PDB Short entry for 3MUR HEADER RNA BINDING PROTEIN/RNA 03-MAY-10 3MUR TITLE CRYSTAL STRUCTURE OF THE C92U MUTANT C-DI-GMP RIBOSWITH BOUND TO C-DI- TITLE 2 GMP 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: C92U MUTANT 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 4 06-SEP-23 3MUR 1 REMARK REVDAT 3 06-OCT-21 3MUR 1 REMARK SEQADV HETSYN LINK REVDAT 2 22-SEP-10 3MUR 1 JRNL REVDAT 1 25-AUG-10 3MUR 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. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 6324 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) : 0.200 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 317 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 232 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 10 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 734 REMARK 3 NUCLEIC ACID ATOMS : 1984 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 72.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.65000 REMARK 3 B22 (A**2) : -5.47000 REMARK 3 B33 (A**2) : 2.49000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.90000 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): 0.519 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.506 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 54.962 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3031 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4576 ; 1.129 ; 2.771 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 89 ; 4.520 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 34 ;34.039 ;23.235 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 150 ;14.584 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;14.554 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 577 ; 0.054 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1531 ; 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): 449 ; 1.354 ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 727 ; 2.376 ;10.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2582 ; 1.302 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3848 ; 2.185 ;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 : 2 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 : P 7 P 93 REMARK 3 ORIGIN FOR THE GROUP (A): -6.1350 18.3268 -38.5607 REMARK 3 T TENSOR REMARK 3 T11: 0.1137 T22: 0.6467 REMARK 3 T33: 0.3397 T12: 0.0967 REMARK 3 T13: -0.0635 T23: 0.0292 REMARK 3 L TENSOR REMARK 3 L11: 11.5566 L22: 23.4223 REMARK 3 L33: 6.7381 L12: 0.9551 REMARK 3 L13: 0.9859 L23: -6.9415 REMARK 3 S TENSOR REMARK 3 S11: 0.4891 S12: 1.3934 S13: 1.2061 REMARK 3 S21: -0.1784 S22: 0.0517 S23: 0.0019 REMARK 3 S31: -0.1876 S32: 0.4667 S33: -0.5408 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 8 R 98 REMARK 3 ORIGIN FOR THE GROUP (A): -7.9593 -2.7314 0.6800 REMARK 3 T TENSOR REMARK 3 T11: 0.1527 T22: 0.0921 REMARK 3 T33: 0.1107 T12: 0.0366 REMARK 3 T13: 0.0393 T23: 0.0260 REMARK 3 L TENSOR REMARK 3 L11: 3.6567 L22: 2.5570 REMARK 3 L33: 2.8477 L12: 0.9615 REMARK 3 L13: -1.4035 L23: -0.4052 REMARK 3 S TENSOR REMARK 3 S11: 0.1009 S12: -0.0748 S13: -0.1977 REMARK 3 S21: 0.0913 S22: -0.0611 S23: 0.2837 REMARK 3 S31: -0.1485 S32: -0.4689 S33: -0.0398 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 3MUR 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_1000059018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-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 : 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 DOUBLE CRYSTAL REMARK 200 OPTICS : PT-COATED 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 : 6324 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%) : 94.7 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.16400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.57900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 42.