HEADER TRANSFERASE/RNA 09-DEC-16 5WT1 TITLE PYROCOCCUS ABYSSI METHYLTRANSFERASE PATRM5A BOUND BY SAH AND COGNATE TITLE 2 TRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA (GUANINE(37)-N1)-METHYLTRANSFERASE TRM5A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: M1G-METHYLTRANSFERASE,TRNA [GM37] METHYLTRANSFERASE; COMPND 5 EC: 2.1.1.228; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (76-MER); COMPND 9 CHAIN: C, F; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI (STRAIN GE5 / ORSAY); SOURCE 3 ORGANISM_TAXID: 272844; SOURCE 4 STRAIN: GE5 / ORSAY; SOURCE 5 GENE: TRM5A, PYRAB01130, PAB2272; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI GE5; SOURCE 11 ORGANISM_TAXID: 272844 KEYWDS METHYLTRANSFERASE, TRM5A, WYOSINE HYPERMODIFICATION, TRANSFERASE-RNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.XIE,C.WANG,Q.JIA REVDAT 3 08-NOV-23 5WT1 1 REMARK REVDAT 2 18-DEC-19 5WT1 1 JRNL REVDAT 1 13-DEC-17 5WT1 0 JRNL AUTH C.WANG,Q.JIA,J.ZENG,R.CHEN,W.XIE JRNL TITL STRUCTURAL INSIGHT INTO THE METHYLTRANSFER MECHANISM OF THE JRNL TITL 2 BIFUNCTIONAL TRM5. JRNL REF SCI ADV V. 3 00195 2017 JRNL REFN ESSN 2375-2548 JRNL PMID 29214216 JRNL DOI 10.1126/SCIADV.1700195 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 40281 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2020 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 40.2218 - 6.2538 0.96 2758 154 0.2115 0.2435 REMARK 3 2 6.2538 - 4.9667 1.00 2800 142 0.2250 0.2351 REMARK 3 3 4.9667 - 4.3398 0.99 2766 138 0.2120 0.2164 REMARK 3 4 4.3398 - 3.9433 1.00 2783 137 0.2226 0.2334 REMARK 3 5 3.9433 - 3.6609 1.00 2746 150 0.2349 0.2757 REMARK 3 6 3.6609 - 3.4452 1.00 2739 166 0.2603 0.2821 REMARK 3 7 3.4452 - 3.2727 0.99 2737 151 0.2613 0.2770 REMARK 3 8 3.2727 - 3.1303 0.99 2708 129 0.2690 0.3096 REMARK 3 9 3.1303 - 3.0099 1.00 2734 139 0.3050 0.3661 REMARK 3 10 3.0099 - 2.9060 1.00 2740 174 0.3134 0.3633 REMARK 3 11 2.9060 - 2.8152 1.00 2748 143 0.3488 0.3881 REMARK 3 12 2.8152 - 2.7347 1.00 2749 129 0.3449 0.3859 REMARK 3 13 2.7347 - 2.6628 1.00 2769 121 0.3507 0.4175 REMARK 3 14 2.6628 - 2.5978 0.92 2484 147 0.3809 0.4534 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) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 8348 REMARK 3 ANGLE : 0.976 12002 REMARK 3 CHIRALITY : 0.056 1491 REMARK 3 PLANARITY : 0.007 1040 REMARK 3 DIHEDRAL : 14.913 4706 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5WT1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1300002266. