HEADER RNA 28-JAN-20 6VMY TITLE STRUCTURE OF THE B. SUBTILIS COBALAMIN RIBOSWITCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: B. SUBTILIS COBALAMIN RIBOSWITCH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS RNA, RIBOSWITCH, COBALAMIN, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR C.W.CHAN,A.MONDRAGON REVDAT 4 06-MAR-24 6VMY 1 REMARK REVDAT 3 29-JUL-20 6VMY 1 JRNL LINK REVDAT 2 01-JUL-20 6VMY 1 JRNL REVDAT 1 10-JUN-20 6VMY 0 JRNL AUTH C.W.CHAN,A.MONDRAGON JRNL TITL CRYSTAL STRUCTURE OF AN ATYPICAL COBALAMIN RIBOSWITCH JRNL TITL 2 REVEALS RNA STRUCTURAL ADAPTABILITY AS BASIS FOR PROMISCUOUS JRNL TITL 3 LIGAND BINDING. JRNL REF NUCLEIC ACIDS RES. V. 48 7569 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32544228 JRNL DOI 10.1093/NAR/GKAA507 REMARK 2 REMARK 2 RESOLUTION. 3.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 86.3 REMARK 3 NUMBER OF REFLECTIONS : 15338 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.263 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.118 REMARK 3 FREE R VALUE TEST SET COUNT : 785 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 124 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 9.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.3760 REMARK 3 BIN FREE R VALUE SET COUNT : 4 REMARK 3 BIN FREE R VALUE : 0.6120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 3183 REMARK 3 HETEROGEN ATOMS : 170 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 129.1 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.69300 REMARK 3 B22 (A**2) : 0.69300 REMARK 3 B33 (A**2) : -2.24800 REMARK 3 B12 (A**2) : 0.34700 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): 1.731 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.470 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3776 ; 0.003 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): 1681 ; 0.001 ; 0.019 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5974 ; 0.807 ; 1.373 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3993 ; 2.165 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1374 ; 8.013 ; 5.073 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 116 ; 1.736 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 611 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2509 ; 0.033 ; 0.034 REMARK 3 GENERAL PLANES OTHERS (A): 832 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 587 ; 0.148 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 75 ; 0.220 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1257 ; 0.253 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 60 ; 0.208 ; 0.200 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3776 ; 1.847 ;13.655 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3771 ; 1.847 ;13.655 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 5974 ; 3.117 ;20.539 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5965 ; 3.118 ;20.539 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 : NULL 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 6VMY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000246516. