HEADER DNA 15-SEP-05 2B1D TITLE 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3' METHIONINE REPRESSOR TITLE 2 BINDING SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*AP*GP*AP*CP*GP*TP*CP*TP*GP*C)-3'; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS SEQUENCE DEPENDENT DNA DEFORMABILITY, PROTEIN-DNA RECOGNITION, DNA EXPDTA X-RAY DIFFRACTION AUTHOR H.M.BERMAN,J.W.LOCASALE,A.A.NAPOLI REVDAT 7 23-AUG-23 2B1D 1 REMARK LINK REVDAT 6 11-OCT-17 2B1D 1 REMARK REVDAT 5 13-JUL-11 2B1D 1 VERSN REVDAT 4 09-JUN-09 2B1D 1 JRNL REVDAT 3 24-FEB-09 2B1D 1 VERSN REVDAT 2 17-JAN-06 2B1D 1 AUTHOR REVDAT 1 27-SEP-05 2B1D 0 JRNL AUTH J.W.LOCASALE,A.A.NAPOLI,S.CHEN,H.M.BERMAN,C.L.LAWSON JRNL TITL SIGNATURES OF PROTEIN-DNA RECOGNITION IN FREE DNA BINDING JRNL TITL 2 SITES. JRNL REF J.MOL.BIOL. V. 386 1054 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19244617 REMARK 2 REMARK 2 RESOLUTION. 2.50 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 7684 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) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.100 REMARK 3 FREE R VALUE TEST SET COUNT : 624 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 4 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2468 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4420 REMARK 3 BIN FREE R VALUE SET COUNT : 203 REMARK 3 BIN FREE R VALUE : 0.5350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1458 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 56 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.71000 REMARK 3 B22 (A**2) : -0.51000 REMARK 3 B33 (A**2) : 1.70000 REMARK 3 B12 (A**2) : -0.63000 REMARK 3 B13 (A**2) : -2.49000 REMARK 3 B23 (A**2) : 0.23000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.787 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.343 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.282 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.384 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1656 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2568 ; 7.661 ; 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): 216 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 766 ; 0.049 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 615 ; 0.228 ; 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): 91 ; 0.350 ; 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): 55 ; 0.247 ; 0.200 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): 1656 ; 8.551 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2568 ;12.396 ; 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 12 REMARK 3 RESIDUE RANGE : B 13 B 24 REMARK 3 ORIGIN FOR THE GROUP (A): -38.1293 -23.7653 27.8991 REMARK 3 T TENSOR REMARK 3 T11: 0.3008 T22: 0.1786 REMARK 3 T33: 0.0670 T12: 0.0685 REMARK 3 T13: -0.0510 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 1.4594 