HEADER DNA/ANTIBIOTIC 16-NOV-15 5ERZ OBSLTE 26-JUL-17 5ERZ 5XEW TITLE CRYSTAL STRUCTURE OF THE [NI2+-(CHROMOMYCIN A3)2]-D(TTCCGCCGCCGAA)2 TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*AP*A)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS NUCLEOTIDE FLIPPING-OUT, CCG TRINUCLEOTIDE REPEATS, CHROMOMYCIN A3, KEYWDS 2 METALLOANTIBIOTICS, MINOR GROOVE BINDING DRUG, DNA-ANTIBIOTIC KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.H.TSENG,P.C.WU,M.H.HOU REVDAT 2 26-JUL-17 5ERZ 1 OBSLTE REMARK REVDAT 1 16-NOV-16 5ERZ 0 JRNL AUTH W.H.TSENG,P.C.WU,M.H.HOU JRNL TITL CRYSTAL STRUCTURE OF THE [NI2+-(CHROMOMYCIN JRNL TITL 2 A3)2]-D(TTCCGCCGCCGAA)2 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 10858 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 546 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 761 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.3200 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 518 REMARK 3 HETEROGEN ATOMS : 169 REMARK 3 SOLVENT ATOMS : 202 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.54000 REMARK 3 B22 (A**2) : 0.54000 REMARK 3 B33 (A**2) : -1.76000 REMARK 3 B12 (A**2) : 0.54000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.760 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 748 ; 0.018 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 429 ; 0.021 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1128 ; 2.486 ; 1.755 REMARK 3 BOND ANGLES OTHERS (DEGREES): 993 ; 1.481 ; 3.000 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): 120 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 370 ; 0.024 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 146 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 4 REMARK 4 5ERZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215365. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.45104 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11436 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 MM SINGLE STRANDED-DNA, 2.0 MM REMARK 280 CHROMOMYCIN A3, 4MM NISO4 6H2O, 50 MM SODIUM-CACODYLATE BUFFER, REMARK 280 5 MM MGCL2, 1 MM SPERMINE, 3 % MPD, PH 6.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -Y,-X,-Z+1/3 REMARK 290 5555 -X+Y,Y,-Z+2/3 REMARK 290 6555 X,X-Y,-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 -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 55.57067 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 27.78533 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 27.78533 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.57067 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 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 HOH A 215 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 309 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 311 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 248 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 DT A 1 N1 DT A 1 C2 0.076 REMARK 500 DT A 1 C4 DT A 1 C5 0.069 REMARK 500 DT A 1 C2 DT A 1 O2 0.077 REMARK 500 DT A 2 C6 DT A 2 N1 -0.044 REMARK 500 DT A 2 C2 DT A 2 O2 0.054 REMARK 500 DG A 5 O3' DC A 6 P -0.077 REMARK 500 DT B 14 N1 DT B 14 C2 0.085 REMARK 500 DT B 14 C2 DT B 14 O2 0.066 REMARK 500 DG B 18 O3' DC B 19 P -0.075 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT A 1 N1 - C2 - N3 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT A 1 C2 - N3 - C4 ANGL. DEV. = -7.2 DEGREES REMARK 500 DT A 1 N3 - C4 - C5 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT A 1 C5 - C6 - N1 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 1 C4 - C5 - C7 