HEADER RNA 04-AUG-20 7JNH TITLE CRYSTAL STRUCTURE OF A DOUBLE-ENE RNA STABILITY ELEMENT IN COMPLEX TITLE 2 WITH A 28-MER POLY(A) RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 28-MER POLY(A) RNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CORE DOUBLE ENE RNA (XTAL CONSTRUCT) FROM ORYZA SATIVA COMPND 7 TRANSPOSON,CORE DOUBLE ENE RNA (XTAL CONSTRUCT) FROM ORYZA SATIVA COMPND 8 TRANSPOSON; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: THE TERMINAL C IS MODIFIED IN THE STRUCTURE,THE COMPND 12 TERMINAL C IS MODIFIED IN THE STRUCTURE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: ORYZA SATIVA; SOURCE 8 ORGANISM_TAXID: 4530 KEYWDS RNA STABILITY, ELEMENT FOR NUCLEAR EXPRESSION (ENE), POLY(A) TAIL, KEYWDS 2 MAJOR-GROOVE TRIPLE HELIX, QUINTUPLE-BASE TRANSITION MOTIF, WC-H A- KEYWDS 3 MINOR INTERACTION, POLY(A) 3-END BINDING POCKET, RNA EXPDTA X-RAY DIFFRACTION AUTHOR S.F.TORABI,A.T.VAIDYA,K.T.TYCOWSKI,S.J.DEGREGORIO,J.WANG,M.D.SHU, AUTHOR 2 T.A.STEITZ,J.A.STEITZ REVDAT 4 03-APR-24 7JNH 1 REMARK REVDAT 3 06-MAR-24 7JNH 1 REMARK REVDAT 2 17-FEB-21 7JNH 1 JRNL REVDAT 1 20-JAN-21 7JNH 0 JRNL AUTH S.F.TORABI,A.T.VAIDYA,K.T.TYCOWSKI,S.J.DEGREGORIO,J.WANG, JRNL AUTH 2 M.D.SHU,T.A.STEITZ,J.A.STEITZ JRNL TITL RNA STABILIZATION BY A POLY(A) TAIL 3'-END BINDING POCKET JRNL TITL 2 AND OTHER MODES OF POLY(A)-RNA INTERACTION. JRNL REF SCIENCE V. 371 2021 JRNL REFN ESSN 1095-9203 JRNL PMID 33414189 JRNL DOI 10.1126/SCIENCE.ABE6523 REMARK 2 REMARK 2 RESOLUTION. 2.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 2.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 11269 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 581 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 564 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.4540 REMARK 3 BIN FREE R VALUE SET COUNT : 22 REMARK 3 BIN FREE R VALUE : 0.4630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 2324 REMARK 3 HETEROGEN ATOMS : 103 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 108.8 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.70000 REMARK 3 B22 (A**2) : 0.70000 REMARK 3 B33 (A**2) : -2.28000 REMARK 3 B12 (A**2) : 0.35000 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): 0.707 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.314 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.290 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.955 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2700 ; 0.008 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): 1301 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4284 ; 1.951 ; 1.392 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3067 ; 1.675 ; 2.983 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): 437 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1282 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 564 ; 0.001 ; 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 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7JNH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9272 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11859 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.890 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 16.40 REMARK 200 R MERGE (I) : 0.14700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 10.20 REMARK 200 R MERGE FOR SHELL (I) : 3.29300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.660 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: DENE REMARK 200 REMARK 200 REMARK: ROD SHAPED CRYSTALS APPEARED WITHIN 7 TO 20 DAYS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM SODIUM CACODYLATE, PH 7.0, 9 MM REMARK 280 MGCL2, 1.8 MM COBALT (III) HEXAMINE CHLORIDE, 0.9 MM SPERMIDINE, REMARK 280 2.5 MM SPERMINE AND 5% PEG 400, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-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 67.39033 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 134.78067 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 67.39033 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 134.78067 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.39033 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 134.78067 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 67.39033 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 134.78067 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: 9430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -179.0 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 A A 17 REMARK 465 A A 18 REMARK 465 A A 19 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 A A 16 C5' C4' O4' C3' O3' C2' O2' REMARK 