HEADER RNA BINDING PROTEIN 20-FEB-20 6Y4B TITLE STRUCTURE OF CYCLODIPEPTIDE SYNTHASE FROM CANDIDATUS GLOMERIBACTER TITLE 2 GIGASPORARUM BOUND TO PHE-TRNAPHE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (77-MER); COMPND 3 CHAIN: F; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: TRNA IS AMINOACYLATED, ADENOSINE 76 IS BOUNDED TO COMPND 6 PHENYLALANINE; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CYCLODIPEPTIDE SYNTHASE; COMPND 9 CHAIN: A; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: CANDIDATUS GLOMERIBACTER GIGASPORARUM BEG34; SOURCE 8 ORGANISM_TAXID: 1070319; SOURCE 9 GENE: CAGGBEG34_30028; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYCLODIPEPTIDE SYNTHASE, TRNA, COMPLEX, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.BOURGEOIS,Y.MECHULAM,E.SCHMITT REVDAT 2 24-JAN-24 6Y4B 1 REMARK REVDAT 1 30-DEC-20 6Y4B 0 JRNL AUTH G.BOURGEOIS,J.SEGUIN,M.BABIN,M.GONDRY,Y.MECHULAM,E.SCHMITT JRNL TITL STRUCTURAL BASIS OF THE INTERACTION BETWEEN CYCLODIPEPTIDE JRNL TITL 2 SYNTHASES AND AMINOACYLATED TRNA SUBSTRATES. JRNL REF RNA V. 26 1589 2020 JRNL REFN ESSN 1469-9001 JRNL PMID 32680846 JRNL DOI 10.1261/RNA.075184.120 REMARK 2 REMARK 2 RESOLUTION. 5.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 5.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 70.7 REMARK 3 NUMBER OF REFLECTIONS : 4315 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.305 REMARK 3 R VALUE (WORKING SET) : 0.304 REMARK 3 FREE R VALUE : 0.316 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 215 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.1600 - 6.3000 0.98 2938 144 0.2826 0.2805 REMARK 3 2 6.3000 - 5.0000 0.41 1162 71 0.4592 0.5531 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.063 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.275 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 214.5 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 139.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 3164 REMARK 3 ANGLE : 0.646 4700 REMARK 3 CHIRALITY : 0.032 619 REMARK 3 PLANARITY : 0.004 386 REMARK 3 DIHEDRAL : 20.260 1241 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -80.2336 69.1408 3.1475 REMARK 3 T TENSOR REMARK 3 T11: 0.2399 T22: 1.3057 REMARK 3 T33: 0.9848 T12: -0.5410 REMARK 3 T13: 0.0676 T23: -0.7505 REMARK 3 L TENSOR REMARK 3 L11: 5.4155 L22: 2.1514 REMARK 3 L33: 1.2426 L12: 0.6872 REMARK 3 L13: 0.1298 L23: -0.2691 REMARK 3 S TENSOR REMARK 3 S11: 0.0865 S12: -1.7098 S13: -0.0667 REMARK 3 S21: 0.4508 S22: -0.0259 S23: 0.6635 REMARK 3 S31: -0.3280 S32: -0.9686 S33: -0.0110 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6Y4B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292106805. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 1.17.1_3660 REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6120 REMARK 200 RESOLUTION RANGE HIGH (A) : 5.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 33.