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40587 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.598 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.91100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 2ZZN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45% MPD, 100 MM MES (PH 6.5), 200 MM REMARK 280 NH4OAC, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 4810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 2 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: 4570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F 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 SER A 333 REMARK 465 G C 1 REMARK 465 G C 2 REMARK 465 G C 3 REMARK 465 C C 70 REMARK 465 C C 71 REMARK 465 C C 72 REMARK 465 A C 73 REMARK 465 C C 74 REMARK 465 C C 75 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 SER B 333 REMARK 465 G F 1 REMARK 465 G F 2 REMARK 465 C F 70 REMARK 465 C F 71 REMARK 465 C F 72 REMARK 465 A F 73 REMARK 465 C F 74 REMARK 465 C F 75 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 MET A 1 CG SD CE REMARK 470 LYS A 5 CG CD CE NZ REMARK 470 VAL A 6 CG1 CG2 REMARK 470 ARG A 7 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 8 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 9 CG CD OE1 OE2 REMARK 470 LYS A 12 CG CD CE NZ REMARK 470 LYS A 13 CG CD CE NZ REMARK 470 SER A 20 OG REMARK 470 GLU A 34 CG CD OE1 OE2 REMARK 470 LYS A 35 CG CD CE NZ REMARK 470 TYR A 36 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 50 CG CD1 CD2 REMARK 470 GLU A 58 CG CD OE1 OE2 REMARK 470 MET A 61 CG SD CE REMARK 470 ARG A 65 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 77 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 78 CG CD OE1 OE2 REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 ILE A 92 CG1 CG2 CD1 REMARK 470 ILE A 97 CG1 CG2 CD1 REMARK 470 PRO A 98 CG CD REMARK 470 GLU A 100 CG CD OE1 OE2 REMARK 470 ARG A 105 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 107 CG1 CG2 REMARK 470 VAL A 109 CG1 CG2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 LYS A 151 CG CD CE NZ REMARK 470 ILE A 214 CG1 CG2 CD1 REMARK 470 GLU A 216 CG CD OE1 OE2 REMARK 470 LYS A 220 CG CD CE NZ REMARK 470 GLU A 223 CG CD OE1 OE2 REMARK 470 ARG A 230 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 236 CG CD CE NZ REMARK 470 LYS A 277 CG CD CE NZ REMARK 470 GLU A 291 CG CD OE1 OE2 REMARK 470 GLU A 307 CG CD OE1 OE2 REMARK 470 LYS B 5 CG CD CE NZ REMARK 470 VAL B 6 CG1 CG2 REMARK 470 ARG B 7 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 8 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 9 CG CD OE1 OE2 REMARK 470 LYS B 13 CG CD CE NZ REMARK 470 VAL B 14 CG1 CG2 REMARK 470 LEU B 15 CG CD1 CD2 REMARK 470 GLU B 16 CG CD OE1 OE2 REMARK 470 LEU B 17 CG CD1 CD2 REMARK 470 LEU B 18 CG CD1 CD2 REMARK 470 LYS B 19 CG CD CE NZ REMARK 470 SER B 20 OG REMARK 470 VAL B 21 CG1 CG2 REMARK 470 ILE B 23 CG1 CG2 CD1 REMARK 470 LEU B 24 CG CD1 CD2 REMARK 470 LYS B 27 CG CD CE NZ REMARK 470 ARG B 28 