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 550 MME, 5 MM MGSO4, 50 MM REMARK 280 MES, PH 6.0, 300 MM NACL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 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 22.63600 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: 3600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 MET P 97 REMARK 465 LYS P 98 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CB SER P 35 OD2 ASP P 79 2554 2.12 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 R 670 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH R 718 O REMARK 620 2 HOH R 719 O 178.9 REMARK 620 3 HOH R 720 O 90.1 90.1 REMARK 620 4 HOH R 721 O 89.6 90.3 178.7 REMARK 620 5 HOH R 722 O 90.6 90.5 90.1 91.2 REMARK 620 6 HOH R 723 O 89.3 89.6 89.8 88.9 179.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG R 671 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH R 724 O REMARK 620 2 HOH R 725 O 178.6 REMARK 620 3 HOH R 726 O 89.1 90.0 REMARK 620 4 HOH R 727 O 89.9 91.0 178.8 REMARK 620 5 HOH R 728 O 90.0 89.1 91.3 88.1 REMARK 620 6 HOH R 729 O 89.1 91.8 88.3 92.2 179.0 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 C2E R 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 670 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG R 671 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: 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: 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: 3MXH RELATED DB: PDB REMARK 900 STRUCTURE OF A C-DI-GMP RIBOSWITCH FROM V. CHOLERAE BOUND TO NATIVE REMARK 900 METALS REMARK 900 RELATED ID: 3IRW RELATED DB: PDB REMARK 900 THE ORIGINAL REPORT OF THE STRUCTURE OF THIS RIBOSWITCH (WILD-TYPE) DBREF 3MUR P 1 98 UNP P09012 SNRPA_HUMAN 1 98 DBREF 3MUR R 8 98 PDB 3MUR 3MUR 8 98 SEQADV 3MUR HIS P 31 UNP P09012 TYR 31 ENGINEERED MUTATION SEQADV 3MUR 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 U C G A U G SEQRES 8 R 92 G MODRES 3MUR GTP R 8 G GUANOSINE-5'-TRIPHOSPHATE HET GTP R 8 32 HET C2E R 1 46 HET MG R 670 1 HET MG R 671 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE 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) HETNAM MG MAGNESIUM ION HETSYN C2E C-DI-GMP; CYCLIC DIGUANOSINE MONOPHOSPHATE FORMUL 2 GTP C10 H16 N5 O14 P3 FORMUL 3 C2E C20 H24 N10 O14 P2 FORMUL 4 MG 2(MG 2+) FORMUL 6 HOH *30(H2 O) HELIX 1 1 LYS P 22 SER P 35 1 14 HELIX 2 2 ARG P 36 GLY P 38 5 3 HELIX 3 3 GLU P 61 GLN P 73 1 13 SHEET 1 A 4 ILE P 40 VAL P 45 0 SHEET 2 A 4 ALA P 55 PHE P 59 -1 O PHE P 56 N LEU P 44 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 1.60 LINK MG MG R 670 O HOH R 718 1555 1555 2.18 LINK MG MG R 670 O HOH R 719 1555 1555 2.19 LINK MG MG R 670 O HOH R 720 1555 1555 2.18 LINK MG MG R 670 O HOH R 721 1555 1555 2.18 LINK MG MG R 670 O HOH R 722 1555 1555 2.18 LINK MG MG R 670 O HOH R 723 1555 1555 2.18 LINK MG MG R 671 O HOH R 724 1555 1555 2.19 LINK MG MG R 671 O HOH R 725 1555 1555 2.18 LINK MG MG R 671 O HOH R 726 1555 1555 2.18 LINK MG MG R 671 O HOH R 727 1555 1555 2.19 LINK MG MG R 671 O HOH R 728 1555 1555 2.18 LINK MG MG R 671 O HOH R 729 1555 1555 2.18 SITE 1 AC1 16 G R 14 A R 16 C R 17 A R 18 SITE 2 AC1 16 G R 19 G R 20 G R 21 C R 46 SITE 3 AC1 16 A R 47 A R 48 A R 49 U R 92 SITE 4 AC1 16 C R 93 MG R 670 HOH R 718 HOH R 722 SITE 1 AC2 7 C2E R 1 HOH R 718 HOH R 719 HOH R 720 SITE 2 AC2 7 HOH R 721 HOH R 722 HOH R 723 SITE 1 AC3 7 G R 57 HOH R 724 HOH R 725 HOH R 726 SITE 2 AC3 7 HOH R 727 HOH R 728 HOH R 729 CRYST1 49.915 45.272 78.616 90.00 94.96 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 0.020034 0.000000 0.001739 0.00000 SCALE2 0.000000 0.022089 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012768 0.00000