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 5.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 5.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : 32.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: 5MLP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 77.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG8000, 0.17 M ACCA, 0.17 M REMARK 280 GUANIDINIUM HYDROCHLORIDE, 0.1 M HEPES PH 7, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 23.13667 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 46.27333 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 34.70500 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 57.84167 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 11.56833 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 23.13667 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 46.27333 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 57.84167 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 34.70500 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 11.56833 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: 4000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, 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 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 A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 ILE A 4 REMARK 465 ALA A 5 REMARK 465 TYR A 6 REMARK 465 PHE A 7 REMARK 465 LYS A 8 REMARK 465 ASN A 70 REMARK 465 ASN A 71 REMARK 465 GLU A 72 REMARK 465 SER A 73 REMARK 465 ALA A 74 REMARK 465 VAL A 269 REMARK 465 GLU A 270 REMARK 465 ASN A 271 REMARK 465 ALA A 272 REMARK 465 LEU A 273 REMARK 465 SER A 274 REMARK 465 GLY A 275 REMARK 465 MET A 276 REMARK 465 PRO A 277 REMARK 465 ASP A 278 REMARK 465 GLU A 279 REMARK 465 GLU A 280 REMARK 465 PHE A 281 REMARK 465 LEU A 282 REMARK 465 ILE A 283 REMARK 465 HIS A 284 REMARK 465 HIS A 285 REMARK 465 THR A 286 REMARK 465 SER A 287 REMARK 465 ASN A 288 REMARK 465 PHE A 289 REMARK 465 SER A 290 REMARK 465 ASN A 291 REMARK 465 HIS A 292 REMARK 465 HIS A 293 REMARK 465 HIS A 294 REMARK 465 HIS A 295 REMARK 465 HIS A 296 REMARK 465 HIS A 297 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 10 CG CD1 CD2 REMARK 470 GLU A 11 CG CD OE1 OE2 REMARK 470 GLN A 12 CG CD OE1 NE2 REMARK 470 PHE A 13 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE A 14 CG1 CG2 CD1 REMARK 470 LEU A 15 CG CD1 CD2 REMARK 470 GLU A 16 CG CD OE1 OE2 REMARK 470 ASN A 17 CG OD1 ND2 REMARK 470 SER A 18 OG REMARK 470 LEU A 19 CG CD1 CD2 REMARK 470 ILE A 20 CG1 CG2 CD1 REMARK 470 LYS A 21 CG CD CE NZ REMARK 470 ASN A 22 CG OD1 ND2 REMARK 470 LYS A 23 CG CD CE NZ REMARK 470 PRO A 24 CG CD REMARK 470 ILE A 25 CG1 CG2 CD1 REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 ILE A 27 CG1 CG2 CD1 REMARK 470 VAL A 28 CG1 CG2 REMARK 470 ILE A 29 CG1 CG2 CD1 REMARK 470 SER A 32 OG REMARK 470 MET A 33 CG SD