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 32 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 33 CG OD1 OD2 REMARK 470 GLU B 34 CG CD OE1 OE2 REMARK 470 LYS B 35 CG CD CE NZ REMARK 470 TYR B 36 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 VAL B 37 CG1 CG2 REMARK 470 ILE B 38 CG1 CG2 CD1 REMARK 470 VAL B 41 CG1 CG2 REMARK 470 THR B 42 OG1 CG2 REMARK 470 THR B 44 OG1 CG2 REMARK 470 ASN B 45 CG OD1 ND2 REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 LEU B 50 CG CD1 CD2 REMARK 470 LEU B 52 CG CD1 CD2 REMARK 470 GLU B 53 CG CD OE1 OE2 REMARK 470 VAL B 54 CG1 CG2 REMARK 470 VAL B 55 CG1 CG2 REMARK 470 ASP B 56 CG OD1 OD2 REMARK 470 VAL B 57 CG1 CG2 REMARK 470 GLU B 58 CG CD OE1 OE2 REMARK 470 LEU B 59 CG CD1 CD2 REMARK 470 MET B 61 CG SD CE REMARK 470 ARG B 65 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 77 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 78 CG CD OE1 OE2 REMARK 470 LYS B 81 CG CD CE NZ REMARK 470 LYS B 82 CG CD CE NZ REMARK 470 LEU B 83 CG CD1 CD2 REMARK 470 ILE B 88 CG1 CG2 CD1 REMARK 470 ILE B 97 CG1 CG2 CD1 REMARK 470 GLU B 100 CG CD OE1 OE2 REMARK 470 ILE B 101 CG1 CG2 CD1 REMARK 470 LEU B 102 CG CD1 CD2 REMARK 470 ARG B 105 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 109 CG1 CG2 REMARK 470 SER B 110 OG REMARK 470 ARG B 113 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 114 CG CD CE NZ REMARK 470 LYS B 120 CG CD CE NZ REMARK 470 ILE B 122 CG1 CG2 CD1 REMARK 470 GLU B 136 CG CD OE1 OE2 REMARK 470 ARG B 145 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 151 CG CD CE NZ REMARK 470 LYS B 158 CG CD CE NZ REMARK 470 LEU B 161 CG CD1 CD2 REMARK 470 LYS B 163 CG CD CE NZ REMARK 470 GLN B 179 CG CD OE1 NE2 REMARK 470 LYS B 205 CG CD CE NZ REMARK 470 ILE B 214 CG1 CG2 CD1 REMARK 470 PHE B 217 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 227 CG CD OE1 OE2 REMARK 470 ARG B 230 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 231 CG OD1 OD2 REMARK 470 LEU B 233 CG CD1 CD2 REMARK 470 LYS B 234 CG CD CE NZ REMARK 470 LYS B 236 CG CD CE NZ REMARK 470 LYS B 238 CG CD CE NZ REMARK 470 GLU B 246 CG CD OE1 OE2 REMARK 470 LYS B 277 CG CD CE NZ REMARK 470 GLU B 307 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2' A F 58 OP2 U F 60 2.05 REMARK 500 NZ LYS B 29 OP2 G F 19 2.08 REMARK 500 O2' A C 58 OP2 U C 60 2.11 REMARK 500 OD2 ASP B 99 NH2 ARG B 124 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG B 232 NE ARG B 232 CZ -0.087 REMARK 500 ARG B 232 CZ ARG B 232 NH1 -0.090 REMARK 500 REMARK 500 REMARK: NULL 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 ARG B 232 CG - CD - NE ANGL. DEV. = 21.7 DEGREES REMARK 500 ARG B 232 NE - CZ - NH1 ANGL. DEV. = -9.2 DEGREES REMARK 500 ARG B 232 NE - CZ - NH2 ANGL. DEV. = 