HEADER RNA 18-JAN-05 1YKQ TITLE CRYSTAL STRUCTURE OF DIELS-ALDER RIBOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIELS-ALDER RIBOZYME; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: 11-MER; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DIELS-ALDER RIBOZYME; COMPND 8 CHAIN: B, D; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: 38-MER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS DERIVED FROM THE IN VITRO SELECTED SOURCE 4 RIBOZYME CATALYZING DIELS-ALDER REACTION BETWEEN TETHERED ANTHRACENE SOURCE 5 AND BIOTINYLATED MALEIMIDE; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 OTHER_DETAILS: THIS SEQUENCE WAS DERIVED FROM THE IN VITRO SELECTED SOURCE 9 RIBOZYME CATALYZING DIELS-ALDER REACTION BETWEEN TETHERED ANTHRACENE SOURCE 10 AND BIOTINYLATED MALEIMIDE KEYWDS CARBON-CARBON BOND, CATALYTIC MECHANISM, RNA CRYSTAL STRUCTURE, KEYWDS 2 DIELS-ALDER REACTION, RIBOZYME, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.SERGANOV,S.KEIPER,L.MALININA,V.TERESHKO,E.SKRIPKIN,C.HOBARTNER, AUTHOR 2 A.POLONSKAIA,A.T.PHAN,R.WOMBACHER,R.MICURA,Z.DAUTER,A.JASCHKE, AUTHOR 3 D.J.PATEL REVDAT 5 23-AUG-23 1YKQ 1 REMARK LINK REVDAT 4 13-JUL-11 1YKQ 1 VERSN REVDAT 3 24-FEB-09 1YKQ 1 VERSN REVDAT 2 22-MAR-05 1YKQ 1 JRNL REVDAT 1 22-FEB-05 1YKQ 0 JRNL AUTH A.SERGANOV,S.KEIPER,L.MALININA,V.TERESHKO,E.SKRIPKIN, JRNL AUTH 2 C.HOBARTNER,A.POLONSKAIA,A.T.PHAN,R.WOMBACHER,R.MICURA, JRNL AUTH 3 Z.DAUTER,A.JASCHKE,D.J.PATEL JRNL TITL STRUCTURAL BASIS FOR DIELS-ALDER RIBOZYME-CATALYZED JRNL TITL 2 CARBON-CARBON BOND FORMATION. JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 218 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 15723077 JRNL DOI 10.1038/NSMB906 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.9999 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) : 3.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 6563 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) : 0.288 REMARK 3 R VALUE (WORKING SET) : 0.286 REMARK 3 FREE R VALUE : 0.324 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 312 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) : 3.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 447 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3640 REMARK 3 BIN FREE R VALUE SET COUNT : 24 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 2078 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 0 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) : 40.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.45000 REMARK 3 B22 (A**2) : -8.91000 REMARK 3 B33 (A**2) : 7.20000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.26000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.671 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.730 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 109.285 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.896 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.852 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2320 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3610 ; 1.612 ; 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): 480 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1018 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1209 ; 0.262 ; 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): 71 ; 0.218 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.098 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 42 ; 0.184 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.262 ; 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): 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): 3325 ; 0.000 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3610 ; 0.000 ; 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 101 A 111 6 REMARK 3 1 C 101 C 111 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 A (A): 230 ; 0.48 ; 5.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 230 ; 0.00 ; 10.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : B D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 201 B 238 6 REMARK 3 1 D 201 D 238 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 2 B (A): 809 ; 0.38 ; 5.00 REMARK 3 LOOSE THERMAL 2 B (A**2): 809 ; 0.00 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 101 A 111 REMARK 3 RESIDUE RANGE : B 201 B 238 REMARK 3 RESIDUE RANGE : A 249 A 249 REMARK 3 RESIDUE RANGE : B 240 B 246 REMARK 3 ORIGIN FOR THE GROUP (A): 34.8903 26.3165 23.0536 REMARK 3 T TENSOR REMARK 3 T11: -0.1432 T22: -0.0335 REMARK 3 T33: -0.2140 T12: -0.1055 REMARK 3 T13: 0.0076 T23: 0.0686 REMARK 3 L TENSOR REMARK 3 L11: 1.9947 L22: 3.8868 REMARK 3 L33: 4.1616 L12: -0.0839 REMARK 3 L13: -1.1069 L23: -0.1312 REMARK 3 S TENSOR REMARK 3 S11: -0.2032 S12: 0.3208 S13: -0.0009 REMARK 3 S21: -0.1677 S22: 0.5006 S23: 0.5116 REMARK 3 S31: 0.4317 S32: -0.0485 S33: -0.2973 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 101 C 111 REMARK 3 RESIDUE RANGE : D 201 D 238 REMARK 3 RESIDUE RANGE : D 340 D 348 REMARK 3 RESIDUE RANGE : C 349 C 349 REMARK 3 ORIGIN FOR THE GROUP (A): 58.1887 33.3438 22.9837 REMARK 3 T TENSOR REMARK 3 T11: -0.0431 T22: 0.0349 REMARK 3 T33: -0.1638 T12: -0.0849 REMARK 3 T13: 0.0227 T23: -0.1458 REMARK 3 L TENSOR REMARK 3 L11: 2.3200 L22: 2.5376 REMARK 3 L33: 4.4194 L12: -0.6245 REMARK 3 L13: 2.5601 L23: -0.8796 REMARK 3 S TENSOR REMARK 3 S11: -0.2539 S12: 0.2170 S13: 0.3499 REMARK 3 S21: -0.4012 S22: 0.3263 S23: -0.4412 REMARK 3 S31: -0.5310 S32: 0.2039 S33: -0.0724 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 : 1.20 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 1YKQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000031626. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : SI(111),(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6744 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.15400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.72900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: DIELS-ALDER RIBOZYME FROM THE RIBOZYME-PRODUCT REMARK 200 COMPLEX, PDB ENTRY 1YLS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400, SODIUM CACODYLATE, MAGNESIUM REMARK 280 ACETATE, 1,6-HEXANDIOL, SODIUM CHLORIDE, CADMIUM CHLORIDE, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 22.12000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 C A 110 O2' REMARK 470 C B 204 O2' REMARK 470 C B 209 O2' REMARK 470 C C 110 O2' REMARK 470 C D 204 O2' REMARK 470 C D 209 O2' 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 U A 106 C2' U A 106 C1' -0.051 REMARK 500 A B 232 O5' A B 232 C5' -0.058 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 G A 101 O4' - C4' - C3' ANGL. DEV. = -8.0 DEGREES REMARK 500 G A 101 C4' - C3' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 G A 101 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 A A 103 C1' - O4' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 A A 103 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 U A 106 C3' - C2' - C1' ANGL. DEV. = -4.7 DEGREES REMARK 500 U A 106 C3' - O3' - P ANGL. DEV. = -9.3 DEGREES REMARK 500 C B 204 C3' - C2' - C1' ANGL. DEV. = -8.3 DEGREES REMARK 500 C B 223 C3' - C2' - C1' ANGL. DEV. = -4.7 DEGREES REMARK 500 A B 230 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 A C 103 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 G C 108 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 G C 108 C4' - C3' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 G D 201 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES REMARK 500 G D 201 C1' - O4' - C4' ANGL. DEV. = -7.8 DEGREES REMARK 500 G D 201 C4' - C3' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 G D 201 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 C D 204 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 G D 227 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 C D 238 C3' - C2' - C1' ANGL. DEV. = -4.5 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 CD A 249 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 101 N7 REMARK 620 2 G A 101 O6 77.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 246 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 213 OP1 REMARK 620 2 G D 213 OP1 78.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 349 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G C 101 N7 REMARK 620 2 G C 101 O6 76.1 REMARK 620 N 1 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 240 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 243 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 249 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD D 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD D 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 348 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 349 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YKV RELATED DB: PDB REMARK 900 RELATED ID: 1YLS RELATED DB: PDB DBREF 1YKQ A 101 111 PDB 1YKQ 1YKQ 101 111 DBREF 1YKQ B 201 238 PDB 1YKQ 1YKQ 201 238 DBREF 1YKQ C 101 111 PDB 1YKQ 1YKQ 101 111 DBREF 1YKQ D 201 238 PDB 1YKQ 1YKQ 201 238 SEQRES 1 A 11 G G A G C U C G C C C SEQRES 1 B 38 G G G C G A G G C C G U G SEQRES 2 B 38 C C A G C U C U U C G G A SEQRES 3 B 38 G C A A U A C U C G G C SEQRES 1 C 11 G G A G C U C G C C C SEQRES 1 D 38 G G G C G A G G C C G U G SEQRES 2 D 38 C C A G C U C U U C G G A SEQRES 3 D 38 G C A A U A C U C G G C HET CD A 249 1 HET MG B 240 1 HET MG B 241 1 HET CD B 242 1 HET CD B 243 1 HET MG B 246 1 HET MG C 349 1 HET MG D 340 1 HET MG D 341 1 HET CD D 342 1 HET CD D 343 1 HET MG D 348 1 HETNAM CD CADMIUM ION HETNAM MG MAGNESIUM ION FORMUL 5 CD 5(CD 2+) FORMUL 6 MG 7(MG 2+) LINK N7 G A 101 CD CD A 249 1555 1555 2.32 LINK O6 G A 101 CD CD A 249 1555 1555 2.60 LINK N7 G B 201 CD CD B 243 1555 1555 2.70 LINK OP1 G B 213 MG MG B 246 1555 1555 2.15 LINK OP2 A B 216 CD CD B 242 1555 1555 2.54 LINK OP2 C B 233 MG MG B 241 1555 1555 2.35 LINK OP1 U B 234 MG MG B 240 1555 1555 1.89 LINK MG MG B 246 OP1 G D 213 1555 1555 2.30 LINK N7 G C 101 MG MG C 349 1555 1555 2.20 LINK O6 G C 101 MG MG C 349 1555 1555 2.58 LINK N7 G D 201 CD CD D 343 1555 1555 2.67 LINK OP2 A D 216 CD CD D 342 1555 1555 2.25 LINK N7 G D 225 MG MG D 348 1555 1555 2.36 LINK OP2 C D 233 MG MG D 341 1555 1555 2.42 LINK OP1 U D 234 MG MG D 340 1555 1555 2.72 SITE 1 AC1 2 U B 234 G B 236 SITE 1 AC2 1 C B 233 SITE 1 AC3 2 A B 216 G B 217 SITE 1 AC4 1 G B 201 SITE 1 AC5 2 G B 213 G D 213 SITE 1 AC6 1 G A 101 SITE 1 AC7 1 U D 234 SITE 1 AC8 1 C D 233 SITE 1 AC9 1 A D 216 SITE 1 BC1 1 G D 201 SITE 1 BC2 1 G D 225 SITE 1 BC3 1 G C 101 CRYST1 77.690 44.240 79.640 90.00 107.12 90.00 P 1 21 1 4 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 0.012872 0.000000 0.003965 0.00000 SCALE2 0.000000 0.022604 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013139 0.00000