ANGL. DEV. = 5.4 DEGREES REMARK 500 DT A 1 C6 - C5 - C7 ANGL. DEV. = -6.6 DEGREES REMARK 500 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT A 2 C6 - N1 - C2 ANGL. DEV. = -4.1 DEGREES REMARK 500 DT A 2 N1 - C2 - N3 ANGL. DEV. = 6.0 DEGREES REMARK 500 DT A 2 C4 - C5 - C7 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT A 2 C6 - C5 - C7 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG A 11 O5' - P - OP2 ANGL. DEV. = -6.5 DEGREES REMARK 500 DA A 13 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 DT B 14 N1 - C2 - N3 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT B 14 C2 - N3 - C4 ANGL. DEV. = -6.6 DEGREES REMARK 500 DT B 14 N3 - C4 - C5 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT B 14 C5 - C6 - N1 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT B 14 C5 - C4 - O4 ANGL. DEV. = -5.9 DEGREES REMARK 500 DT B 14 C4 - C5 - C7 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT B 14 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT B 15 O4' - C1' - N1 ANGL. DEV. = 10.8 DEGREES REMARK 500 DT B 15 N1 - C2 - N3 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT B 15 C2 - N3 - C4 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT B 15 N3 - C4 - C5 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT B 15 C5 - C4 - O4 ANGL. DEV. = -7.3 DEGREES REMARK 500 DT B 15 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 304 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 305 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A 306 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A 307 DISTANCE = 7.00 ANGSTROMS REMARK 525 HOH A 308 DISTANCE = 7.38 ANGSTROMS REMARK 525 HOH A 309 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH A 310 DISTANCE = 8.30 ANGSTROMS REMARK 525 HOH A 311 DISTANCE = 8.33 ANGSTROMS REMARK 525 HOH A 312 DISTANCE = 8.74 ANGSTROMS REMARK 525 HOH A 313 DISTANCE = 8.89 ANGSTROMS REMARK 525 HOH B 282 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH B 283 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH B 284 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH B 285 DISTANCE = 7.73 ANGSTROMS REMARK 525 HOH B 286 DISTANCE = 7.76 ANGSTROMS REMARK 525 HOH B 287 DISTANCE = 8.08 ANGSTROMS REMARK 525 HOH B 288 DISTANCE = 8.87 ANGSTROMS REMARK 525 HOH B 289 DISTANCE = 9.56 ANGSTROMS 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 108 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 8 N7 REMARK 620 2 HOH A 205 O 95.6 REMARK 620 3 HOH A 208 O 91.6 159.9 REMARK 620 4 HOH A 219 O 82.8 93.5 68.8 REMARK 620 5 HOH A 236 O 93.5 85.1 113.2 175.9 REMARK 620 6 HOH A 249 O 159.6 92.4 75.1 78.0 106.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 107 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 21 N7 REMARK 620 2 HOH B 208 O 90.6 REMARK 620 3 HOH B 206 O 93.1 162.7 REMARK 620 4 HOH B 222 O 83.8 73.8 89.8 REMARK 620 5 HOH B 228 O 92.7 115.4 81.3 170.3 REMARK 620 6 HOH A 254 O 171.6 88.3 90.4 103.9 80.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 107 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CPH A 103 O1 REMARK 620 2 CPH A 103 O9 88.3 REMARK 620 3 CPH B 103 O1 87.8 94.4 REMARK 620 4 CPH B 103 O9 94.5 176.9 87.1 REMARK 620 5 HOH A 203 O 91.2 94.1 171.5 84.6 REMARK 620 6 HOH B 207 O 171.1 83.0 90.9 94.2 91.4 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 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues 1GL A REMARK 800 101 through ERI A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues 1GL B REMARK 800 101 through ERI B 106 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ES0 RELATED