L22: 0.1132 REMARK 3 L33: 4.2628 L12: 0.6864 REMARK 3 L13: 0.9726 L23: 0.0495 REMARK 3 S TENSOR REMARK 3 S11: 0.2173 S12: 0.1279 S13: -0.0979 REMARK 3 S21: -0.0937 S22: 0.0663 S23: -0.0369 REMARK 3 S31: 0.4700 S32: 0.1208 S33: -0.2835 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 12 REMARK 3 RESIDUE RANGE : D 13 D 24 REMARK 3 ORIGIN FOR THE GROUP (A): -33.2810 -8.0540 30.4043 REMARK 3 T TENSOR REMARK 3 T11: 0.0902 T22: 0.1852 REMARK 3 T33: 0.2189 T12: 0.0292 REMARK 3 T13: 0.0314 T23: 0.0773 REMARK 3 L TENSOR REMARK 3 L11: 3.4059 L22: 0.9713 REMARK 3 L33: 0.6450 L12: 0.2768 REMARK 3 L13: 0.0540 L23: -0.0573 REMARK 3 S TENSOR REMARK 3 S11: -0.0388 S12: 0.2407 S13: 0.4342 REMARK 3 S21: 0.0112 S22: 0.0090 S23: -0.1388 REMARK 3 S31: 0.0587 S32: 0.0294 S33: 0.0297 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 1 E 12 REMARK 3 RESIDUE RANGE : F 13 F 24 REMARK 3 ORIGIN FOR THE GROUP (A): -46.9346 -9.1296 46.0194 REMARK 3 T TENSOR REMARK 3 T11: 0.2498 T22: 0.0004 REMARK 3 T33: 0.1975 T12: -0.0103 REMARK 3 T13: 0.0197 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.8677 L22: 6.9103 REMARK 3 L33: 1.2868 L12: 1.0628 REMARK 3 L13: 0.0350 L23: -0.0484 REMARK 3 S TENSOR REMARK 3 S11: 0.0270 S12: 0.0243 S13: 0.1806 REMARK 3 S21: -0.0404 S22: -0.1275 S23: 0.3281 REMARK 3 S31: -0.0751 S32: -0.0493 S33: 0.1005 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 2B1D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034553. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1004 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7790 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: NDB ID BD0001 (PDB ID 423D) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SODIUM CACODYLATE, COBALT REMARK 280 HEXAMINE, MAGNESIUM CHLORIDE, PH 5.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 IN SAME ASYMMETRIC UNIT 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 OP1 DA A 5 O HOH A 2546 2.07 REMARK 500 O2 DC A 6 N2 DG B 19 2.11 REMARK 500 O6 DG C 11 N4 DC D 14 2.17 REMARK 500 N2 DG C 11 O2 DC D 14 2.19 REMARK 500 O6 DG C 1 N4 DC D 24 2.19 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 DA A 3 N9 DA A 3 C4 0.041 REMARK 500 DC A 6 C2 DC A 6 O2 0.059 REMARK 500 DG B 19 N1 DG B 19 C2 0.053 REMARK 500 DT B 20 C4 DT B 20 O4 -0.066 REMARK 500 DA C 3 C5 DA C 3 C6 0.054 REMARK 500 DG C 7 C6 DG C 7 O6 -0.058 REMARK 500 DT D 20 C4 DT D 20 O4 -0.118 REMARK 500 DG E 1 C6 DG E 1 O6 0.059 REMARK 500 DC E 2 C4 DC E 2 N4 0.055 REMARK 500 DT F 22 C4 DT F 22 C5 -0.059 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 DC A 6 C1' - O4' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 DC A 6 C3' - C2' - C1' ANGL. DEV. = -6.5 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 9 O5' - P - OP1 ANGL. DEV. = -6.3 DEGREES REMARK 500 DG B 16 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DG C 1 