CE REMARK 470 GLN A 34 CG CD OE1 NE2 REMARK 470 SER A 35 OG REMARK 470 PRO A 36 CG CD REMARK 470 GLN A 38 CG CD OE1 NE2 REMARK 470 ILE A 39 CG1 CG2 CD1 REMARK 470 SER A 40 OG REMARK 470 ASN A 41 CG OD1 ND2 REMARK 470 GLU A 42 CG CD OE1 OE2 REMARK 470 HIS A 43 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 44 CG CD CE NZ REMARK 470 GLN A 45 CG CD OE1 NE2 REMARK 470 SER A 46 OG REMARK 470 ASP A 48 CG OD1 OD2 REMARK 470 SER A 49 OG REMARK 470 PHE A 50 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 51 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 53 CG CD1 CD2 CE1 CE2 CZ REMARK 470 VAL A 54 CG1 CG2 REMARK 470 ASP A 55 CG OD1 OD2 REMARK 470 LEU A 56 CG CD1 CD2 REMARK 470 LEU A 57 CG CD1 CD2 REMARK 470 ARG A 58 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 THR A 60 OG1 CG2 REMARK 470 ASN A 61 CG OD1 ND2 REMARK 470 GLU A 62 CG CD OE1 OE2 REMARK 470 GLN A 63 CG CD OE1 NE2 REMARK 470 CYS A 64 SG REMARK 470 ILE A 65 CG1 CG2 CD1 REMARK 470 ARG A 66 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 67 CG OD1 OD2 REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 ASN A 69 CG OD1 ND2 REMARK 470 ILE A 75 CG1 CG2 CD1 REMARK 470 ARG A 76 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 77 CG1 CG2 CD1 REMARK 470 SER A 78 OG REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 LEU A 80 CG CD1 CD2 REMARK 470 ILE A 81 CG1 CG2 CD1 REMARK 470 VAL A 82 CG1 CG2 REMARK 470 VAL A 83 CG1 CG2 REMARK 470 ASP A 86 CG OD1 OD2 REMARK 470 LEU A 88 CG CD1 CD2 REMARK 470 HIS A 89 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 91 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 92 CG OD1 ND2 REMARK 470 LEU A 93 CG CD1 CD2 REMARK 470 ARG A 94 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 95 CG CD1 CD2 REMARK 470 ASN A 98 CG OD1 ND2 REMARK 470 VAL A 99 CG1 CG2 REMARK 470 SER A 100 OG REMARK 470 THR A 101 OG1 CG2 REMARK 470 THR A 102 OG1 CG2 REMARK 470 GLU A 103 CG CD OE1 OE2 REMARK 470 GLU A 105 CG CD OE1 OE2 REMARK 470 SER A 106 OG REMARK 470 GLU A 107 CG CD OE1 OE2 REMARK 470 LEU A 111 CG CD1 CD2 REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 VAL A 116 CG1 CG2 REMARK 470 ASN A 119 CG OD1 ND2 REMARK 470 ARG A 120 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 121 CG CD OE1 NE2 REMARK 470 PHE A 122 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 123 CG CD1 CD2 REMARK 470 GLU A 124 CG CD OE1 OE2 REMARK 470 ILE A 126 CG1 CG2 CD1 REMARK 470 GLN A 128 CG CD OE1 NE2 REMARK 470 CYS A 129 SG REMARK 470 ILE A 131 CG1 CG2 CD1 REMARK 470 SER A 132 OG REMARK 470 TYR A 133 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 134 CG CD CE NZ REMARK 470 VAL A 135 CG1 CG2 REMARK 470 ILE A 136 CG1 CG2 CD1 REMARK 470 HIS A 137 CG ND1 CD2 CE1 NE2 REMARK 470 TRP A 138 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 138 CZ3 CH2 REMARK 470 GLU A 139 CG CD OE1 OE2 REMARK 470 GLU A 140 CG CD OE1 OE2 REMARK 