DB: PDB DBREF 5ERZ A 1 13 PDB 5ERZ 5ERZ 1 13 DBREF 5ERZ B 14 26 PDB 5ERZ 5ERZ 14 26 SEQRES 1 A 13 DT DT DC DC DG DC DC DG DC DC DG DA DA SEQRES 1 B 13 DT DT DC DC DG DC DC DG DC DC DG DA DA HET 1GL A 101 11 HET ARI A 102 12 HET CPH A 103 28 HET CDR A 104 9 HET CDR A 105 9 HET ERI A 106 14 HET NI A 107 1 HET NI A 108 1 HET 1GL B 101 11 HET ARI B 102 12 HET CPH B 103 28 HET CDR B 104 9 HET CDR B 105 9 HET ERI B 106 14 HET NI B 107 1 HETNAM 1GL 4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE HETNAM ARI [O4]-ACETOXY-2,3-DIDEOXYFUCOSE HETNAM CPH (1S)-5-DEOXY-1-O-METHYL-1-C-[(2R,3S)-3,5,7,10- HETNAM 2 CPH TETRAHYDROXY-6-METHYL-4-OXO-1,2,3,4- HETNAM 3 CPH TETRAHYDROANTHRACEN-2-YL]-D-XYLULOSE HETNAM CDR 2,3-DIDEOXYFUCOSE HETNAM ERI 4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO- HETNAM 2 ERI HEXOPYRANOSE HETNAM NI NICKEL (II) ION HETSYN CPH NONE FORMUL 3 1GL 2(C7 H14 O4) FORMUL 3 ARI 2(C8 H14 O4) FORMUL 4 CPH 2(C21 H24 O9) FORMUL 5 CDR 4(C6 H12 O3) FORMUL 5 ERI 2(C9 H16 O5) FORMUL 6 NI 3(NI 2+) FORMUL 12 HOH *202(H2 O) LINK N7 DG A 8 NI NI A 108 1555 1555 2.10 LINK N7 DG B 21 NI NI B 107 1555 1555 2.11 LINK OGL ARI A 102 C6 CPH A 103 1555 1555 1.49 LINK O1 CPH A 103 NI NI A 107 1555 1555 2.02 LINK O9 CPH A 103 NI NI A 107 1555 1555 1.98 LINK NI NI A 107 O1 CPH B 103 1555 1555 2.04 LINK NI NI A 107 O9 CPH B 103 1555 1555 1.96 LINK NI NI A 107 O HOH A 203 1555 1555 2.15 LINK NI NI A 107 O HOH B 207 1555 1555 2.15 LINK NI NI A 108 O HOH A 205 1555 1555 2.03 LINK NI NI A 108 O HOH A 208 1555 1555 2.10 LINK NI NI A 108 O HOH A 219 1555 1555 1.99 LINK NI NI A 108 O HOH A 236 1555 1555 1.85 LINK NI NI A 108 O HOH A 249 1555 1555 2.42 LINK OGL ARI B 102 C6 CPH B 103 1555 1555 1.49 LINK C3 CDR B 105 O1 ERI B 106 1555 1555 1.51 LINK O1 1GL B 101 C3 ARI B 102 1555 1555 1.55 LINK O1 1GL A 101 C3 ARI A 102 1555 1555 1.57 LINK C2 CPH A 103 OGL CDR A 104 1555 1555 1.57 LINK C3 CDR A 105 O1 ERI A 106 1555 1555 1.58 LINK C3 CDR A 104 OGL CDR A 105 1555 1555 1.61 LINK C2 CPH B 103 OGL CDR B 104 1555 1555 1.61 LINK C3 CDR B 104 OGL CDR B 105 1555 1555 1.64 LINK NI NI B 107 O HOH B 208 1555 1555 2.13 LINK NI NI B 107 O HOH B 206 1555 1555 2.12 LINK NI NI B 107 O HOH B 222 1555 1555 2.17 LINK NI NI B 107 O HOH B 228 1555 1555 1.80 LINK NI NI B 107 O HOH A 254 1555 6565 2.33 SITE 1 AC1 4 CPH A 103 HOH A 203 CPH B 103 HOH B 207 SITE 1 AC2 6 DG A 8 HOH A 205 HOH A 208 HOH A 219 SITE 2 AC2 6 HOH A 236 HOH A 249 SITE 1 AC3 6 HOH A 254 DG B 21 HOH B 206 HOH B 208 SITE 2 AC3 6 HOH B 222 HOH B 228 SITE 1 AC4 27 DG A 5 DC A 6 DC A 7 DG A 8 SITE 2 AC4 27 DC A 9 DC A 10 DG A 11 DA A 12 SITE 3 AC4 27 NI A 107 HOH A 203 HOH A 206 HOH A 207 SITE 4 AC4 27 HOH A 213 HOH A 220 HOH A 223 HOH A 225 SITE 5 AC4 27 HOH A 229 HOH A 232 HOH A 239 DG B 18 SITE 6 AC4 27 DC B 19 DC B 23 ARI B 102 CPH B 103 SITE 7 AC4 27 CDR B 105 ERI B 106 HOH B 207 SITE 1 AC5 37 DG A 5 DC A 6 DC A 7 DG A 8 SITE 2 AC5 37 DC A 9 DC A 10 DG A 11 DA A 12 SITE 3 AC5 37 NI A 107 HOH A 203 HOH A 204 HOH A 206 SITE 4 AC5 37 HOH A 207 HOH A 212 HOH A 213 HOH A 218 SITE 5 AC5 37 HOH A 220 HOH A 223 HOH A 225 HOH A 229 SITE 6 AC5 37 HOH A 232 HOH A 235 HOH A 238 HOH A 239 SITE 7 AC5 37 DG B 18 DC B 19 DG B 21 DC B 22 SITE 8 AC5 37 DC B 23 DG B 24 DA B 25 HOH B 202 SITE 9 AC5 37 HOH B 207 HOH B 210 HOH B 211 HOH B 221 SITE 10 AC5 37 HOH B 224 CRYST1 48.291 48.291 83.356 90.00 90.00 120.00 P 32 1 2 12 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 0.020708 0.011956 0.000000 0.00000 SCALE2 0.000000 0.023911 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011997 0.00000