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 - 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : KOHZU MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15338 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.253 REMARK 200 RESOLUTION RANGE LOW (A) : 39.213 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 47.00 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 43.8 REMARK 200 DATA REDUNDANCY IN SHELL : 54.00 REMARK 200 R MERGE FOR SHELL (I) : 4.12900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS 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 (%): 77.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PURIFIED RNA WAS INCUBATED AT ROOM REMARK 280 TEMPERATURE FOR 30 MINUTES IN 25 MM TRIS-HCL, PH 8.0, 50 MM REMARK 280 POTASSIUM CHLORIDE, 10 MM MAGNESIUM CHLORIDE, 0.5 MM REMARK 280 ADENOSYLCOBALAMIN PRIOR TO CRYSTALLIZATION IN 50 MM SODIUM REMARK 280 CACODYLATE, 15% (V/V) PEG 400, 0.2 MM COBALT HEXAMINE, 80 MM REMARK 280 MAGNESIUM ACETATE, 1 MM SPERMINE BETWEEN PH 6.0 TO PH 6.5 AT 14C REMARK 280 BY VAPOR DIFFUSION IN A HANGING DROP FORMAT, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 174.36467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 87.18233 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 130.77350 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.59117 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 217.95583 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 174.36467 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 87.18233 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 43.59117 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 130.77350 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 217.95583 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: A 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 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 A 413 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 517 O REMARK 620 2 HOH A 518 O 89.9 REMARK 620 3 HOH A 523 O 90.0 89.2 REMARK 620 4 HOH A 527 O 89.9 179.6 90.5 REMARK 620 5 HOH A 544 O 179.8 90.3 90.1 89.9 REMARK 620 6 HOH A 547 O 89.9 90.5 179.7 89.8 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 414 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 504 O REMARK 620 2 HOH A 505 O 88.5 REMARK 620 3 HOH A 510 O 91.1 90.0 REMARK 620 4 HOH A 519 O 89.7 90.0 179.2 REMARK 620 5 HOH A 529 O 91.5 179.3 89.3 90.7 REMARK 620 6 HOH A 530 O 178.4 90.3 89.9 89.3 89.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 415 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 507 O REMARK 620 2 HOH A 511 O 179.6 REMARK 620 3 HOH A 512 O 90.2 89.9 REMARK 620 4 HOH A 515 O 90.0 90.4 89.4 REMARK 620 5 HOH A 533 O 90.2 89.7 179.4 90.2 REMARK 620 6 HOH A 539 O 89.4 90.3 89.9 179.0 90.