HEADER RNA BINDING PROTEIN/RNA 07-MAY-10 3MXH TITLE NATIVE STRUCTURE OF A C-DI-GMP RIBOSWITCH FROM V. CHOLERAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A; COMPND 3 CHAIN: P; COMPND 4 FRAGMENT: UNP RESIDUES 1-98; COMPND 5 SYNONYM: U1 SNRNP A, U1-A, U1A; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: C-DI-GMP RIBOSWITCH; COMPND 10 CHAIN: R; COMPND 11 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: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: IN VITRO TRANSCRIBED FROM LINEAR DNA KEYWDS RNA, RIBOSWITCH, C-DI-GMP, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.A.STROBEL,K.D.SMITH REVDAT 3 06-SEP-23 3MXH 1 REMARK SEQADV HETSYN LINK REVDAT 2 22-SEP-10 3MXH 1 JRNL REVDAT 1 25-AUG-10 3MXH 0 JRNL AUTH K.D.SMITH,S.V.LIPCHOCK,A.L.LIVINGSTON,C.A.SHANAHAN, JRNL AUTH 2 S.A.STROBEL JRNL TITL STRUCTURAL AND BIOCHEMICAL DETERMINANTS OF LIGAND BINDING BY JRNL TITL 2 THE C-DI-GMP RIBOSWITCH . JRNL REF BIOCHEMISTRY V. 49 7351 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20690679 JRNL DOI 10.1021/BI100671E REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 15201 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 816 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1019 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.4650 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.4130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 712 REMARK 3 NUCLEIC ACID ATOMS : 1984 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.92000 REMARK 3 B22 (A**2) : -0.50000 REMARK 3 B33 (A**2) : -1.98000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.33000 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): 0.247 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.204 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.433 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3020 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4567 ; 0.936 ; 2.777 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 86 ; 5.313 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 34 ;37.972 ;23.235 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 144 ;14.270 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;17.356 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 573 ; 0.046 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1519 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 434 ; 0.918 ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 703 ; 1.576 ;10.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2586 ; 1.382 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3863 ; 2.122 ;10.000 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 : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : R 8 R 20 REMARK 3 ORIGIN FOR THE GROUP (A): -14.2399 -4.3803 22.3020 REMARK 3 T TENSOR REMARK 3 T11: 0.4632 T22: 0.2931 REMARK 3 T33: 0.1569 T12: 0.0199 REMARK 3 T13: 0.1601 T23: 0.0195 REMARK 3 L TENSOR REMARK 3 L11: 17.1276 L22: 7.0041 REMARK 3 L33: 7.0560 L12: 2.5107 REMARK 3 L13: 1.1895 L23: -1.9606 REMARK 3 S TENSOR REMARK 3 S11: 0.1639 S12: -0.8546 S13: -0.5377 REMARK 3 S21: 0.8490 S22: -0.1776 S23: 0.4128 REMARK 3 S31: 0.0910 S32: -0.3856 S33: 0.0137 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : R 21 R 65 REMARK 3 ORIGIN FOR THE GROUP (A): -2.2192 -1.7566 -6.0709 REMARK 3 T TENSOR REMARK 3 T11: 0.2817 T22: 0.1041 REMARK 3 T33: 0.1784 T12: 0.0457 REMARK 3 T13: -0.0720 T23: 0.0279 REMARK 3 L TENSOR REMARK 3 L11: 2.2231 L22: 2.5465 REMARK 3 L33: 2.2971 L12: 0.7402 REMARK 3 L13: -1.4779 L23: -0.0342 REMARK 3 S TENSOR REMARK 3 S11: -0.0468 S12: 0.4048 S13: -0.0374 REMARK 3 S21: -0.4174 S22: 0.0628 S23: 0.1106 REMARK 3 S31: -0.0508 S32: -0.2331 S33: -0.0160 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : R 75 R 98 REMARK 3 ORIGIN FOR THE GROUP (A): -15.0206 -4.0060 2.9990 REMARK 3 T TENSOR REMARK 3 T11: 0.2549 T22: 0.2456 REMARK 3 T33: 0.3190 T12: 0.0814 REMARK 3 T13: 0.0189 T23: 0.0222 REMARK 3 L TENSOR REMARK 3 L11: 2.0878 L22: 2.3987 REMARK 3 L33: 5.0541 L12: 0.7014 REMARK 3 L13: 0.6373 L23: -0.4760 REMARK 3 S TENSOR REMARK 3 S11: -0.0147 S12: 0.2956 S13: 0.0208 REMARK 3 S21: -0.1695 S22: 0.0196 S23: 0.3893 REMARK 3 S31: -0.3833 S32: -0.6250 S33: -0.0049 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : R 660 R 669 REMARK 3 ORIGIN FOR THE GROUP (A): -17.7168 10.0842 -32.7336 REMARK 3 T TENSOR REMARK 3 T11: 0.3427 T22: 0.5249 REMARK 3 T33: 1.1319 T12: 0.0481 REMARK 3 T13: -0.0876 T23: -0.0748 REMARK 3 L TENSOR REMARK 3 L11: 9.2811 L22: 3.3611 REMARK 3 L33: 5.4248 L12: 2.4823 REMARK 3 L13: -3.6152 L23: -4.2577 REMARK 3 S TENSOR REMARK 3 S11: 0.9414 S12: -0.0554 S13: 1.7623 REMARK 3 S21: 0.2947 S22: 0.4019 S23: 1.1096 REMARK 3 S31: -0.4251 S32: -0.3753 S33: -1.3432 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : P 7 P 93 REMARK 3 ORIGIN FOR THE GROUP (A): -7.0168 16.3283 -40.3012 REMARK 3 T TENSOR REMARK 3 T11: 0.2482 T22: 0.3578 REMARK 3 T33: 0.7960 T12: 0.0520 REMARK 3 T13: -0.0008 T23: 0.0215 REMARK 3 L TENSOR REMARK 3 L11: 8.5598 L22: 26.6322 REMARK 3 L33: 10.8829 L12: 1.6941 REMARK 3 L13: -1.4201 L23: -7.7860 REMARK 3 S TENSOR REMARK 3 S11: 0.5642 S12: 0.5106 S13: 1.8324 REMARK 3 S21: -0.9445 S22: -0.0686 S23: 0.4835 REMARK 3 S31: -0.6197 S32: 0.2963 S33: -0.4956 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3MXH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1000059116. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A 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 : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : VERTICALLY FOCUSING MIRROR 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15201 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.52800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: PDB ENTRY 3IRW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG550MME, 50 MM MES, PH 6.0, 5 MM REMARK 280 MGSO4, 300 MM NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K 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 22.82600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, R 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 MET P 1 REMARK 465 ALA P 2 REMARK 465 VAL P 3 REMARK 465 PRO P 4 REMARK 465 GLU P 5 REMARK 465 THR P 6 REMARK 465 ILE P 94 REMARK 465 ALA P 95 REMARK 465 LYS P 96 REMARK 465 MET P 97 REMARK 465 LYS P 98 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 A R 48 O4' - C1' - N9 ANGL. DEV. = 6.2 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 THR P 89 115.32 -165.90 REMARK 500 SER P 91 -91.60 -77.07 REMARK 500 ASP P 92 -126.61 42.63 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 P 99 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH P 109 O REMARK 620 2 HOH P 110 O 179.9 REMARK 620 3 HOH P 111 O 89.9 89.9 REMARK 620 4 HOH P 112 O 90.0 90.1 179.8 REMARK 620 5 HOH P 113 O 90.0 90.0 90.0 90.2 REMARK 620 6 HOH P 114 O 90.1 89.9 90.1 89.7 179.