HEADER DNA 04-FEB-04 1S9B TITLE CRYSTAL STRUCTURE ANALYSIS OF THE B-DNA GAATTCG COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*AP*AP*TP*TP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DOUBLE HELIX, CUBIC DNA, NICKEL, DNA EXPDTA X-RAY DIFFRACTION AUTHOR N.VALLS,I.USON,C.GOUYETTE,J.A.SUBIRANA REVDAT 6 03-APR-24 1S9B 1 REMARK REVDAT 5 14-FEB-24 1S9B 1 REMARK LINK REVDAT 4 24-FEB-09 1S9B 1 VERSN REVDAT 3 05-OCT-04 1S9B 1 JRNL REVDAT 2 14-SEP-04 1S9B 1 REMARK REVDAT 1 07-SEP-04 1S9B 0 JRNL AUTH N.VALLS,I.USON,C.GOUYETTE,J.A.SUBIRANA JRNL TITL A CUBIC ARRANGEMENT OF DNA DOUBLE HELICES BASED ON JRNL TITL 2 NICKEL-GUANINE INTERACTIONS JRNL REF J.AM.CHEM.SOC. V. 126 7812 2004 JRNL REFN ISSN 0002-7863 JRNL PMID 15212528 JRNL DOI 10.1021/JA049393I REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 1388 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) : 0.281 REMARK 3 R VALUE (WORKING SET) : 0.281 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 69 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) : 2.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 54 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4250 REMARK 3 BIN FREE R VALUE SET COUNT : 3 REMARK 3 BIN FREE R VALUE : 0.8990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 284 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 20 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.150 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.361 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.207 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.090 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.905 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 396 ; 0.019 ; 0.023 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 488 ; 3.124 ; 3.000 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): 42 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 150 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 110 ; 0.231 ; 0.200 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): 14 ; 0.202 ; 0.200 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): 8 ; 0.245 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.078 ; 0.200 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): 35 ; 0.568 ; 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): 325 ; 2.890 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 488 ; 4.730 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 7 0 REMARK 3 1 B 1 B 7 0 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 142 ; 0.07 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 142 ; 0.21 ; 0.50 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: NULL REMARK 4 REMARK 4 1S9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021529. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-02; 10-SEP-02 REMARK 200 TEMPERATURE (KELVIN) : NULL; NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; ESRF REMARK 200 BEAMLINE : BM14; BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000; 1.48475, 1.48563, REMARK 200 1.31155 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1491 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.810 REMARK 200 RESOLUTION RANGE LOW (A) : 22.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09500 REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: IDEAL B-DNA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, NICKEL CHLORIDE, CACODYLATE, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 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 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+1/2 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 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 35.43350 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 35.43350 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 35.43350 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 35.43350 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 35.43350 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 35.43350 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 35.43350 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 35.43350 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 35.43350 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 35.43350 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 35.43350 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 35.43350 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 35.43350 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 35.43350 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 35.43350 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 35.43350 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 35.43350 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 35.43350 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 35.43350 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 35.43350 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 35.43350 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 35.43350 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 35.43350 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 35.43350 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 35.43350 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 35.43350 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 35.43350 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 35.43350 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 35.43350 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 35.43350 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 35.43350 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 35.43350 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 35.43350 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 35.43350 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 35.43350 