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 416 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 501 O REMARK 620 2 HOH A 506 O 88.7 REMARK 620 3 HOH A 508 O 90.1 90.0 REMARK 620 4 HOH A 520 O 90.8 179.5 90.2 REMARK 620 5 HOH A 528 O 179.3 90.6 89.9 89.9 REMARK 620 6 HOH A 534 O 90.2 89.7 179.5 90.1 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 417 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 514 O REMARK 620 2 HOH A 521 O 89.9 REMARK 620 3 HOH A 531 O 90.0 89.7 REMARK 620 4 HOH A 537 O 179.8 90.3 89.9 REMARK 620 5 HOH A 538 O 90.2 179.8 90.1 89.7 REMARK 620 6 HOH A 545 O 89.9 90.3 179.9 90.2 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 418 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 502 O REMARK 620 2 HOH A 503 O 179.1 REMARK 620 3 HOH A 509 O 89.9 90.6 REMARK 620 4 HOH A 513 O 91.1 89.7 89.6 REMARK 620 5 HOH A 532 O 89.7 89.7 179.5 90.1 REMARK 620 6 HOH A 543 O 89.7 89.6 90.1 179.2 90.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 419 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 525 O REMARK 620 2 HOH A 526 O 89.6 REMARK 620 3 HOH A 535 O 90.0 90.0 REMARK 620 4 HOH A 541 O 89.6 90.0 179.6 REMARK 620 5 HOH A 546 O 179.4 89.9 89.8 90.6 REMARK 620 6 HOH A 548 O 90.2 179.8 90.0 90.0 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 420 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 516 O REMARK 620 2 HOH A 522 O 90.1 REMARK 620 3 HOH A 524 O 179.7 89.9 REMARK 620 4 HOH A 536 O 90.0 89.9 90.3 REMARK 620 5 HOH A 540 O 89.8 179.8 90.1 89.9 REMARK 620 6 HOH A 542 O 89.9 90.3 89.8 179.8 89.9 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 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NCO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NCO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NCO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NCO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NCO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NCO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NCO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B1Z A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 420 DBREF1 6VMY A 203 349 GB CP046047.1 DBREF2 6VMY A CP046047.1 832641 832787 SEQADV 6VMY GTP A 202 GB CP046047. CLONING ARTIFACT SEQRES 1 A 148 GTP G U C A A A U A G G U G SEQRES 2 A 148 C C G G U C C G U G A A C SEQRES 3 A 148 A A C A G C C G G C U U A SEQRES 4 A 148 A A A G G G A A A C C G G SEQRES 5 A 148 U A A A A G C C G G U G C SEQRES 6 A 148 G G U C C C G C C A C U G SEQRES 7 A 148 U A A U U G G C C A A G C SEQRES 8 A 148 G C C A A G A G C C A G G SEQRES 9 A 148 A U A C C U G C C U G U U SEQRES 10 A 148 U G A U C A G C A C G A A SEQRES 11 A 148 U U C U G C G A G G A C A SEQRES 12 A 148 G A U G A HET GTP A 202 32 HET MG A 401 1 HET MG A 402 1 HET MG A 403 1 HET MG A 404 1 HET NCO A 405 7 HET NCO A 406 7 HET NCO A 407 7 HET NCO A 408 7 HET NCO A 409 7 HET NCO A 410 7 HET NCO A 411 7 HET B1Z A 412 109 HET MG A 413 1 HET MG A 414 1 HET MG A 415 1 HET MG A 416 1 HET MG A 417 1 HET MG A 418 1 HET MG A 419 1 HET MG A 420 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NCO COBALT HEXAMMINE(III) HETNAM B1Z ADENOSYLCOBALAMIN HETSYN B1Z COBAMAMIDE FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 MG 12(MG 2+) FORMUL 6 NCO 7(CO H18 N6 