PDB Short entry for 3EGZ HEADER RNA 11-SEP-08 3EGZ TITLE CRYSTAL STRUCTURE OF AN IN VITRO EVOLVED TETRACYCLINE APTAMER AND TITLE 2 ARTIFICIAL RIBOSWITCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: U1 SNRNP PROTEIN A, U1A PROTEIN, U1-A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TETRACYCLINE APTAMER AND ARTIFICIAL RIBOSWITCH; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SNRPA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: IN VITRO EVOLVED APTAMER KEYWDS TETRACYCLINE, APTAMER, RIBOSWITCH, ANTIBIOTIC, RNA EXPDTA X-RAY DIFFRACTION AUTHOR H.XIAO,T.E.EDWARDS,A.R.FERRE-D'AMARE REVDAT 5 20-OCT-21 3EGZ 1 REMARK SEQADV LINK REVDAT 4 25-OCT-17 3EGZ 1 REMARK REVDAT 3 15-SEP-10 3EGZ 1 JRNL REVDAT 2 24-FEB-09 3EGZ 1 VERSN REVDAT 1 28-OCT-08 3EGZ 0 JRNL AUTH H.XIAO,T.E.EDWARDS,A.R.FERRE-D'AMARE JRNL TITL STRUCTURAL BASIS FOR SPECIFIC, HIGH-AFFINITY TETRACYCLINE JRNL TITL 2 BINDING BY AN IN VITRO EVOLVED APTAMER AND ARTIFICIAL JRNL TITL 3 RIBOSWITCH JRNL REF CHEM.BIOL. V. 15 1125 2008 JRNL REFN ISSN 1074-5521 JRNL PMID 18940672 JRNL DOI 10.1016/J.CHEMBIOL.2008.09.004 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0067 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 21171 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2156 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1347 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE SET COUNT : 158 REMARK 3 BIN FREE R VALUE : 0.4340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 727 REMARK 3 NUCLEIC ACID ATOMS : 1380 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 146 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.12000 REMARK 3 B22 (A**2) : 1.12000 REMARK 3 B33 (A**2) : -2.24000 REMARK 3 B12 (A**2) : 0.00000 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): 0.235 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.207 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.146 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.694 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2321 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1057 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3461 ; 1.987 ; 2.701 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2668 ; 1.270 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 90 ; 6.360 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 33 ;32.527 ;23.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 140 ;15.349 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;15.365 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 442 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1511 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 297 ; 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): 455 ; 0.780 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 181 ; 0.143 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 735 ; 1.519 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1866 ; 2.081 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2726 ; 3.276 ; 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 : 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 REMARK 4 REMARK 4 3EGZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000049310. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-08 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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9570,0.9797,0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21415 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 29.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.00800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 37.