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG R 2 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH R 734 O REMARK 620 2 HOH R 735 O 179.7 REMARK 620 3 HOH R 736 O 89.9 90.4 REMARK 620 4 HOH R 737 O 90.0 89.7 179.7 REMARK 620 5 HOH R 738 O 89.9 90.1 90.1 90.1 REMARK 620 6 HOH R 739 O 90.5 89.6 89.7 90.0 179.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG R 4 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH R 100 O REMARK 620 2 HOH R 161 O 67.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG R 5 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G R 42 O6 REMARK 620 2 HOH R 740 O 83.8 REMARK 620 3 HOH R 741 O 96.2 179.8 REMARK 620 4 HOH R 742 O 82.7 90.4 89.8 REMARK 620 5 HOH R 743 O 96.5 89.5 90.4 179.3 REMARK 620 6 HOH R 744 O 170.1 90.0 90.0 89.6 91.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG R 670 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A R 48 OP2 REMARK 620 2 HOH R 729 O 158.8 REMARK 620 3 HOH R 730 O 110.5 90.4 REMARK 620 4 HOH R 731 O 69.9 89.1 179.5 REMARK 620 5 HOH R 732 O 88.0 88.9 89.5 90.4 REMARK 620 6 HOH R 733 O 92.6 90.6 90.3 89.8 179.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG P 99 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C2E R 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 670 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MUM RELATED DB: PDB REMARK 900 STRUCTURE OF THE G20A MUTANT C-DI-GMP RIBOSWITH BOUND TO C-DI-GMP REMARK 900 RELATED ID: 3MUR RELATED DB: PDB REMARK 900 STRUCTURE OF THE C92U MUTANT C-DI-GMP RIBOSWITH BOUND TO C-DI-GMP REMARK 900 RELATED ID: 3MUT RELATED DB: PDB REMARK 900 STRUCTURE OF THE G20A/C92U MUTANT C-DI-GMP RIBOSWITH BOUND TO C-DI- REMARK 900 GMP REMARK 900 RELATED ID: 3MUV RELATED DB: PDB REMARK 900 STRUCTURE OF THE G20A/C92U MUTANT C-DI-GMP RIBOSWITH BOUND TO C-DI- REMARK 900 AMP REMARK 900 RELATED ID: 3IRW RELATED DB: PDB REMARK 900 THE ORIGINAL REPORT OF THE STRUCTURE OF THIS RIBOSWITCH (WILD-TYPE) DBREF 3MXH P 1 98 UNP P09012 SNRPA_HUMAN 1 98 DBREF 3MXH R 8 98 PDB 3MXH 3MXH 8 98 SEQADV 3MXH HIS P 31 UNP P09012 TYR 31 ENGINEERED MUTATION SEQADV 3MXH ARG P 36 UNP P09012 GLN 36 ENGINEERED MUTATION SEQRES 1 P 98 MET ALA VAL PRO GLU THR ARG PRO ASN HIS THR ILE TYR SEQRES 2 P 98 ILE ASN ASN LEU ASN GLU LYS ILE LYS LYS ASP GLU LEU SEQRES 3 P 98 LYS LYS SER LEU HIS ALA ILE PHE SER ARG PHE GLY GLN SEQRES 4 P 98 ILE LEU ASP ILE LEU VAL SER ARG SER LEU LYS MET ARG SEQRES 5 P 98 GLY GLN ALA PHE VAL ILE PHE LYS GLU VAL SER SER ALA SEQRES 6 P 98 THR ASN ALA LEU ARG SER MET GLN GLY PHE PRO PHE TYR SEQRES 7 P 98 ASP LYS PRO MET ARG ILE GLN TYR ALA LYS THR ASP SER SEQRES 8 P 98 ASP ILE ILE ALA LYS MET LYS SEQRES 1 R 92 GTP G U C A C G C A C A G G SEQRES 2 R 92 G C A A A C C A U U C G A SEQRES 3 R 92 A A G A G U G