3+) FORMUL 13 B1Z C72 H101 CO N18 O17 P FORMUL 22 HOH *48(H2 O) LINK O3' GTP A 202 P G A 203 1555 1555 1.61 LINK MG MG A 413 O HOH A 517 1555 1555 2.18 LINK MG MG A 413 O HOH A 518 1555 1555 2.18 LINK MG MG A 413 O HOH A 523 1555 1555 2.18 LINK MG MG A 413 O HOH A 527 1555 1555 2.18 LINK MG MG A 413 O HOH A 544 1555 1555 2.18 LINK MG MG A 413 O HOH A 547 1555 1555 2.18 LINK MG MG A 414 O HOH A 504 1555 1555 2.18 LINK MG MG A 414 O HOH A 505 1555 1555 2.18 LINK MG MG A 414 O HOH A 510 1555 1555 2.18 LINK MG MG A 414 O HOH A 519 1555 1555 2.18 LINK MG MG A 414 O HOH A 529 1555 1555 2.18 LINK MG MG A 414 O HOH A 530 1555 1555 2.18 LINK MG MG A 415 O HOH A 507 1555 1555 2.18 LINK MG MG A 415 O HOH A 511 1555 1555 2.18 LINK MG MG A 415 O HOH A 512 1555 1555 2.18 LINK MG MG A 415 O HOH A 515 1555 1555 2.18 LINK MG MG A 415 O HOH A 533 1555 1555 2.18 LINK MG MG A 415 O HOH A 539 1555 1555 2.18 LINK MG MG A 416 O HOH A 501 1555 1555 2.18 LINK MG MG A 416 O HOH A 506 1555 1555 2.18 LINK MG MG A 416 O HOH A 508 1555 1555 2.18 LINK MG MG A 416 O HOH A 520 1555 1555 2.18 LINK MG MG A 416 O HOH A 528 1555 1555 2.18 LINK MG MG A 416 O HOH A 534 1555 1555 2.18 LINK MG MG A 417 O HOH A 514 1555 1555 2.18 LINK MG MG A 417 O HOH A 521 1555 1555 2.18 LINK MG MG A 417 O HOH A 531 1555 1555 2.18 LINK MG MG A 417 O HOH A 537 1555 6564 2.18 LINK MG MG A 417 O HOH A 538 1555 1555 2.18 LINK MG MG A 417 O HOH A 545 1555 1555 2.18 LINK MG MG A 418 O HOH A 502 1555 1555 2.18 LINK MG MG A 418 O HOH A 503 1555 1555 2.18 LINK MG MG A 418 O HOH A 509 1555 1555 2.18 LINK MG MG A 418 O HOH A 513 1555 1555 2.18 LINK MG MG A 418 O HOH A 532 1555 1555 2.18 LINK MG MG A 418 O HOH A 543 1555 1555 2.18 LINK MG MG A 419 O HOH A 525 1555 1555 2.18 LINK MG MG A 419 O HOH A 526 1555 1555 2.18 LINK MG MG A 419 O HOH A 535 1555 1555 2.18 LINK MG MG A 419 O HOH A 541 1555 1555 2.18 LINK MG MG A 419 O HOH A 546 1555 1555 2.18 LINK MG MG A 419 O HOH A 548 1555 1555 2.18 LINK MG MG A 420 O HOH A 516 1555 1555 2.18 LINK MG MG A 420 O HOH A 522 1555 1555 2.18 LINK MG MG A 420 O HOH A 524 1555 1555 2.18 LINK MG MG A 420 O HOH A 536 1555 1555 2.18 LINK MG MG A 420 O HOH A 540 1555 1555 2.18 LINK MG MG A 420 O HOH A 542 1555 1555 2.18 SITE 1 AC1 1 G A 244 SITE 1 AC2 1 C A 343 SITE 1 AC3 4 G A 212 U A 213 U A 311 C A 313 SITE 1 AC4 6 G A 268 C A 271 C A 272 G A 273 SITE 2 AC4 6 C A 274 NCO A 408 SITE 1 AC5 3 G A 222 U A 223 G A 224 SITE 1 AC6 3 G A 267 C A 270 NCO A 406 SITE 1 AC7 4 G A 217 G A 218 U A 219 C A 230 SITE 1 AC8 2 G A 329 A A 330 SITE 1 AC9 6 A A 231 G A 305 A A 306 U A 307 SITE 2 AC9 6 A A 308 B1Z A 412 SITE 1 AD1 14 G A 245 G A 246 A A 247 G A 268 SITE 2 AD1 14 U A 269 A A 276 G A 305 A A 306 SITE 3 AD1 14 A A 308 C A 310 C A 334 U A 335 SITE 4 AD1 14 G A 336 NCO A 411 SITE 1 AD2 6 HOH A 517 HOH A 518 HOH A 523 HOH A 527 SITE 2 AD2 6 HOH A 544 HOH A 547 SITE 1 AD3 7 A A 258 HOH A 504 HOH A 505 HOH A 510 SITE 2 AD3 7 HOH A 519 HOH A 529 HOH A 530 SITE 1 AD4 7 G A 252 HOH A 507 HOH A 511 HOH A 512 SITE 2 AD4 7 HOH A 515 HOH A 533 HOH A 539 SITE 1 