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.80 REMARK 200 R MERGE FOR SHELL (I) : 0.53200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 MM RNA, 0.33 MM SELENOMETHIONINE REMARK 280 LABELED U1A-RBD DOUBLE MUTANT, 0.5 MM CHLOROTETRACYCLINE, 50 MM REMARK 280 TRIS PH 7.5, 5 MM MGCL2, 0.25 MM SPERMINE; 1UL MACROMOLECULAR REMARK 280 COMPLEX:1 UL RESERVOIR; 50 MM HEPES-KOH PH 7.0, 20 MM MGCL2, REMARK 280 12.5-15% PEG 8000; CRYO 30% GLYCEROL, 50 MM HEPES-KOH PH 7.0, 20 REMARK 280 MM MGCL2, 15% PEG 8000, 0.5 MM SPERMINE, 0.5 MM REMARK 280 CHLOROTETRACYCLINE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 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 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 60.41750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 60.41750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 60.41750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 60.41750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 60.41750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.41750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 60.41750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.41750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 20160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 54890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -383.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 120.83500 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 60.41750 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 60.41750 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 -60.41750 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 60.41750 REMARK 350 BIOMT3 4 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 MG MG A 510 LIES ON A SPECIAL POSITION. REMARK 375 MG MG B 505 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 327 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 434 LIES ON A SPECIAL POSITION. 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 MSE A 196 REMARK 465 ALA A 197 REMARK 465 VAL A 198 REMARK 465 PRO A 199 REMARK 465 GLU A 200 REMARK 465 MSE A 292 REMARK 465 LYS A 293 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 ARG A 202 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 245 CG CD CE NZ REMARK 470 LYS A 291 CG CD CE NZ REMARK 470 U B 43 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U B 43 C6 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 CG2 THR A 261 NH1 ARG A 265 2.07 REMARK 500 OP2 G B 9 O HOH B 313 2.10 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 G B 1 P G B 1 OP3 -0.124 REMARK 500 A B 17 O5' A B 17 C5' -0.065 REMARK 500 G B 31 O5' G B 31 C5' -0.060 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 ARG A 278 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 G B 1 OP1 - P - OP2 ANGL. DEV. = -13.6 DEGREES REMARK 500 G B 1 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 A B 2 C1' - O4' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 A B 2 C4' - C3' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 A B 2 O4' - C1' - C2' ANGL. DEV. = -8.0 DEGREES REMARK 500 G B 3 C3' - C2' - C1' ANGL. DEV. = -7.2 DEGREES REMARK 500 G B 3 N9 - C1' - C2' ANGL. DEV. = -9.1 DEGREES REMARK 500 A B 8 O4' - C1' - N9 ANGL. DEV. = -5.6 DEGREES REMARK 500 A B 13 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 A B 17 O5' - C5' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 A B 17 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 U B 18 C5' - C4' - C3' ANGL. DEV. = -10.1 DEGREES REMARK 500 U B 18 C1' - O4' - C4' ANGL. DEV. = -8.3 DEGREES REMARK 500 U B 18 C4' - C3' - C2' ANGL. DEV. = -13.1 DEGREES REMARK 500 C B 20 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 G B 31 O5' - P - OP2 ANGL. DEV. = -6.0 DEGREES REMARK 500 G B 31 O4' - C1' - N9 ANGL. DEV. = -5.8 DEGREES REMARK 500 G B 39 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 C B 40 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 C B 44 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 C B 50 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 274 -2.89 77.71 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 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 8 OP1 REMARK 620 2 HOH B 312 O 87.1 REMARK 620 3 HOH B 320 O 89.1 154.4 REMARK 620 4 HOH B 321 O 77.9 79.3 75.2 REMARK 620 5 HOH B 322 O 165.7 89.0 88.5 87.