8.3 DEGREES REMARK 500 U F 45 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 A F 59 O4' - C1' - N9 ANGL. DEV. = 4.7 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 VAL B 194 30.34 -89.09 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 SAH A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAH B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WT3 RELATED DB: PDB DBREF 5WT1 A 1 333 UNP Q9V2G1 TRM5A_PYRAB 1 333 DBREF1 5WT1 C 1 75 GB HE613800.1 DBREF2 5WT1 C HE613800.1 150080 150005 DBREF 5WT1 B 1 333 UNP Q9V2G1 TRM5A_PYRAB 1 333 DBREF1 5WT1 F 1 75 GB HE613800.1 DBREF2 5WT1 F HE613800.1 150080 150005 SEQRES 1 A 333 MET SER GLY VAL LYS VAL ARG ARG GLU ASP ALA LYS LYS SEQRES 2 A 333 VAL LEU GLU LEU LEU LYS SER VAL GLY ILE LEU ASP GLY SEQRES 3 A 333 LYS ARG LYS ALA ILE ARG ASP GLU LYS TYR VAL ILE PHE SEQRES 4 A 333 PRO VAL THR ASP THR ASN ILE ALA LYS SER LEU GLY LEU SEQRES 5 A 333 GLU VAL VAL ASP VAL GLU LEU PRO MET ARG PRO GLU ARG SEQRES 6 A 333 GLN ILE TYR LYS ASN LEU GLU ASP LEU LEU PRO ARG GLU SEQRES 7 A 333 ILE PHE LYS LYS LEU GLY ARG LEU ASP ILE VAL GLY ASP SEQRES 8 A 333 ILE ALA ILE VAL SER ILE PRO ASP GLU ILE LEU SER GLU SEQRES 9 A 333 ARG GLU VAL ILE VAL SER ALA ILE ARG LYS LEU TYR PRO SEQRES 10 A 333 LYS VAL LYS VAL ILE ALA ARG ARG GLY PHE HIS SER GLY SEQRES 11 A 333 LEU TYR ARG ILE ARG GLU LEU GLU VAL ILE TRP GLY GLU SEQRES 12 A 333 ASN ARG LEU HIS THR ILE HIS LYS GLU ASN GLY VAL LEU SEQRES 13 A 333 ILE LYS VAL ASP LEU SER LYS VAL PHE PHE ASN PRO ARG SEQRES 14 A 333 MET LYS GLY GLU ARG TYR ARG ILE ALA GLN LEU VAL ASN SEQRES 15 A 333 ASP GLY GLU ARG ILE LEU VAL PRO PHE ALA GLY VAL ILE SEQRES 16 A 333 PRO TYR PRO LEU VAL ILE ALA ARG PHE LYS ASN VAL GLU SEQRES 17 A 333 VAL TYR ALA VAL GLU ILE ASN GLU PHE ALA VAL LYS LEU SEQRES 18 A 333 ALA GLU GLU ASN LEU GLU LEU ASN ARG ASP ARG LEU LYS SEQRES 19 A 333 GLY LYS ILE LYS ILE ILE HIS GLY ASP VAL PHE GLU VAL SEQRES 20 A 333 LEU PRO ASN LEU PRO ASN PHE ASP ARG VAL VAL SER PRO SEQRES 21 A 333 THR PRO LYS GLY VAL ASP ALA LEU SER LEU THR LEU SER SEQRES 22 A 333 LYS ALA GLU LYS PHE LEU HIS TYR TYR ASP PHE VAL HIS SEQRES 23 A 333 GLU SER GLU ILE GLU ARG PHE ARG GLU ARG VAL LEU GLU SEQRES 24 A 333 GLU CYS ARG ARG GLN GLY LYS GLU CYS ARG VAL SER VAL SEQRES 25 A 333 ARG LYS VAL SER ASP TYR LYS PRO HIS VAL TYR LYS VAL SEQRES 26 A 333 CYS ALA ASP VAL GLU ILE LEU SER SEQRES 1 C 76 G G G G C G G U A G C U C SEQRES 2 C 76 A G C C U G G G A G A G C SEQRES 3 C 76 A C C G G A C U G A A G A SEQRES 4 C 76 U C C G G G U G U C G G G SEQRES 5 C 76 G G U U C A A A U C C C C SEQRES 6 C 76 C C C G C C C C A C C SEQRES 1 B 333 MET SER GLY VAL LYS VAL ARG ARG GLU ASP ALA LYS LYS SEQRES 2 B 333 VAL LEU GLU LEU LEU LYS SER VAL GLY ILE LEU ASP GLY SEQRES 3 