AD5 7 A A 303 HOH A 501 HOH A 506 HOH A 508 SITE 2 AD5 7 HOH A 520 HOH A 528 HOH A 534 SITE 1 AD6 6 HOH A 514 HOH A 521 HOH A 531 HOH A 537 SITE 2 AD6 6 HOH A 538 HOH A 545 SITE 1 AD7 7 U A 335 HOH A 502 HOH A 503 HOH A 509 SITE 2 AD7 7 HOH A 513 HOH A 532 HOH A 543 SITE 1 AD8 6 HOH A 525 HOH A 526 HOH A 535 HOH A 541 SITE 2 AD8 6 HOH A 546 HOH A 548 SITE 1 AD9 6 HOH A 516 HOH A 522 HOH A 524 HOH A 536 SITE 2 AD9 6 HOH A 540 HOH A 542 CRYST1 118.282 118.282 261.547 90.00 90.00 120.00 P 65 2 2 12 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 0.008454 0.004881 0.000000 0.00000 SCALE2 0.000000 0.009762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003823 0.00000 CONECT 1 2 3 4 5 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 5 1 6 CONECT 6 5 7 8 9 CONECT 7 6 CONECT 8 6 CONECT 9 6 10 CONECT 10 9 11 12 13 CONECT 11 10 CONECT 12 10 CONECT 13 10 14 CONECT 14 13 15 CONECT 15 14 16 17 CONECT 16 15 21 CONECT 17 15 18 19 CONECT 18 17 33 CONECT 19 17 20 21 CONECT 20 19 CONECT 21 16 19 22 CONECT 22 21 23 32 CONECT 23 22 24 CONECT 24 23 25 CONECT 25 24 26 32 CONECT 26 25 27 28 CONECT 27 26 CONECT 28 26 29 CONECT 29 28 30 31 CONECT 30 29 CONECT 31 29 32 CONECT 32 22 25 31 CONECT 33 18 CONECT 3189 3190 3191 3192 3193 CONECT 3189 3194 3195 CONECT 3190 3189 CONECT 3191 3189 CONECT 3192 3189 CONECT 3193 3189 CONECT 3194 3189 CONECT 3195 3189 CONECT 3196 3197 3198 3199 3200 CONECT 3196 3201 3202 CONECT 3197 3196 CONECT 3198 3196 CONECT 3199 3196 CONECT 3200 3196 CONECT 3201 3196 CONECT 3202 3196 CONECT 3203 3204 3205 3206 3207 CONECT 3203 3208 3209 CONECT 3204 3203 CONECT 3205 3203 CONECT 3206 3203 CONECT 3207 3203 CONECT 3208 3203 CONECT 3209 3203 CONECT 3210 3211 3212 3213 3214 CONECT 3210 3215 3216 CONECT 3211 3210 CONECT 3212 3210 CONECT 3213 3210 CONECT 3214 3210 CONECT 3215 3210 CONECT 3216 3210 CONECT 3217 3218 3219 3220 3221 CONECT 3217 3222 3223 CONECT 3218 3217 CONECT 3219 3217 CONECT 3220 3217 CONECT 3221 3217 CONECT 3222 3217 CONECT 3223 3217 CONECT 3224 3225 3226 3227 3228 CONECT 3224 3229 3230 CONECT 3225 3224 CONECT 3226 3224 CONECT 3227 3224 CONECT 3228 3224 CONECT 3229 3224 CONECT 3230 3224 CONECT 3231 3232 3233 3234 3235 CONECT 3231 3236 3237 CONECT 3232 3231 CONECT 3233 3231 CONECT 3234 3231 CONECT 3235 3231 CONECT 3236 3231 CONECT 3237 3231 CONECT 3238 3281 3297 3312 3327 CONECT 3239 3268 3269 3270 3271 CONECT 3239 3295 3324 CONECT 3240 3241 3260 3267 3268 CONECT 3241 3240 3242 3272 3273 CONECT 3242 3241 3243 3283 CONECT 3243 3242 3244 3268 CONECT 3244 3243 3245 3288 CONECT 3245 3244 3246 3269 CONECT 3246 3245 3247 3289 3290 CONECT 3247 3246 3248 3300 CONECT 3248 3247 3251 3269 CONECT 3249 3333 CONECT 3250 3325 CONECT 3251 3248 3252 CONECT 3252 3251 3253 3270 CONECT 3253 3252 3254 3305 3306 CONECT 3254 3253 3255 3307 CONECT 3255 3254 3256 3270 CONECT 3256 3255 3257 3317 CONECT 3257 3256 3258 3271 CONECT 3258 3257 3259 3318 3319 CONECT 3259 3258 3260 3329 CONECT 3260 3240 3259 3271 CONECT 3261 3277 3334 3345 CONECT 3262 3279 3333 CONECT 3263 3335 CONECT 3264 3266 3278 3343 CONECT 3265 