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 505 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 11 OP1 REMARK 620 2 HOH B 334 O 66.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 13 OP2 REMARK 620 2 HOH B 409 O 92.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 15 OP2 REMARK 620 2 HOH B 429 O 75.7 REMARK 620 3 HOH B 430 O 108.7 155.7 REMARK 620 4 HOH B 443 O 161.6 90.9 78.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 512 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 21 OP2 REMARK 620 2 HOH B 438 O 100.3 REMARK 620 3 HOH B 439 O 108.3 78.3 REMARK 620 4 CTC B 601 O11 93.8 84.7 154.1 REMARK 620 5 CTC B 601 O12 163.0 84.1 88.7 70.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 511 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 30 N7 REMARK 620 2 HOH B 389 O 118.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 509 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 37 O4 REMARK 620 2 HOH B 340 O 89.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 506 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 54 OP1 REMARK 620 2 A B 55 OP2 86.4 REMARK 620 3 HOH B 313 O 91.7 166.2 REMARK 620 4 HOH B 323 O 87.3 97.6 96.0 REMARK 620 5 HOH B 427 O 163.0 76.6 105.1 93.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 507 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 57 OP2 REMARK 620 2 HOH B 314 O 80.1 REMARK 620 3 HOH B 315 O 80.0 71.6 REMARK 620 4 HOH B 335 O 169.8 100.1 90.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 301 O REMARK 620 2 HOH B 302 O 102.1 REMARK 620 3 HOH B 303 O 81.1 115.1 REMARK 620 4 HOH B 304 O 74.0 161.1 83.0 REMARK 620 5 HOH B 305 O 160.3 96.6 96.6 86.3 REMARK 620 6 HOH B 306 O 92.8 88.2 156.6 73.7 81.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 508 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 337 O REMARK 620 2 HOH B 338 O 111.3 REMARK 620 3 HOH B 349 O 173.5 66.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CTC B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 512 DBREF 3EGZ A 196 293 UNP P09012 SNRPA_HUMAN 1 98 DBREF 3EGZ B 1 65 PDB 3EGZ 3EGZ 1 65 SEQADV 3EGZ HIS A 226 UNP P09012 TYR 31 ENGINEERED MUTATION SEQADV 3EGZ ARG A 231 UNP P09012 GLN 36 ENGINEERED MUTATION SEQRES 1 A 98 MSE ALA VAL PRO GLU THR ARG PRO ASN HIS THR ILE TYR SEQRES 2 A 98 ILE ASN ASN LEU ASN GLU LYS ILE LYS LYS ASP GLU LEU SEQRES 3 A 98 LYS LYS SER LEU HIS ALA ILE PHE SER ARG PHE GLY GLN SEQRES 4 A 98 ILE LEU ASP ILE LEU VAL SER ARG SER LEU LYS MSE ARG SEQRES 5 A 98 GLY GLN ALA PHE VAL ILE PHE LYS GLU VAL SER SER ALA SEQRES 6 A 98 THR ASN ALA LEU ARG SER MSE GLN GLY PHE PRO PHE TYR SEQRES 7 A 98 ASP LYS PRO MSE ARG ILE GLN TYR ALA LYS THR ASP SER SEQRES 8 A 98 ASP ILE ILE ALA LYS MSE LYS SEQRES 1 B 65 G A G G G A G A G G U G A SEQRES 2 B 65 A G A A U A C G A C C A C SEQRES 3 B 65 C U A G G U A C C A U U G SEQRES 4 B 65 C A C U C C G G U A C C U SEQRES 5 B 65 A A A A C A U A C C C U C MODRES 3EGZ MSE A 246 MET SELENOMETHIONINE MODRES 3EGZ MSE A 267 MET SELENOMETHIONINE MODRES 3EGZ MSE A 277 MET SELENOMETHIONINE HET MSE A 246 8 HET MSE A 267 8 HET MSE A 277 8 HET MG A 510 1 HET CTC B 601 33 HET MG B 