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 HETATM 1 PG GTP A 202 -50.287 -17.664 -3.537 1.00182.60 P HETATM 2 O1G GTP A 202 -50.926 -18.431 -4.669 1.00179.17 O HETATM 3 O2G GTP A 202 -49.792 -18.562 -2.430 1.00181.07 O HETATM 4 O3G GTP A 202 -51.161 -16.543 -3.028 1.00182.79 O HETATM 5 O3B GTP A 202 -48.973 -16.959 -4.159 1.00188.36 O HETATM 6 PB GTP A 202 -48.682 -16.262 -5.572 1.00192.52 P HETATM 7 O1B GTP A 202 -49.047 -17.222 -6.655 1.00190.61 O HETATM 8 O2B GTP A 202 -49.290 -14.898 -5.565 1.00192.81 O HETATM 9 O3A GTP A 202 -47.085 -16.122 -5.539 1.00198.96 O HETATM 10 PA GTP A 202 -46.265 -15.386 -4.356 1.00205.07 P HETATM 11 O1A GTP A 202 -47.081 -14.250 -3.858 1.00207.05 O HETATM 12 O2A GTP A 202 -45.837 -16.444 -3.406 1.00201.86 O HETATM 13 O5' GTP A 202 -44.950 -14.759 -5.004 1.00206.10 O HETATM 14 C5' GTP A 202 -44.085 -13.880 -4.253 1.00206.57 C HETATM 15 C4' GTP A 202 -42.639 -14.265 -4.464 1.00208.41 C HETATM 16 O4' GTP A 202 -42.485 -15.690 -4.243 1.00211.94 O HETATM 17 C3' GTP A 202 -42.091 -14.029 -5.863 1.00209.50 C HETATM 18 O3' GTP A 202 -41.646 -12.688 -6.063 1.00212.15 O HETATM 19 C2' GTP A 202 -40.959 -15.048 -5.958 1.00209.68 C HETATM 20 O2' GTP A 202 -39.738 -14.599 -5.407 1.00205.82 O HETATM 21 C1' GTP A 202 -41.502 -16.211 -5.121 1.00212.11 C HETATM 22 N9 GTP A 202 -42.118 -17.271 -5.915 1.00213.94 N HETATM 23 C8 GTP A 202 -43.392 -17.769 -5.778 1.00212.95 C HETATM 24 N7 GTP A 202 -43.663 -18.723 -6.627 1.00212.95 N HETATM 25 C5 GTP A 202 -42.497 -18.868 -7.366 1.00214.73 C HETATM 26 C6 GTP A 202 -42.189 -19.751 -8.434 1.00215.14 C HETATM 27 O6 GTP A 202 -42.911 -20.608 -8.957 1.00217.15 O HETATM 28 N1 GTP A 202 -40.890 -19.562 -8.895 1.00213.49 N HETATM 29 C2 GTP A 202 -39.999 -18.645 -8.394 1.00212.25 C HETATM 30 N2 GTP A 202 -38.790 -18.614 -8.974 1.00211.55 N HETATM 31 N3 GTP A 202 -40.273 -17.817 -7.398 1.00212.31 N HETATM 32 C4 GTP A 202 -41.532 -17.982 -6.936 1.00213.95 C