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG A 106 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 106 C3' - O3' - P ANGL. DEV. = 14.1 DEGREES REMARK 500 DC A 107 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 DC A 108 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DC A 108 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DC A 108 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 109 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT A 109 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG A 110 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DT A 111 O4' - C1' - N1 ANGL. DEV. = 11.8 DEGREES REMARK 500 DA A 112 C5' - C4' - C3' ANGL. DEV. = 7.2 DEGREES REMARK 500 DA A 112 C3' - O3' - P ANGL. DEV. = 13.2 DEGREES REMARK 500 DG A 115 C3' - O3' - P ANGL. DEV. = 11.9 DEGREES REMARK 500 DC A 117 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC A 117 O4' - C1' - N1 ANGL. DEV. = 7.6 DEGREES REMARK 500 DA A 118 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 DT A 119 O4' - C1' - C2' ANGL. DEV. = 3.5 DEGREES REMARK 500 DT A 119 C3' - O3' - P ANGL. DEV. = 10.8 DEGREES REMARK 500 DC A 120 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 119 C3' - O3' - P ANGL. DEV. = 10.7 DEGREES REMARK 500 DC B 120 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG B 121 C3' - O3' - P ANGL. DEV. = 13.8 DEGREES REMARK 500 DC B 124 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 124 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DG C 210 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 DC C 211 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES REMARK 500 DC C 211 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 DC C 211 C3' - O3' - P ANGL. DEV. = 11.4 DEGREES REMARK 500 DT C 212 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT C 212 C3' - O3' - P ANGL. DEV. = 10.8 DEGREES REMARK 500 DG C 213 C3' - C2' - C1' ANGL. DEV. = -5.7 DEGREES REMARK 500 DG C 213 O4' - C1' - N9 ANGL. DEV. = 11.0 DEGREES REMARK 500 DG C 213 C3' - O3' - P ANGL. DEV. = 9.7 DEGREES REMARK 500 DC C 214 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT D 101 OP1 - P - OP2 ANGL. DEV. = -10.5 DEGREES REMARK 500 DT D 101 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT D 101 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DC D 102 O4' - C1' - N1 ANGL. DEV. = 13.6 DEGREES REMARK 500 DC D 102 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 DT D 103 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 59 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 4B8D A 101 121 PDB 4B8D 4B8D 101 121 DBREF 4B8D B 119 125 PDB 4B8D 4B8D 119 125 DBREF 4B8D C 209 214 PDB 4B8D 4B8D 209 214 DBREF 4B8D D 101 108 PDB 4B8D 4B8D 101 108 SEQRES 1 A 21 DG DA DG DC DA DG DC DC DT DG DT DA DC SEQRES 2 A 21 DG DG DA DC DA DT DC DA SEQRES 1 B 7 DC DC DG DT DA DC DA SEQRES 1 C 6 DG DG DC DT DG DC SEQRES 1 D 8 DT DC DT DG DA DT DG DT CRYST1 106.437 106.437 95.154 90.00 90.00 120.00 H 3 9 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 0.009395 0.005424 0.000000 0.00000 SCALE2 0.000000 0.010849 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010509 0.00000