G G A C G C SEQRES 4 R 92 A A A G C C U C C G G C C SEQRES 5 R 92 U A A A C C A U U G C A C SEQRES 6 R 92 U C C G G U A G G U A G C SEQRES 7 R 92 G G G G U U A C C G A U G SEQRES 8 R 92 G MODRES 3MXH GTP R 8 G GUANOSINE-5'-TRIPHOSPHATE HET GTP R 8 32 HET MG P 99 1 HET C2E R 1 46 HET MG R 670 1 HET MG R 2 1 HET MG R 4 1 HET MG R 5 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM C2E 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10, HETNAM 2 C2E 12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3, HETNAM 3 C2E 2-D:3',2'-J][1,3,7,9,2, HETNAM 4 C2E 8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO- HETNAM 5 C2E 1,9-DIHYDRO-6H-PURIN-6-ONE) HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 MG 5(MG 2+) FORMUL 4 C2E C20 H24 N10 O14 P2 FORMUL 9 HOH *169(H2 O) HELIX 1 1 LYS P 22 SER P 35 1 14 HELIX 2 2 GLU P 61 MET P 72 1 12 SHEET 1 A 4 ILE P 40 LEU P 44 0 SHEET 2 A 4 ALA P 55 PHE P 59 -1 O ILE P 58 N LEU P 41 SHEET 3 A 4 THR P 11 ASN P 15 -1 N ILE P 14 O ALA P 55 SHEET 4 A 4 ARG P 83 TYR P 86 -1 O GLN P 85 N TYR P 13 SHEET 1 B 2 PRO P 76 PHE P 77 0 SHEET 2 B 2 LYS P 80 PRO P 81 -1 O LYS P 80 N PHE P 77 LINK O3' GTP R 8 P G R 9 1555 1555 1.61 LINK MG MG P 99 O HOH P 109 1555 1555 2.18 LINK MG MG P 99 O HOH P 110 1555 1555 2.18 LINK MG MG P 99 O HOH P 111 1555 1555 2.18 LINK MG MG P 99 O HOH P 112 1555 1555 2.18 LINK MG MG P 99 O HOH P 113 1555 1555 2.18 LINK MG MG P 99 O HOH P 114 1555 1555 2.18 LINK MG MG R 2 O HOH R 734 1555 1555 2.19 LINK MG MG R 2 O HOH R 735 1555 1555 2.18 LINK MG MG R 2 O HOH R 736 1555 1555 2.18 LINK MG MG R 2 O HOH R 737 1555 1555 2.18 LINK MG MG R 2 O HOH R 738 1555 1555 2.18 LINK MG MG R 2 O HOH R 739 1555 1555 2.17 LINK MG MG R 4 O HOH R 100 1555 1555 2.21 LINK MG MG R 4 O HOH R 161 1555 1555 2.42 LINK MG MG R 5 O6 G R 42 1555 1555 2.40 LINK MG MG R 5 O HOH R 740 1555 1555 2.18 LINK MG MG R 5 O HOH R 741 1555 1555 2.18 LINK MG MG R 5 O HOH R 742 1555 1555 2.18 LINK MG MG R 5 O HOH R 743 1555 1555 2.18 LINK MG MG R 5 O HOH R 744 1555 1555 2.18 LINK OP2 A R 48 MG MG R 670 1555 1555 2.18 LINK MG MG R 670 O HOH R 729 1555 1555 2.18 LINK MG MG R 670 O HOH R 730 1555 1555 2.18 LINK MG MG R 670 O HOH R 731 1555 1555 2.18 LINK MG MG R 670 O HOH R 732 1555 1555 2.18 LINK MG MG R 670 O HOH R 733 1555 1555 2.18 SITE 1 AC1 7 ARG P 70 HOH P 109 HOH P 110 HOH P 111 SITE 2 AC1 7 HOH P 112 HOH P 113 HOH P 114 SITE 1 AC2 23 MG R 2 G R 14 A R 16 C R 17 SITE 2 AC2 23 A R 18 G R 20 G R 21 C R 46 SITE 3 AC2 23 A R 47 A R 48 A R 49 C R 92 SITE 4 AC2 23 C R 93 HOH R 140 HOH R 671 HOH R 673 SITE 5 AC2 23 HOH R 676 HOH R 687 HOH R 717 HOH R 732 SITE 6 AC2 23 HOH R 734 HOH R 736 HOH R 738 SITE 1 AC3 7 A R 47 A R 48 HOH R 729 HOH R 730 SITE 2 AC3 7 HOH R 731 HOH R 732 HOH R 733 SITE 1 AC4 7 C2E R 1 HOH R 734 HOH R 735 HOH R 736 SITE 2 AC4 7 HOH R 737 HOH R 738 HOH R 739 SITE 1 AC5 4 HOH R 70 U R 81 HOH R 100 HOH R 161 SITE 1 AC6 6 G R 42 HOH R 740 HOH R 741 HOH R 742 SITE 2 AC6 6 HOH R 743 HOH R 744 CRYST1 50.243 45.652 80.248 90.00 93.74 90.00 P 1 21 1 2 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 0.019903 0.000000 0.001300 0.00000 SCALE2 0.000000 0.021905 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012488 0.00000