B 333 LYS ARG LYS ALA ILE ARG ASP GLU LYS TYR VAL ILE PHE SEQRES 4 B 333 PRO VAL THR ASP THR ASN ILE ALA LYS SER LEU GLY LEU SEQRES 5 B 333 GLU VAL VAL ASP VAL GLU LEU PRO MET ARG PRO GLU ARG SEQRES 6 B 333 GLN ILE TYR LYS ASN LEU GLU ASP LEU LEU PRO ARG GLU SEQRES 7 B 333 ILE PHE LYS LYS LEU GLY ARG LEU ASP ILE VAL GLY ASP SEQRES 8 B 333 ILE ALA ILE VAL SER ILE PRO ASP GLU ILE LEU SER GLU SEQRES 9 B 333 ARG GLU VAL ILE VAL SER ALA ILE ARG LYS LEU TYR PRO SEQRES 10 B 333 LYS VAL LYS VAL ILE ALA ARG ARG GLY PHE HIS SER GLY SEQRES 11 B 333 LEU TYR ARG ILE ARG GLU LEU GLU VAL ILE TRP GLY GLU SEQRES 12 B 333 ASN ARG LEU HIS THR ILE HIS LYS GLU ASN GLY VAL LEU SEQRES 13 B 333 ILE LYS VAL ASP LEU SER LYS VAL PHE PHE ASN PRO ARG SEQRES 14 B 333 MET LYS GLY GLU ARG TYR ARG ILE ALA GLN LEU VAL ASN SEQRES 15 B 333 ASP GLY GLU ARG ILE LEU VAL PRO PHE ALA GLY VAL ILE SEQRES 16 B 333 PRO TYR PRO LEU VAL ILE ALA ARG PHE LYS ASN VAL GLU SEQRES 17 B 333 VAL TYR ALA VAL GLU ILE ASN GLU PHE ALA VAL LYS LEU SEQRES 18 B 333 ALA GLU GLU ASN LEU GLU LEU ASN ARG ASP ARG LEU LYS SEQRES 19 B 333 GLY LYS ILE LYS ILE ILE HIS GLY ASP VAL PHE GLU VAL SEQRES 20 B 333 LEU PRO ASN LEU PRO ASN PHE ASP ARG VAL VAL SER PRO SEQRES 21 B 333 THR PRO LYS GLY VAL ASP ALA LEU SER LEU THR LEU SER SEQRES 22 B 333 LYS ALA GLU LYS PHE LEU HIS TYR TYR ASP PHE VAL HIS SEQRES 23 B 333 GLU SER GLU ILE GLU ARG PHE ARG GLU ARG VAL LEU GLU SEQRES 24 B 333 GLU CYS ARG ARG GLN GLY LYS GLU CYS ARG VAL SER VAL SEQRES 25 B 333 ARG LYS VAL SER ASP TYR LYS PRO HIS VAL TYR LYS VAL SEQRES 26 B 333 CYS ALA ASP VAL GLU ILE LEU SER SEQRES 1 F 76 G G G G C G G U A G C U C SEQRES 2 F 76 A G C C U G G G A G A G C SEQRES 3 F 76 A C C G G A C U G A A G A SEQRES 4 F 76 U C C G G G U G U C G G G SEQRES 5 F 76 G G U U C A A A U C C C C SEQRES 6 F 76 C C C G C C C C A C C HET SAH A 401 26 HET SAH B 401 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 5 SAH 2(C14 H20 N6 O5 S) FORMUL 7 HOH *60(H2 O) HELIX 1 AA1 ASP A 10 GLY A 22 1 13 HELIX 2 AA2 ASP A 43 LEU A 50 1 8 HELIX 3 AA3 PRO A 63 ILE A 67 5 5 HELIX 4 AA4 PRO A 76 LEU A 83 1 8 HELIX 5 AA5 PRO A 98 GLU A 100 5 3 HELIX 6 AA6 ILE A 101 TYR A 116 1 16 HELIX 7 AA7 ASN A 167 ARG A 169 5 3 HELIX 8 AA8 MET A 170 VAL A 181 1 12 HELIX 9 AA9 ILE A 195 LYS A 205 1 11 HELIX 10 AB1 ASN A 215 ARG A 230 1 16 HELIX 11 AB2 ASP A 243 LEU A 248 1 6 HELIX 12 AB3 PRO A 249 LEU A 251 5 3 HELIX 13 AB4 ALA A 267 LYS A 274 1 8 HELIX 14 AB5 GLU A 289 GLN A 304 1 16 HELIX 15 AB6 ASP B 10 GLY B 22 1 13 HELIX 16 AB7 ASP B 43 GLY B 51 1 9 HELIX 17 AB8 PRO B 63 ILE B 67 5 5 HELIX 18 AB9 PRO B 76 LEU B 83 1 8 HELIX 19 AC1 PRO B 98 LEU B 102 5 5 HELIX 20 AC2 GLU B 104 TYR B 116 1 13 HELIX 21 AC3 ASN B 167 ARG B 169 5 3 HELIX 22 AC4 MET B 170 VAL