470 A A 16 C1' N9 C8 N7 C5 C6 N6 REMARK 470 A A 16 N1 C2 N3 C4 REMARK 470 A A 20 P OP1 OP2 O5' C5' C4' O4' REMARK 470 A A 20 C3' C2' O2' C1' N9 C8 N7 REMARK 470 A A 20 C5 C6 N6 N1 C2 N3 C4 REMARK 470 A B 21 OP2 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 OP2 A A 15 O2' A B 14 1.90 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 B 3 C2' - C3' - O3' ANGL. DEV. = 16.9 DEGREES REMARK 500 A B 21 O5' - P - OP1 ANGL. DEV. = 7.8 DEGREES REMARK 500 U B 25 C2' - C3' - O3' ANGL. DEV. = 9.8 DEGREES REMARK 500 U B 60 O5' - P - OP2 ANGL. DEV. = 8.0 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 MG B 118 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 201 O REMARK 620 2 HOH A 203 O 90.0 REMARK 620 3 HOH A 204 O 88.5 90.3 REMARK 620 4 HOH B 204 O 91.7 87.3 177.5 REMARK 620 5 HOH B 206 O 87.4 177.2 90.3 92.2 REMARK 620 6 HOH B 213 O 179.0 90.7 92.2 87.6 92.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 116 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 202 O REMARK 620 2 HOH A 205 O 92.9 REMARK 620 3 HOH B 201 O 176.9 86.2 REMARK 620 4 HOH B 203 O 88.4 93.0 88.7 REMARK 620 5 HOH B 207 O 90.8 87.9 92.2 178.8 REMARK 620 6 HOH B 208 O 89.0 175.8 92.1 90.8 88.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 117 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 202 O REMARK 620 2 HOH B 205 O 178.4 REMARK 620 3 HOH B 209 O 90.4 91.2 REMARK 620 4 HOH B 210 O 90.7 88.9 92.9 REMARK 620 5 HOH B 211 O 90.4 89.9 87.7 178.7 REMARK 620 6 HOH B 212 O 90.7 87.7 178.2 88.5 90.9 REMARK 620 N 1 2 3 4 5 DBREF 7JNH A 1 28 PDB 7JNH 7JNH 1 28 DBREF1 7JNH B 5 40 GB AL442105.2 DBREF2 7JNH B AL442105.2 27466 27501 DBREF1 7JNH B 51 82 GB AL442105.2 DBREF2 7JNH B AL442105.2 27424 27455 SEQADV 7JNH G B 1 GB AL442105. INSERTION SEQADV 7JNH G B 2 GB AL442105. INSERTION SEQADV 7JNH G B 3 GB AL442105. INSERTION SEQADV 7JNH C B 4 GB AL442105. INSERTION SEQADV 7JNH G B 41 GB AL442105. LINKER SEQADV 7JNH G B 42 GB AL442105. LINKER SEQADV 7JNH C B 43 GB AL442105. LINKER SEQADV 7JNH G B 44 GB AL442105. LINKER SEQADV 7JNH A B 45 GB AL442105. LINKER SEQADV 7JNH A B 46 GB AL442105. LINKER SEQADV 7JNH A B 47 GB AL442105. LINKER SEQADV 7JNH G B 48 GB AL442105. LINKER SEQADV 7JNH U B 49 GB AL442105. LINKER SEQADV 7JNH C B 50 GB AL442105. LINKER SEQADV 7JNH G B 83 GB AL442105. INSERTION SEQADV 7JNH C B 84 GB AL442105. INSERTION SEQADV 7JNH C B 85 GB AL442105. INSERTION SEQADV 7JNH CCC B 86 GB AL442105. INSERTION SEQRES 1 A 28 A A A A A A A A A A A A A SEQRES 2 A 28 A A A A A A A A A A A A A SEQRES 3 A 28 A A SEQRES 1 B 86 G G G C U G A G U U U U U SEQRES 2 B 86 A C A U G A C A A A G U U SEQRES 3 B 86 U U U A A C G A G G C A G SEQRES 4 B 86 C G G C G A A A G U C G C SEQRES 5 B 86 U G U A C U C U U U U C U SEQRES 6 B 86 U U G U C A U G G U U U U SEQRES 7 B 86 C U C A G C C CCC HET CCC B 86 23 HET SR A 101 1 HET SR A 102 1 HET SR A 103 1 HET NCO A 104 7 HET SR B 101 1 HET SR B 102 1 HET SR B 103 1 HET NCO B 104 7 HET NCO B 105 7 HET NCO B 106 7 HET NCO B 107 7 HET NCO B 108 7 HET NCO B 109 7 HET NCO B 110 7 HET NCO B 111 7 HET NCO B 112 7 HET NCO B 113 7 HET NCO B 114 7 HET SPD B 115 10 HET MG B 116 1 HET MG B 117 1 HET MG B 118 1 HETNAM CCC CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM SR STRONTIUM ION HETNAM NCO COBALT HEXAMMINE(III) HETNAM SPD SPERMIDINE HETNAM MG MAGNESIUM ION HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 2 CCC C9 H13 N3 O10 P2 FORMUL 3 SR 6(SR 2+) FORMUL 6 NCO 12(CO H18 N6 3+) FORMUL 21 SPD C7 H19 N3 FORMUL 22 MG 3(MG 2+) FORMUL 25 HOH *18(H2 O) LINK O3' C B 85 P CCC B 86 1555 1555 1.60 LINK O HOH A 201 MG MG B 118 10556 1555 2.17 LINK O HOH A 202 MG MG B 116 6554 1555 2.18 LINK O HOH A 203 MG MG B 118 10556 1555 2.18 LINK O HOH A 204 MG MG B 118 10556 1555 2.19 LINK O HOH A 205 MG MG B 116 6554 1555 2.18 LINK MG MG B 116 O HOH B 201 1555 1555 2.18 LINK MG MG B 116 O HOH B 203 1555 6554 2.19 LINK MG MG B 116 O HOH B 207 1555 1555 2.18 LINK MG MG B 116 O HOH B 208 1555 1555 2.19 LINK MG MG B 117 O HOH B 202 1555 1555 2.19 LINK MG MG B 117 O HOH B 205 1555 1555 2.18 LINK MG MG B 117 O HOH B 209 1555 1555 2.19 LINK MG MG B 117 O HOH B 210 1555 1555 2.20 LINK MG MG B 117 O HOH B 211 1555 1555 2.19 LINK MG MG B 117 O HOH B 212 1555 1555 2.18 LINK MG MG B 118 O HOH B 204 1555 1555 2.18 LINK MG MG B 118 O HOH B 206 1555 1555 2.19 LINK MG MG B 118 O HOH B 213 1555 1555 2.19 CRYST1 93.973 93.973 202.171 90.00 90.00 120.00 P 64 2 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 0.010641 0.006144 0.000000 0.00000 SCALE2 0.000000 0.012288 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004946 0.00000