501 1 HET MG B 502 1 HET MG B 503 1 HET MG B 504 1 HET MG B 505 1 HET MG B 506 1 HET MG B 507 1 HET MG B 508 1 HET MG B 509 1 HET MG B 511 1 HET MG B 512 1 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM CTC 7-CHLOROTETRACYCLINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 3 MG 12(MG 2+) FORMUL 4 CTC C22 H23 CL N2 O8 FORMUL 16 HOH *146(H2 O) HELIX 1 1 LYS A 217 SER A 230 1 14 HELIX 2 2 ARG A 231 GLY A 233 5 3 HELIX 3 3 GLU A 256 GLN A 268 1 13 SHEET 1 A 4 ILE A 235 VAL A 240 0 SHEET 2 A 4 ALA A 250 PHE A 254 -1 O ILE A 253 N LEU A 236 SHEET 3 A 4 THR A 206 ASN A 210 -1 N ILE A 209 O ALA A 250 SHEET 4 A 4 ARG A 278 TYR A 281 -1 O GLN A 280 N TYR A 208 SHEET 1 B 2 PRO A 271 PHE A 272 0 SHEET 2 B 2 LYS A 275 PRO A 276 -1 O LYS A 275 N PHE A 272 LINK C LYS A 245 N MSE A 246 1555 1555 1.32 LINK C MSE A 246 N ARG A 247 1555 1555 1.31 LINK C SER A 266 N MSE A 267 1555 1555 1.33 LINK C MSE A 267 N GLN A 268 1555 1555 1.33 LINK C PRO A 276 N MSE A 277 1555 1555 1.32 LINK C MSE A 277 N ARG A 278 1555 1555 1.33 LINK OP1 A B 8 MG MG B 502 1555 1555 2.19 LINK OP1 U B 11 MG MG B 505 1555 1555 2.49 LINK OP2 A B 13 MG MG B 504 1555 1555 1.93 LINK OP2 G B 15 MG MG B 503 1555 1555 2.10 LINK OP2 G B 21 MG MG B 512 1555 1555 1.98 LINK N7 G B 30 MG MG B 511 1555 1555 2.34 LINK O4 U B 37 MG MG B 509 1555 1555 2.74 LINK OP1 A B 54 MG MG B 506 1555 1555 2.43 LINK OP2 A B 55 MG MG B 506 1555 1555 2.29 LINK OP2 C B 57 MG MG B 507 1555 1555 2.33 LINK O HOH B 301 MG MG B 501 1555 1555 2.12 LINK O HOH B 302 MG MG B 501 1555 1555 2.01 LINK O HOH B 303 MG MG B 501 1555 1555 2.20 LINK O HOH B 304 MG MG B 501 1555 1555 2.16 LINK O HOH B 305 MG MG B 501 1555 1555 2.11 LINK O HOH B 306 MG MG B 501 1555 1555 2.16 LINK O HOH B 312 MG MG B 502 1555 1555 2.16 LINK O HOH B 313 MG MG B 506 1555 1555 2.31 LINK O HOH B 314 MG MG B 507 1555 1555 2.26 LINK O HOH B 315 MG MG B 507 1555 1555 2.14 LINK O HOH B 320 MG MG B 502 1555 1555 1.97 LINK O HOH B 321 MG MG B 502 1555 1555 2.12 LINK O HOH B 322 MG MG B 502 1555 1555 2.28 LINK O HOH B 323 MG MG B 506 1555 1555 2.34 LINK O HOH B 334 MG MG B 505 1555 1555 2.96 LINK O HOH B 335 MG MG B 507 1555 1555 2.23 LINK O HOH B 337 MG MG B 508 1555 1555 2.32 LINK O HOH B 338 MG MG B 508 1555 1555 2.09 LINK O HOH B 340 MG MG B 509 1555 1555 2.88 LINK O HOH B 349 MG MG B 508 1555 1555 2.27 LINK O HOH B 389 MG MG B 511 1555 1555 2.80 LINK O HOH B 409 MG MG B 504 1555 1555 2.26 LINK O HOH B 427 MG MG B 506 1555 1555 2.13 LINK O HOH B 429 MG MG B 503 1555 1555 1.96 LINK O HOH B 430 MG MG B 503 1555 1555 2.13 LINK O HOH B 438 MG MG B 512 1555 1555 2.28 LINK O HOH B 439 MG MG B 512 1555 1555 1.98 LINK O HOH B 443 MG MG B 503 1555 1555 1.82 LINK MG MG B 512 O11 CTC B 601 1555 1555 2.00 LINK MG MG B 512 O12 CTC B 601 1555 1555 2.21 SITE 1 AC1 11 G B 7 G B 15 U B 18 G B 21 SITE 2 AC1 11 A B 22 U B 59 A B 60 C B 61 SITE 3 AC1 11 HOH B 438 HOH B 439 MG B 512 SITE 1 AC2 6 HOH B 301 HOH B 302 HOH B 303 HOH B 304 SITE 2 AC2 6 HOH B 305 HOH B 306 SITE 1 AC3 5 A B 8 HOH B 312 HOH B 320 HOH B 321 SITE 2 AC3 5 HOH B 322 SITE 1 AC4 4 G B 15 HOH B 429 HOH B 430 HOH B 443 SITE 1 AC5 2 A B 13 HOH B 409 SITE 1 AC6 2 U B 11 HOH B 334 SITE 1 AC7 5 A B 54 A B 55 HOH B 313 HOH B 323 SITE 2 AC7 5 HOH B 427 SITE 1 AC8 4 C B 57 HOH B 314 HOH B 315 HOH B 335 SITE 1 AC9 3 HOH B 337 HOH B 338 HOH B 349 SITE 1 BC1 2 U B 37 HOH B 340 SITE 1 BC2 3 A B 29 G B 30 HOH B 389 SITE 1 BC3 4 G B 21 HOH B 438 HOH B 439 CTC B 601 CRYST1 120.835 120.835 55.279 90.00 90.00 90.00 P 4 21 2 8 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 0.008276 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008276 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018090 0.00000