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 35.43350 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: 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 DA A 2 O3' DA A 2 C3' -0.045 REMARK 500 DA A 3 O3' DA A 3 C3' -0.056 REMARK 500 DT A 4 O3' DT A 4 C3' -0.044 REMARK 500 DA B 2 N3 DA B 2 C4 -0.048 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' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 1 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 2 O5' - C5' - C4' ANGL. DEV. = -9.4 DEGREES REMARK 500 DA A 2 C3' - O3' - P ANGL. DEV. = -8.4 DEGREES REMARK 500 DA A 3 O5' - C5' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DA A 3 O4' - C1' - C2' ANGL. DEV. = -7.9 DEGREES REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = -7.4 DEGREES REMARK 500 DT A 5 C2 - N3 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT A 5 N3 - C4 - O4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 5 C5 - C4 - O4 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC A 6 N3 - C4 - N4 ANGL. DEV. = -6.0 DEGREES REMARK 500 DC A 6 C2 - N1 - C1' ANGL. DEV. = -6.7 DEGREES REMARK 500 DG A 7 C4 - C5 - N7 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG A 7 C5 - N7 - C8 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG A 7 N1 - C6 - O6 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 7 C5 - C6 - O6 ANGL. DEV. = -6.2 DEGREES REMARK 500 DG B 1 C6 - N1 - C2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG B 1 N1 - C6 - O6 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 1 C5 - C6 - O6 ANGL. DEV. = -6.6 DEGREES REMARK 500 DA B 2 O5' - C5' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 DA B 2 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DA B 2 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 DA B 2 C6 - N1 - C2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA B 3 O4' - C1' - C2' ANGL. DEV. = -7.9 DEGREES REMARK 500 DA B 3 O4' - C1' - N9 ANGL. DEV. = -6.9 DEGREES REMARK 500 DT B 4 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 DT B 4 N1 - C2 - N3 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT B 4 C2 - N3 - C4 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT B 4 C5 - C6 - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT B 4 C5 - C4 - O4 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT B 4 C4 - C5 - C7 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC B 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 7 C5 - C6 - O6 ANGL. DEV. = -4.0 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 NI A 101 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 N7 REMARK 620 2 HOH A 102 O 142.3 REMARK 620 3 HOH A 110 O 94.3 84.6 REMARK 620 4 HOH A 111 O 59.5 150.0 71.0 REMARK 620 5 HOH A 112 O 59.7 132.9 142.3 72.1 REMARK 620 6 HOH A 113 O 134.0 82.9 99.5 84.1 84.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 103 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 7 N7 REMARK 620 2 HOH A 109 O 66.2 REMARK 620 3 HOH A 119 O 153.1 129.7 REMARK 620 4 HOH A 120 O 82.4 146.9 83.3 REMARK 620 5 HOH A 121 O 117.1 101.3 83.6 83.2 REMARK 620 6 HOH A 122 O 63.2 83.1 94.7 92.3 175.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 102 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 1 N7 REMARK 620 2 DG B 1 O6 71.8 REMARK 620 3 HOH B 114 O 124.2 54.9 REMARK 620 4 HOH B 115 O 125.4 121.0 97.6 REMARK 620 5 HOH B 116 O 68.0 78.1 84.9 158.2 REMARK 620 6 HOH B 117 O 145.4 138.2 83.4 61.3 97.7 REMARK 620 7 HOH B 118 O 65.9 137.7 163.2 84.0 87.5 82.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 104 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 7 N7 REMARK 620 2 HOH B 101 O 89.6 REMARK 620 3 HOH B 103 O 114.5 83.4 REMARK 620 4 HOH B 123 O 57.8 113.7 159.8 REMARK 620 5 HOH B 124 O 134.8 84.8 109.3 83.9 REMARK 620 6 HOH B 125 O 85.5 162.0 114.4 49.5 86.4 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 NI A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 104 DBREF 1S9B A 1 7 PDB 1S9B 1S9B 1 7 DBREF 1S9B B 1 7 PDB 1S9B 1S9B 1 7 SEQRES 1 A 7 DG DA DA DT DT DC DG SEQRES 1 B 7 DG DA DA DT DT DC DG HET NI A 101 1 HET NI A 103 1 HET NI B 102 1 HET NI B 104 1 HETNAM NI NICKEL (II) ION FORMUL 3 NI 4(NI 2+) FORMUL 7 HOH *20(H2 O) LINK N7 DG A 1 NI NI A 101 1555 1555 2.04 LINK N7 DG A 7 NI NI A 103 1555 1555 2.03 LINK NI NI A 101 O HOH A 102 1555 1555 2.02 LINK NI NI A 101 O HOH A 110 1555 1555 1.97 LINK NI NI A 101 O HOH A 111 1555 1555 1.99 LINK NI NI A 101 O HOH A 112 1555 1555 2.00 LINK NI NI A 101 O HOH A 113 1555 1555 2.02 LINK NI NI A 103 O HOH A 109 1555 1555 2.02 LINK NI NI A 103 O HOH A 119 1555 1555 2.01 LINK NI NI A 103 O HOH A 120 1555 1555 2.03 LINK NI NI A 103 O HOH A 121 1555 1555 2.01 LINK NI NI A 103 O HOH A 122 1555 1555 2.02 LINK N7 DG B 1 NI NI B 102 1555 1555 2.00 LINK O6 DG B 1 NI NI B 102 1555 1555 2.77 LINK N7 DG B 7 NI NI B 104 1555 1555 1.98 LINK O HOH B 101 NI NI B 104 1555 1555 2.01 LINK NI NI B 102 O HOH B 114 1555 1555 2.01 LINK NI NI B 102 O HOH B 115 1555 1555 2.00 LINK NI NI B 102 O HOH B 116 1555 1555 1.99 LINK NI NI B 102 O HOH B 117 1555 1555 2.03 LINK NI NI B 102 O HOH B 118 1555 1555 2.03 LINK O HOH B 103 NI NI B 104 1555 1555 2.02 LINK NI NI B 104 O HOH B 123 1555 1555 2.00 LINK NI NI B 104 O HOH B 124 1555 1555 1.99 LINK NI NI B 104 O HOH B 125 1555 1555 1.98 SITE 1 AC1 6 DG A 1 HOH A 102 HOH A 110 HOH A 111 SITE 2 AC1 6 HOH A 112 HOH A 113 SITE 1 AC2 6 DG B 1 HOH B 114 HOH B 115 HOH B 116 SITE 2 AC2 6 HOH B 117 HOH B 118 SITE 1 AC3 6 DG A 7 HOH A 109 HOH A 119 HOH A 120 SITE 2 AC3 6 HOH A 121 HOH A 122 SITE 1 AC4 6 DG B 7 HOH B 101 HOH B 103 HOH B 123 SITE 2 AC4 6 HOH B 124 HOH B 125 CRYST1 70.867 70.867 70.867 90.00 90.00 90.00 I 2 3 48 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 0.014111 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014111 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014111 0.00000