470 LEU A 141 CG CD1 CD2 REMARK 470 LYS A 142 CG CD CE NZ REMARK 470 SER A 143 OG REMARK 470 VAL A 144 CG1 CG2 REMARK 470 PHE A 146 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 147 CG OD1 ND2 REMARK 470 ARG A 148 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 149 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 150 CG CD1 CD2 REMARK 470 GLN A 151 CG CD OE1 NE2 REMARK 470 ILE A 152 CG1 CG2 CD1 REMARK 470 VAL A 153 CG1 CG2 REMARK 470 GLU A 154 CG CD OE1 OE2 REMARK 470 GLU A 155 CG CD OE1 OE2 REMARK 470 GLU A 156 CG CD OE1 OE2 REMARK 470 TYR A 157 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 158 CG CD OE1 OE2 REMARK 470 LYS A 159 CG CD CE NZ REMARK 470 PRO A 160 CG CD REMARK 470 ASN A 161 CG OD1 ND2 REMARK 470 SER A 162 OG REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 PHE A 164 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER A 166 OG REMARK 470 ILE A 167 CG1 CG2 CD1 REMARK 470 ILE A 168 CG1 CG2 CD1 REMARK 470 ASP A 169 CG OD1 OD2 REMARK 470 ASN A 170 CG OD1 ND2 REMARK 470 LEU A 171 CG CD1 CD2 REMARK 470 THR A 172 OG1 CG2 REMARK 470 GLN A 173 CG CD OE1 NE2 REMARK 470 THR A 174 OG1 CG2 REMARK 470 HIS A 175 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 176 CG CD1 CD2 REMARK 470 GLU A 177 CG CD OE1 OE2 REMARK 470 LYS A 178 CG CD CE NZ REMARK 470 LEU A 179 CG CD1 CD2 REMARK 470 VAL A 180 CG1 CG2 REMARK 470 ASN A 181 CG OD1 ND2 REMARK 470 PHE A 182 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 183 CG CD1 CD2 REMARK 470 LEU A 184 CG CD1 CD2 REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 THR A 186 OG1 CG2 REMARK 470 ARG A 187 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 188 CG OD1 OD2 REMARK 470 SER A 189 OG REMARK 470 SER A 190 OG REMARK 470 PHE A 191 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR A 192 OG1 CG2 REMARK 470 GLN A 193 CG CD OE1 NE2 REMARK 470 GLU A 194 CG CD OE1 OE2 REMARK 470 ASP A 195 CG OD1 OD2 REMARK 470 CYS A 196 SG REMARK 470 VAL A 197 CG1 CG2 REMARK 470 SER A 198 OG REMARK 470 THR A 200 OG1 CG2 REMARK 470 ARG A 201 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 TYR A 203 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 204 CG CD1 CD2 REMARK 470 LEU A 205 CG CD1 CD2 REMARK 470 GLU A 206 CG CD OE1 OE2 REMARK 470 GLU A 207 CG CD OE1 OE2 REMARK 470 SER A 210 OG REMARK 470 PHE A 212 CG CD1 CD2 CE1 CE2 CZ REMARK 470 PHE A 214 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER A 216 OG REMARK 470 LEU A 217 CG CD1 CD2 REMARK 470 LYS A 218 CG CD CE NZ REMARK 470 ASP A 220 CG OD1 OD2 REMARK 470 MET A 222 CG SD CE REMARK 470 THR A 223 OG1 CG2 REMARK 470 SER A 229 OG REMARK 470 PRO A 230 CG CD REMARK 470 PHE A 232 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 233 CG CD CE NZ REMARK 470 TYR A 234 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE A 235 CG1 CG2 CD1 REMARK 470 TYR A 236 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 