B 181 1 12 HELIX 23 AC5 ILE B 195 LYS B 205 1 11 HELIX 24 AC6 ASN B 215 ASN B 229 1 15 HELIX 25 AC7 ASP B 243 LEU B 248 1 6 HELIX 26 AC8 PRO B 249 LEU B 251 5 3 HELIX 27 AC9 ALA B 267 LYS B 274 1 8 HELIX 28 AD1 GLU B 289 GLN B 304 1 16 SHEET 1 AA1 4 ILE A 31 ARG A 32 0 SHEET 2 AA1 4 TYR A 36 VAL A 41 -1 O ILE A 38 N ILE A 31 SHEET 3 AA1 4 SER A 2 ARG A 7 -1 N VAL A 6 O VAL A 37 SHEET 4 AA1 4 GLU A 53 VAL A 55 -1 O VAL A 55 N GLY A 3 SHEET 1 AA2 4 LEU A 86 VAL A 89 0 SHEET 2 AA2 4 ILE A 92 VAL A 95 -1 O ILE A 94 N ASP A 87 SHEET 3 AA2 4 VAL A 121 HIS A 128 1 O VAL A 121 N ALA A 93 SHEET 4 AA2 4 ARG A 135 GLY A 142 -1 O GLU A 138 N ARG A 124 SHEET 1 AA3 2 HIS A 147 GLU A 152 0 SHEET 2 AA3 2 VAL A 155 ASP A 160 -1 O VAL A 159 N THR A 148 SHEET 1 AA4 7 LYS A 236 HIS A 241 0 SHEET 2 AA4 7 GLU A 208 GLU A 213 1 N ALA A 211 O ILE A 240 SHEET 3 AA4 7 ARG A 186 PRO A 190 1 N ILE A 187 O TYR A 210 SHEET 4 AA4 7 PHE A 254 SER A 259 1 O VAL A 258 N LEU A 188 SHEET 5 AA4 7 ALA A 275 HIS A 286 1 O HIS A 280 N VAL A 257 SHEET 6 AA4 7 VAL A 322 ILE A 331 -1 O VAL A 329 N LEU A 279 SHEET 7 AA4 7 CYS A 308 LYS A 319 -1 N SER A 311 O ASP A 328 SHEET 1 AA5 3 VAL B 4 ARG B 7 0 SHEET 2 AA5 3 TYR B 36 PHE B 39 -1 O VAL B 37 N VAL B 6 SHEET 3 AA5 3 ILE B 31 ARG B 32 -1 N ILE B 31 O ILE B 38 SHEET 1 AA6 4 ASP B 87 VAL B 89 0 SHEET 2 AA6 4 ILE B 92 VAL B 95 -1 O ILE B 92 N VAL B 89 SHEET 3 AA6 4 VAL B 121 SER B 129 1 O ALA B 123 N ALA B 93 SHEET 4 AA6 4 ILE B 134 GLY B 142 -1 O GLU B 138 N ARG B 124 SHEET 1 AA7 2 HIS B 147 GLU B 152 0 SHEET 2 AA7 2 VAL B 155 ASP B 160 -1 O VAL B 159 N THR B 148 SHEET 1 AA8 7 LYS B 236 HIS B 241 0 SHEET 2 AA8 7 GLU B 208 GLU B 213 1 N ALA B 211 O ILE B 240 SHEET 3 AA8 7 ARG B 186 PRO B 190 1 N ILE B 187 O TYR B 210 SHEET 4 AA8 7 PHE B 254 SER B 259 1 O VAL B 258 N LEU B 188 SHEET 5 AA8 7 ALA B 275 HIS B 286 1 O GLU B 276 N PHE B 254 SHEET 6 AA8 7 VAL B 322 ILE B 331 -1 O VAL B 329 N LEU B 279 SHEET 7 AA8 7 CYS B 308 LYS B 319 -1 N SER B 311 O ASP B 328 CISPEP 1 LEU A 83 GLY A 84 0 10.36 CISPEP 2 LEU B 83 GLY B 84 0 7.10 SITE 1 AC1 15 LEU A 131 TYR A 132 PHE A 165 ARG A 174 SITE 2 AC1 15 PHE A 191 ALA A 192 PRO A 196 TYR A 197 SITE 3 AC1 15 GLU A 213 ILE A 214 GLY A 242 ASP A 243 SITE 4 AC1 15 VAL A 244 PRO A 260 HOH A 510 SITE 1 AC2 17 LEU B 131 TYR B 132 PHE B 165 MET B 170 SITE 2 AC2 17 ARG B 174 PHE B 191 ALA B 192 PRO B 196 SITE 3 AC2 17 TYR B 197 GLU B 213 ILE B 214 GLY B 242 SITE 4 AC2 17 ASP B 243 VAL B 244 PRO B 260 PRO B 262 SITE 5 AC2 17 HOH B 502 CRYST1 102.096 57.017 115.807 90.00 101.53 90.00 P 1 2 1 4 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 0.009795 0.000000 0.001998 0.00000 SCALE2 0.000000 0.017539 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008813 0.00000