3280 3323 CONECT 3266 3264 3282 3336 CONECT 3267 3240 CONECT 3268 3239 3240 3243 CONECT 3269 3239 3245 3248 CONECT 3270 3239 3252 3255 CONECT 3271 3239 3257 3260 CONECT 3272 3241 CONECT 3273 3241 3274 CONECT 3274 3273 3275 3276 CONECT 3275 3274 CONECT 3276 3274 CONECT 3277 3261 3293 3338 CONECT 3278 3264 3295 CONECT 3279 3262 3294 CONECT 3280 3265 3296 3297 CONECT 3281 3238 3298 CONECT 3282 3266 3298 3340 CONECT 3283 3242 3284 CONECT 3284 3283 3285 CONECT 3285 3284 3286 3287 CONECT 3286 3285 CONECT 3287 3285 CONECT 3288 3244 CONECT 3289 3246 CONECT 3290 3246 3291 CONECT 3291 3290 3292 3299 CONECT 3292 3291 CONECT 3293 3277 3309 3342 CONECT 3294 3279 3311 CONECT 3295 3239 3278 3346 CONECT 3296 3280 CONECT 3297 3238 3280 CONECT 3298 3281 3282 3313 CONECT 3299 3291 CONECT 3300 3247 3301 CONECT 3301 3300 3302 CONECT 3302 3301 3303 3304 CONECT 3303 3302 CONECT 3304 3302 CONECT 3305 3253 CONECT 3306 3253 CONECT 3307 3254 3308 CONECT 3308 3307 3314 CONECT 3309 3293 3324 3334 CONECT 3310 3325 3346 CONECT 3311 3294 3326 3345 CONECT 3312 3238 CONECT 3313 3298 3328 3336 CONECT 3314 3308 3315 3316 CONECT 3315 3314 CONECT 3316 3314 CONECT 3317 3256 CONECT 3318 3258 CONECT 3319 3258 3320 CONECT 3320 3319 3321 CONECT 3321 3320 3322 3323 CONECT 3322 3321 CONECT 3323 3265 3321 CONECT 3324 3239 3309 CONECT 3325 3250 3310 3335 CONECT 3326 3311 3333 3337 CONECT 3327 3238 CONECT 3328 3313 3344 CONECT 3329 3259 3330 CONECT 3330 3329 3331 3332 CONECT 3331 3330 CONECT 3332 3330 CONECT 3333 3249 3262 3326 CONECT 3334 3261 3309 CONECT 3335 3263 3325 3339 CONECT 3336 3266 3313 CONECT 3337 3326 3341 CONECT 3338 3277 CONECT 3339 3335 3343 CONECT 3340 3282 CONECT 3341 3337 3345 CONECT 3342 3293 CONECT 3343 3264 3339 3346 CONECT 3344 3328 CONECT 3345 3261 3311 3341 CONECT 3346 3295 3310 3343 CONECT 3347 3371 3372 3377 3381 CONECT 3347 3398 3401 CONECT 3348 3358 3359 3364 3373 CONECT 3348 3383 3384 CONECT 3349 3361 3365 3366 3369 CONECT 3349 3387 3393 CONECT 3350 3355 3360 3362 3374 CONECT 3350 3382 3388 CONECT 3351 3368 3375 3385 3392 CONECT 3351 3399 CONECT 3352 3356 3357 3363 3367 CONECT 3352 3386 3397 CONECT 3353 3379 3380 3389 3395 CONECT 3353 3400 3402 CONECT 3354 3370 3376 3378 3390 CONECT 3354 3394 3396 CONECT 3355 3350 CONECT 3356 3352 CONECT 3357 3352 CONECT 3358 3348 CONECT 3359 3348 CONECT 3360 3350 CONECT 3361 3349 CONECT 3362 3350 CONECT 3363 3352 CONECT 3364 3348 CONECT 3365 3349 CONECT 3366 3349 CONECT 3367 3352 CONECT 3368 3351 CONECT 3369 3349 CONECT 3370 3354 CONECT 3371 3347 CONECT 3372 3347 CONECT 3373 3348 CONECT 3374 3350 CONECT 3375 3351 CONECT 3376 3354 CONECT 3377 3347 CONECT 3378 3354 CONECT 3379 3353 CONECT 3380 3353 CONECT 3381 3347 CONECT 3382 3350 CONECT 3383 3348 CONECT 3384 3348 CONECT 3385 3351 CONECT 3386 3352 CONECT 3387 3349 CONECT 3388 3350 CONECT 3389 3353 CONECT 3390 3354 CONECT 3392 3351 CONECT 3393 3349 CONECT 3394 3354 CONECT 3395 3353 CONECT 3396 3354 CONECT 3397 3352 CONECT 3398 3347 CONECT 3399 3351 CONECT 3400 3353 CONECT 3401 3347 CONECT 3402 3353 MASTER 437 0 21 0 0 0 31 6 3401 1 262 12 END