237 CG OD1 OD2 REMARK 470 THR A 238 OG1 CG2 REMARK 470 TYR A 239 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 240 CG CD1 CD2 REMARK 470 SER A 241 OG REMARK 470 GLU A 242 CG CD OE1 OE2 REMARK 470 SER A 243 OG REMARK 470 ASN A 244 CG OD1 ND2 REMARK 470 PRO A 245 CG CD REMARK 470 LEU A 246 CG CD1 CD2 REMARK 470 PRO A 247 CG CD REMARK 470 PHE A 248 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE A 249 CG1 CG2 CD1 REMARK 470 GLU A 250 CG CD OE1 OE2 REMARK 470 TYR A 251 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 MET A 253 CG SD CE REMARK 470 ARG A 254 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 257 CG CD CE NZ REMARK 470 LYS A 258 CG CD CE NZ REMARK 470 LEU A 259 CG CD1 CD2 REMARK 470 PRO A 260 CG CD REMARK 470 SER A 261 OG REMARK 470 PHE A 262 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TRP A 263 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 263 CZ3 CH2 REMARK 470 LYS A 264 CG CD CE NZ REMARK 470 GLU A 265 CG CD OE1 OE2 REMARK 470 GLU A 266 CG CD OE1 OE2 REMARK 470 SER A 267 OG REMARK 470 PRO A 268 CG CD 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 G F 5 N3 - C4 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 C F 17 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 PRO A 36 N - CA - CB ANGL. DEV. = 7.3 DEGREES REMARK 500 PRO A 247 N - CA - CB ANGL. DEV. = 7.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 35 -77.57 -59.88 REMARK 500 SER A 40 -108.09 56.97 REMARK 500 GLU A 79 81.05 53.09 REMARK 500 ARG A 90 -68.16 -95.15 REMARK 500 VAL A 99 -122.88 51.09 REMARK 500 ASN A 119 41.26 -146.73 REMARK 500 TRP A 138 -72.89 -63.78 REMARK 500 LYS A 142 22.89 -74.73 REMARK 500 ASP A 220 -128.98 67.79 REMARK 500 SER A 243 -51.54 -132.14 REMARK 500 REMARK 500 REMARK: NULL DBREF 6Y4B F 1 76 PDB 6Y4B 6Y4B 1 76 DBREF 6Y4B A 1 291 UNP G2JBB2 G2JBB2_9BURK 1 291 SEQADV 6Y4B HIS A 292 UNP G2JBB2 EXPRESSION TAG SEQADV 6Y4B HIS A 293 UNP G2JBB2 EXPRESSION TAG SEQADV 6Y4B HIS A 294 UNP G2JBB2 EXPRESSION TAG SEQADV 6Y4B HIS A 295 UNP G2JBB2 EXPRESSION TAG SEQADV 6Y4B HIS A 296 UNP G2JBB2 EXPRESSION TAG SEQADV 6Y4B HIS A 297 UNP G2JBB2 EXPRESSION TAG SEQRES 1 F 76 G C C C G G A 4SU A G C U C SEQRES 2 F 76 A G H2U C G G H2U A G A G C A SEQRES 3 F 76 G G G G A PSU U G A A A A PSU SEQRES 4 F 76 C C C C G U G U C C U U G SEQRES 5 F 76 G 5MU PSU C G A U U C C G A G SEQRES 6 F 76 U C C G G G C A C C A SEQRES 1 A 297 MET ALA LYS ILE ALA TYR PHE LYS GLY LEU GLU GLN PHE SEQRES 2 A 297 ILE LEU GLU ASN SER LEU ILE LYS ASN LYS PRO ILE LYS SEQRES 3 A 297 ILE VAL ILE GLY ILE SER MET GLN SER PRO HIS GLN ILE SEQRES 4 A 297 SER ASN GLU HIS LYS GLN SER GLY ASP SER PHE ARG ALA SEQRES 5 A 297 PHE VAL ASP LEU LEU ARG LYS THR ASN GLU GLN CYS ILE SEQRES 6 A 297 ARG ASP GLU ASN ASN ASN GLU SER ALA ILE ARG ILE SER SEQRES 7 A 297 GLU LEU ILE VAL VAL ILE THR ASP GLY LEU HIS ARG HIS SEQRES 8 A 297 ASN LEU