O5' - C5' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 DC C 6 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG F 13 O5' - C5' - C4' ANGL. DEV. = -12.4 DEGREES REMARK 500 DC F 14 O3' - P - OP2 ANGL. DEV. = 7.3 DEGREES REMARK 500 DC F 14 O5' - P - OP1 ANGL. DEV. = -5.7 DEGREES 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 DG A 1 0.11 SIDE CHAIN REMARK 500 DT A 10 0.08 SIDE CHAIN REMARK 500 DT B 20 0.08 SIDE CHAIN REMARK 500 DT B 22 0.10 SIDE CHAIN REMARK 500 DG C 4 0.08 SIDE CHAIN REMARK 500 DT C 8 0.07 SIDE CHAIN REMARK 500 DG D 19 0.06 SIDE CHAIN REMARK 500 DA E 3 0.10 SIDE CHAIN REMARK 500 DG E 11 0.05 SIDE CHAIN REMARK 500 DC E 12 0.06 SIDE CHAIN REMARK 500 DG F 13 0.08 SIDE CHAIN REMARK 500 DA F 17 0.06 SIDE CHAIN 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 MG B2383 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2646 O REMARK 620 2 HOH A2647 O 89.0 REMARK 620 3 HOH A2649 O 87.5 84.2 REMARK 620 4 HOH B2645 O 177.7 88.8 91.5 REMARK 620 5 HOH B2648 O 94.0 174.9 91.7 88.2 REMARK 620 6 HOH B2650 O 90.6 89.8 173.8 90.1 94.3 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 MG B 2383 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 2505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO F 2506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO C 2507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B1B RELATED DB: PDB REMARK 900 5'-D(*GP*CP*GP*TP*GP*GP*GP*CP*AP*C)-3' ZIF268 BINDING SITE REMARK 900 RELATED ID: 2B1C RELATED DB: PDB REMARK 900 5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*CP*C)-3' ZIF268 BINDING SITE DBREF 2B1D A 1 12 PDB 2B1D 2B1D 1 12 DBREF 2B1D B 13 24 PDB 2B1D 2B1D 13 24 DBREF 2B1D C 1 12 PDB 2B1D 2B1D 1 12 DBREF 2B1D D 13 24 PDB 2B1D 2B1D 13 24 DBREF 2B1D E 1 12 PDB 2B1D 2B1D 1 12 DBREF 2B1D F 13 24 PDB 2B1D 2B1D 13 24 SEQRES 1 A 12 DG DC DA DG DA DC DG DT DC DT DG DC SEQRES 1 B 12 DG DC DA DG DA DC DG DT DC DT DG DC SEQRES 1 C 12 DG DC DA DG DA DC DG DT DC DT DG DC SEQRES 1 D 12 DG DC DA DG DA DC DG DT DC DT DG DC SEQRES 1 E 12 DG DC DA DG DA DC DG DT DC DT DG DC SEQRES 1 F 12 DG DC DA DG DA DC DG DT DC DT DG DC HET NCO A2505 7 HET MG B2383 1 HET NCO C2507 7 HET NCO F2506 7 HETNAM NCO COBALT HEXAMMINE(III) HETNAM MG MAGNESIUM ION FORMUL 7 NCO 3(CO H18 N6 3+) FORMUL 8 MG MG 2+ FORMUL 11 HOH *56(H2 O) LINK O HOH A2646 MG MG B2383 1555 1555 1.97 LINK O HOH A2647 MG MG B2383 1555 1555 2.08 LINK O HOH A2649 MG MG B2383 1555 1555 2.07 LINK MG MG B2383 O HOH B2645 1555 1555 2.08 LINK MG MG B2383 O HOH B2648 1555 1555 2.06 LINK MG MG B2383 O HOH B2650 1555 1555 2.12 SITE 1 AC1 6 HOH A2646 HOH A2647 HOH A2649 HOH B2645 SITE 2 AC1 6 HOH B2648 HOH B2650 SITE 1 AC2 5 DA A 3 DG A 4 HOH A2512 DT B 20 SITE 2 AC2 5 DG C 4 SITE 1 AC3 6 DA A 3 DA C 3 DT E 8 DA F 15 SITE 2 AC3 6 DG F 16 DA F 17 SITE 1 AC4 6 DG A 4 DA C 3 DG C 4 HOH C2636 