HEADER RNA 15-AUG-12 4GMA TITLE CRYSTAL STRUCTURE OF THE ADENOSYLCOBALAMIN RIBOSWITCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENOSYLCOBALAMIN RIBOSWITCH; COMPND 3 CHAIN: Z; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: MARINE METAGENOME; SOURCE 4 ORGANISM_TAXID: 408172; SOURCE 5 OTHER_DETAILS: RNA WAS TRANSCRIBED VIA IN VITRO T7 RNA POLYMERASE KEYWDS ADENOSYLCOBALAMIN, RIBOSWITCH, ADOCBL, RNA EXPDTA X-RAY DIFFRACTION AUTHOR F.E.REYES,J.E.JOHNSON,J.T.POLASKI,R.T.BATEY REVDAT 4 28-FEB-24 4GMA 1 REMARK REVDAT 3 28-JUN-17 4GMA 1 REMARK REVDAT 2 26-DEC-12 4GMA 1 JRNL REVDAT 1 17-OCT-12 4GMA 0 JRNL AUTH J.E.JOHNSON,F.E.REYES,J.T.POLASKI,R.T.BATEY JRNL TITL B12 COFACTORS DIRECTLY STABILIZE AN MRNA REGULATORY SWITCH. JRNL REF NATURE V. 492 133 2012 JRNL REFN ISSN 0028-0836 JRNL PMID 23064232 JRNL DOI 10.1038/NATURE11607 REMARK 2 REMARK 2 RESOLUTION. 3.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 8706 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) : 0.263 REMARK 3 R VALUE (WORKING SET) : 0.262 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 REMARK 3 FREE R VALUE TEST SET COUNT : 411 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 9 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 3.94 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 4.41 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.23 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE : 0.2869 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 131 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 4140 REMARK 3 HETEROGEN ATOMS : 109 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 220.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.76200 REMARK 3 B22 (A**2) : -23.21900 REMARK 3 B33 (A**2) : 28.98100 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 1.310 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : NULL ; NULL ; NULL REMARK 3 BOND ANGLES : NULL ; NULL ; NULL REMARK 3 TORSION ANGLES : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS : NULL ; NULL ; NULL REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : NULL ; NULL ; NULL REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : NULL ; NULL ; NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL REMARK 3 OTHER TORSION ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { Z|301 - Z|301 } REMARK 3 ORIGIN FOR THE GROUP (A): -9.5088 -23.0948 26.6162 REMARK 3 T TENSOR REMARK 3 T11: 0.1415 T22: 0.0853 REMARK 3 T33: 0.0382 T12: 0.0456 REMARK 3 T13: -0.0916 T23: -0.0130 REMARK 3 L TENSOR REMARK 3 L11: 0.7708 L22: 0.8266 REMARK 3 L33: 1.0460 L12: -0.2893 REMARK 3 L13: -0.4552 L23: -0.1621 REMARK 3 S TENSOR REMARK 3 S11: -0.0030 S12: -0.0056 S13: 0.0187 REMARK 3 S21: -0.0027 S22: 0.0083 S23: 0.0023 REMARK 3 S31: 0.0006 S32: -0.0030 S33: -0.0053 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { Z|3 - Z|210 } REMARK 3 ORIGIN FOR THE GROUP (A): -8.9583 -29.9450 23.8196 REMARK 3 T TENSOR REMARK 3 T11: -0.1967 T22: -0.2211 REMARK 3 T33: -0.2560 T12: 0.2184 REMARK 3 T13: -0.0403 T23: -0.0222 REMARK 3 L TENSOR REMARK 3 L11: 3.4947 L22: 3.7970 REMARK 3 L33: 3.8119 L12: -0.3385 REMARK 3 L13: 1.6254 L23: 0.0074 REMARK 3 S TENSOR REMARK 3 S11: 0.1073 S12: 0.2685 S13: -0.1319 REMARK 3 S21: -0.3478 S22: -0.0049 S23: 0.2327 REMARK 3 S31: 0.4504 S32: -0.5674 S33: -0.1024 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4GMA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074361. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8706 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.940 REMARK 200 RESOLUTION RANGE LOW (A) : 88.374 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04800 REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.49800 REMARK 200 R SYM FOR SHELL (I) : 0.49800 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% ISOPROPANOL, 300 MM MAGNESIUM REMARK 280 CHLORIDE, 100 MM SODIUM HEPES PH 7.5, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 1.000000 0.000000 0.000000 48.32400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 121.77250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 48.32400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 121.77250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 48.32400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 121.77250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 48.32400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 121.77250 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z 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 G Z 1 REMARK 465 G Z 2 REMARK 465 A Z 25 REMARK 465 U Z 26 REMARK 465 U Z 27 REMARK 465 G Z 28 REMARK 465 C Z 29 REMARK 465 A Z 30 REMARK 465 C Z 31 REMARK 465 U Z 32 REMARK 465 G Z 107 REMARK 465 U Z 108 REMARK 465 A Z 109 REMARK 465 U Z 179 REMARK 465 U Z 180 REMARK 465 A Z 181 REMARK 465 G Z 182 REMARK 465 A Z 183 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 Z 96 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES REMARK 500 G Z 98 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 A Z 145 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B1Z Z 301 DBREF 4GMA Z 1 210 PDB 4GMA 4GMA 1 210 SEQRES 1 Z 210 G G U U A A A G C C U U A SEQRES 2 Z 210 U G G U C G C U A C C A U SEQRES 3 Z 210 U G C A C U C C G G U A G SEQRES 4 Z 210 C G U U A A A A G G G A A SEQRES 5 Z 210 G A C G G G U G A G A A U SEQRES 6 Z 210 C C C G C G C A G C C C C SEQRES 7 Z 210 C G C U A C U G U G A G G SEQRES 8 Z 210 G A G G A C G A A G C C C SEQRES 9 Z 210 U A G U A A G C C A C U G SEQRES 10 Z 210 C C G A A A G G U G G G A SEQRES 11 Z 210 A G G C A G G G U G G A G SEQRES 12 Z 210 G A U G A G U C C C G A G SEQRES 13 Z 210 C C A G G A G A C C U G C SEQRES 14 Z 210 C A U A A G G U U U U A G SEQRES 15 Z 210 A A G U U C G C C U U C G SEQRES 16 Z 210 G G G G G A A G G U G A A SEQRES 17 Z 210 C A HET B1Z Z 301 109 HETNAM B1Z ADENOSYLCOBALAMIN HETSYN B1Z COBAMAMIDE FORMUL 2 B1Z C72 H101 CO N18 O17 P SITE 1 AC1 15 G Z 49 G Z 50 A Z 51 G Z 74 SITE 2 AC1 15 C Z 75 C Z 81 U Z 82 A Z 83 SITE 3 AC1 15 G Z 117 G Z 161 A Z 162 A Z 164 SITE 4 AC1 15 C Z 166 U Z 193 C Z 194 CRYST1 96.648 243.545 87.102 90.00 90.00 90.00 C 2 2 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 0.010347 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011481 0.00000