ARG LEU TYR LYS ASN VAL SER THR THR GLU ALA SEQRES 9 A 297 GLU SER GLU ALA ALA GLY LEU GLY GLN LYS TRP VAL ALA SEQRES 10 A 297 ASP ASN ARG GLN PHE LEU GLU ALA ILE GLY GLN CYS GLY SEQRES 11 A 297 ILE SER TYR LYS VAL ILE HIS TRP GLU GLU LEU LYS SER SEQRES 12 A 297 VAL ALA PHE ASN ARG TYR LEU GLN ILE VAL GLU GLU GLU SEQRES 13 A 297 TYR GLU LYS PRO ASN SER GLU PHE ARG SER ILE ILE ASP SEQRES 14 A 297 ASN LEU THR GLN THR HIS LEU GLU LYS LEU VAL ASN PHE SEQRES 15 A 297 LEU LEU GLU THR ARG ASP SER SER PHE THR GLN GLU ASP SEQRES 16 A 297 CYS VAL SER ALA THR ARG LYS TYR LEU LEU GLU GLU ALA SEQRES 17 A 297 ALA SER ALA PHE GLU PHE ALA SER LEU LYS ALA ASP GLY SEQRES 18 A 297 MET THR TYR PRO GLY PRO CYS SER PRO GLY PHE LYS TYR SEQRES 19 A 297 ILE TYR ASP THR TYR LEU SER GLU SER ASN PRO LEU PRO SEQRES 20 A 297 PHE ILE GLU TYR GLY MET ARG GLY GLY LYS LYS LEU PRO SEQRES 21 A 297 SER PHE TRP LYS GLU GLU SER PRO VAL GLU ASN ALA LEU SEQRES 22 A 297 SER GLY MET PRO ASP GLU GLU PHE LEU ILE HIS HIS THR SEQRES 23 A 297 SER ASN PHE SER ASN HIS HIS HIS HIS HIS HIS HET 4SU F 8 20 HET H2U F 16 20 HET H2U F 20 20 HET PSU F 32 20 HET PSU F 39 20 HET 5MU F 54 21 HET PSU F 55 20 HET PHE F 101 11 HETNAM 4SU 4-THIOURIDINE-5'-MONOPHOSPHATE HETNAM H2U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM PHE PHENYLALANINE FORMUL 1 4SU C9 H13 N2 O8 P S FORMUL 1 H2U 2(C9 H15 N2 O9 P) FORMUL 1 PSU 3(C9 H13 N2 O9 P) FORMUL 1 5MU C10 H15 N2 O9 P FORMUL 3 PHE C9 H11 N O2 HELIX 1 AA1 GLU A 11 PHE A 13 5 3 HELIX 2 AA2 ILE A 14 LEU A 19 1 6 HELIX 3 AA3 SER A 46 LYS A 59 1 14 HELIX 4 AA4 SER A 100 ASN A 119 1 20 HELIX 5 AA5 ASN A 119 CYS A 129 1 11 HELIX 6 AA6 HIS A 137 SER A 143 1 7 HELIX 7 AA7 PHE A 146 TYR A 157 1 12 HELIX 8 AA8 GLU A 163 LEU A 184 1 22 HELIX 9 AA9 THR A 186 SER A 190 5 5 HELIX 10 AB1 THR A 192 LYS A 218 1 27 HELIX 11 AB2 GLY A 231 TYR A 239 1 9 HELIX 12 AB3 LEU A 240 SER A 243 5 4 SHEET 1 AA1 2 ILE A 27 VAL A 28 0 SHEET 2 AA1 2 GLY A 221 MET A 222 1 O GLY A 221 N VAL A 28 SHEET 1 AA2 2 GLY A 30 ILE A 31 0 SHEET 2 AA2 2 VAL A 83 ILE A 84 1 O VAL A 83 N ILE A 31 LINK O3' A F 7 P 4SU F 8 1555 1555 1.61 LINK O3' 4SU F 8 P A F 9 1555 1555 1.61 LINK O3' G F 15 P H2U F 16 1555 1555 1.61 LINK O3' H2U F 16 P C F 17 1555 1555 1.61 LINK O3' G F 19 P H2U F 20 1555 1555 1.62 LINK O3' H2U F 20 P A F 21 1555 1555 1.61 LINK O3' A F 31 P PSU F 32 1555 1555 1.61 LINK O3' PSU F 32 P U F 33 1555 1555 1.61 LINK O3' A F 38 P PSU F 39 1555 1555 1.61 LINK O3' PSU F 39 P C F 40 1555 1555 1.61 LINK O3' G F 53 P 5MU F 54 1555 1555 1.61 LINK O3' 5MU F 54 P PSU F 55 1555 1555 1.61 LINK O3' PSU F 55 P C F 56 1555 1555 1.61 LINK O3' A F 76 C PHE F 101 1555 1555 1.48 CRYST1 254.834 254.834 69.410 90.00 90.00 120.00 P 61 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 0.003924 0.002266 0.000000 0.00000 SCALE2 0.000000 0.004531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014407 0.00000