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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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