SITE 2 AC4 6 DT D 20 DC E 6 CRYST1 39.980 40.346 40.255 82.15 69.13 81.44 P 1 6 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 0.025010 -0.003760 -0.009230 0.00000 SCALE2 0.000000 0.025060 -0.002280 0.00000 SCALE3 0.000000 0.000000 0.026700 0.00000 TER 244 DC A 12 TER 488 DC B 24 TER 732 DC C 12 TER 976 DC D 24 TER 1220 DC E 12 TER 1464 DC F 24 HETATM 1465 CO NCO A2505 -41.315 -21.151 35.841 1.00 63.82 CO HETATM 1466 N1 NCO A2505 -42.248 -22.506 36.880 1.00 64.83 N HETATM 1467 N2 NCO A2505 -40.365 -19.842 34.699 1.00 71.12 N HETATM 1468 N3 NCO A2505 -42.267 -19.675 36.781 1.00 55.47 N HETATM 1469 N4 NCO A2505 -42.810 -21.151 34.581 1.00 49.30 N HETATM 1470 N5 NCO A2505 -40.398 -22.515 34.791 1.00 69.82 N HETATM 1471 N6 NCO A2505 -39.838 -21.067 37.092 1.00 55.15 N HETATM 1472 MG MG B2383 -36.415 -20.367 19.840 1.00 51.86 MG HETATM 1473 CO NCO C2507 -40.054 -9.828 35.873 1.00 64.69 CO HETATM 1474 N1 NCO C2507 -40.444 -8.267 36.923 1.00 61.67 N HETATM 1475 N2 NCO C2507 -39.656 -11.461 34.720 1.00 55.79 N HETATM 1476 N3 NCO C2507 -40.412 -11.070 37.360 1.00 53.88 N HETATM 1477 N4 NCO C2507 -38.186 -9.756 36.480 1.00 50.02 N HETATM 1478 N5 NCO C2507 -39.678 -8.643 34.317 1.00 73.84 N HETATM 1479 N6 NCO C2507 -41.877 -9.997 35.207 1.00 56.49 N HETATM 1480 CO NCO F2506 -44.522 -15.677 41.283 1.00 72.74 CO HETATM 1481 N1 NCO F2506 -44.178 -13.866 40.662 1.00 64.73 N HETATM 1482 N2 NCO F2506 -44.881 -17.507 41.992 1.00 73.68 N HETATM 1483 N3 NCO F2506 -43.411 -15.416 42.857 1.00 83.46 N HETATM 1484 N4 NCO F2506 -42.980 -16.363 40.311 1.00 77.70 N HETATM 1485 N5 NCO F2506 -45.685 -16.026 39.684 1.00 88.98 N HETATM 1486 N6 NCO F2506 -46.122 -15.103 42.292 1.00 76.37 N HETATM 1487 O HOH A2512 -38.176 -22.683 39.041 1.00 75.44 O HETATM 1488 O HOH A2524 -31.133 -23.922 29.510 1.00 72.55 O HETATM 1489 O HOH A2531 -32.856 -16.971 38.543 1.00 70.00 O HETATM 1490 O HOH A2543 -29.265 -20.421 33.621 1.00 77.73 O HETATM 1491 O HOH A2546 -33.000 -12.262 33.596 1.00 75.04 O HETATM 1492 O HOH A2553 -42.199 -21.165 39.813 1.00 71.31 O HETATM 1493 O HOH A2554 -35.492 -31.013 18.966 1.00 87.15 O HETATM 1494 O HOH A2562 -46.582 -29.328 23.414 1.00 80.59 O HETATM 1495 O HOH A2571 -42.760 -19.400 43.582 1.00 84.15 O HETATM 1496 O HOH A2610 -39.001 -19.055 31.679 1.00 58.14 O HETATM 1497 O HOH A2634 -48.331 -26.450 20.383 1.00142.21 O HETATM 1498 O HOH A2646 -36.195 -22.056 20.833 1.00 67.89 O HETATM 1499 O HOH A2647 -37.329 -19.543 21.516 1.00 66.96 O HETATM 1500 O HOH A2649 -34.669 -19.720 20.732 1.00 64.24 O HETATM 1501 O HOH B2511 -42.057 -29.049 25.745 1.00109.52 O HETATM 1502 O HOH B2518 -40.630 -30.164 10.696 1.00 80.91 O HETATM 1503 O HOH B2519 -43.961 -17.985 26.157 1.00 76.89 O HETATM 1504 O HOH B2575 -29.825 -18.703 35.997 1.00100.98 O HETATM 1505 O HOH B2606 -32.447 -27.233 30.009 1.00 77.48 O HETATM 1506 O HOH B2632 -45.939 -20.782 17.167 1.00 81.24 O HETATM 1507 O HOH B2645 -36.658 -18.545 18.865 1.00 66.28 O HETATM 1508 O HOH B2648 -35.394 -21.040 18.187 1.00 61.80 O HETATM 1509 O HOH B2650 -38.304 -21.002 19.131 1.00 61.09 O HETATM 1510 O HOH C2528 -46.703 -17.915 36.490 1.00 81.42 O HETATM 1511 O HOH C2534 -37.535 -8.479 19.723 1.00114.60 O HETATM 1512 O HOH C2555 -27.612 -3.470 24.127 1.00 95.43 O HETATM 1513 O HOH C2615 -33.846 -11.385 18.955 1.00 93.65 O HETATM 1514 O HOH C2625 -36.126 -1.226 18.317 1.00106.49 O HETATM 1515 O HOH C2631 -38.645 -8.064 22.156 1.00123.22 O HETATM 1516 O HOH C2635 -21.087 -9.241 38.083 1.00122.58 O HETATM 1517 O HOH C2636 -37.041 -10.672 33.394 1.00 76.24 O HETATM 1518 O HOH D2537 -29.199 -2.399 34.011 1.00109.55 O HETATM 1519 O HOH D2547 -48.452 -8.805 14.951 1.00165.63 O HETATM 1520 O HOH D2567 -45.068 -7.096 17.685 1.00 91.97 O HETATM 1521 O HOH D2581 -26.536 -12.115 26.048 1.00 74.60 O HETATM 1522 O HOH D2585 -48.119 -3.858 19.858 1.00127.09 O HETATM 1523 O HOH D2620 -41.966 -7.485 24.350 1.00 85.67 O HETATM 1524 O HOH D2624 -40.925 -1.673 21.250 1.00101.67 O HETATM 1525 O HOH D2630 -53.712 -15.300 19.918 1.00110.75 O HETATM 1526 O HOH D2637 -32.606 -2.091 30.116 1.00112.02 O HETATM 1527 O HOH D2638 -21.048 -11.318 35.003 1.00104.78 O HETATM 1528 O HOH D2639 -37.340 -4.404 25.493 1.00104.37 O HETATM 1529 O HOH D2641 -47.626 -11.432 17.592 1.00107.70 O HETATM 1530 O HOH E2522 -40.853 -16.615 48.851 1.00 89.32 O HETATM 1531 O HOH E2576 -44.095 -19.311 52.538 1.00 93.10 O HETATM 1532 O HOH E2603 -53.676 -20.050 47.110 1.00123.61 O HETATM 1533 O HOH E2640 -44.427 -22.306 49.068 1.00 91.89 O HETATM 1534 O HOH E2642 -42.240 -17.831 46.651 1.00 96.05 O HETATM 1535 O HOH F2509 -43.225 5.604 41.708 1.00 87.65 O HETATM 1536 O HOH F2527 -49.811 -12.373 41.212 1.00 78.00 O HETATM 1537 O HOH F2536 -48.366 -2.464 53.494 1.00 71.41 O HETATM 1538 O HOH F2601 -34.209 -2.115 52.458 1.00117.01 O HETATM 1539 O HOH F2611 -45.247 -26.502 50.904 1.00 81.97 O HETATM 1540 O HOH F2621 -49.748 -25.171 40.594 1.00 96.78 O HETATM 1541 O HOH F2643 -53.911 -17.041 47.909 1.00 96.62 O HETATM 1542 O HOH F2644 -41.262 -5.969 49.329 1.00111.66 O CONECT 1465 1466 1467 1468 1469 CONECT 1465 1470 1471 CONECT 1466 1465 CONECT 1467 1465 CONECT 1468 1465 CONECT 1469 1465 CONECT 1470 1465 CONECT 1471 1465 CONECT 1472 1498 1499 1500 1507 CONECT 1472 1508 1509 CONECT 1473 1474 1475 1476 1477 CONECT 1473 1478 1479 CONECT 1474 1473 CONECT 1475 1473 CONECT 1476 1473 CONECT 1477 1473 CONECT 1478 1473 CONECT 1479 1473 CONECT 1480 1481 1482 1483 1484 CONECT 1480 1485 1486 CONECT 1481 1480 CONECT 1482 1480 CONECT 1483 1480 CONECT 1484 1480 CONECT 1485 1480 CONECT 1486 1480 CONECT 1498 1472 CONECT 1499 1472 CONECT 1500 1472 CONECT 1507 1472 CONECT 1508 1472 CONECT 1509 1472 MASTER 429 0 4 0 0 0 8 6 1536 6 32 6 END