HEADER TRANSFERASE 13-APR-23 8SH4 TITLE CRYSTAL STRUCTURE OF THE TRNA (M1G37) METHYLTRANSFERASE APOENZYME FROM TITLE 2 ANAPLASMA PHAGOCYTOPHILUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANAPLASMA PHAGOCYTOPHILUM; SOURCE 3 ORGANISM_TAXID: 948; SOURCE 4 GENE: TRMD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METHYLTRANSFERASE, APOENZYME, TRMD, SPOUT, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.JANNOTTA,D.EDELE,D.LEVANTI,M.CARSON,G.PRUCHA,J.CAESAR,C.PICCHIELLO, AUTHOR 2 K.COLLINS,E.GARLAND,J.HANDLEY-PENDLETON,V.HERNANDEZ,S.LEFFLER, AUTHOR 3 D.WILLIAMS,V.STOJANOFF,A.PEREZ,J.HALLORAN,R.BOLEN REVDAT 1 17-APR-24 8SH4 0 SPRSDE 17-APR-24 8SH4 6UEV JRNL AUTH C.JANNOTTA,D.EDELE,D.LEVANTI,M.CARSON,G.PRUCHA,J.CAESAR, JRNL AUTH 2 K.COLLINS,E.GARLAND,J.HANDLEY-PENDLETON,V.HERNANDEZ, JRNL AUTH 3 S.LEFFLER,D.WILLIAMS,V.STOJANOFF,A.PEREZ,J.HALLORAN,R.BOLEN JRNL TITL CRYSTAL STRUCTURE OF THE M1G37 TRNA METHYLTRANSFERASE JRNL TITL 2 APOENZYME FROM ANAPLASMA PHAGOCYTOPHILUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.1_4122: ???) 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 3 NUMBER OF REFLECTIONS : 10377 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 506 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 34.4000 - 4.6000 1.00 2927 148 0.1913 0.2449 REMARK 3 2 4.6000 - 3.6500 1.00 2782 135 0.1853 0.2282 REMARK 3 3 3.6500 - 3.1900 0.92 2533 138 0.2291 0.3025 REMARK 3 4 3.1900 - 2.9000 0.60 1629 85 0.2922 0.3312 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 77.57 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 : 0.009 1680 REMARK 3 ANGLE : 1.130 2285 REMARK 3 CHIRALITY : 0.054 261 REMARK 3 PLANARITY : 0.008 298 REMARK 3 DIHEDRAL : 6.397 237 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 8SH4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000268714. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9201 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11321 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.676 REMARK 200 RESOLUTION RANGE LOW (A) : 34.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : 15.50 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.19.1_4122 REMARK 200 STARTING MODEL: 3KNU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG 3350, 0.5ML OF 0.1M SODIUM REMARK 280 CITRATE, 10% GLYCEROL, ETHYLENE GLYCOL AS CRYOPROTECTANT, PH 4.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 45.61500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.36500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.36500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 68.42250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.36500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.36500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.80750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.36500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.36500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 68.42250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.36500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.36500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.80750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 45.61500 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 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 LYS A 27 CG CD CE NZ REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 HIS A 46 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 LEU A 165 CG CD1 CD2 REMARK 470 LYS A 166 CG CD CE NZ REMARK 470 GLN A 167 CG CD OE1 NE2 REMARK 470 GLU A 168 CG CD OE1 OE2 REMARK 470 SER A 169 OG REMARK 470 MET A 170 CG SD CE REMARK 470 GLU A 171 CG CD OE1 OE2 REMARK 470 LEU A 174 CG CD1 CD2 REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 THR A 214 OG1 CG2 REMARK 470 ARG A 217 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O THR A 52 HG1 THR A 180 7555 1.48 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 MET A 1 113.11 -161.27 REMARK 500 SER A 20 -130.74 59.10 REMARK 500 ARG A 89 60.24 -118.04 REMARK 500 PHE A 114 -142.06 60.86 REMARK 500 GLN A 167 -56.12 74.82 REMARK 500 GLU A 171 -58.46 69.31 REMARK 500 GLU A 175 -130.74 50.36 REMARK 500 PRO A 182 171.72 -58.82 REMARK 500 ILE A 213 -56.20 65.29 REMARK 500 ALA A 216 48.16 -79.47 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8SH4 A 1 217 UNP A0A182A739_ANAPH DBREF2 8SH4 A A0A182A739 1 217 SEQADV 8SH4 SER A 0 UNP A0A182A73 EXPRESSION TAG SEQRES 1 A 218 SER MET ILE PHE ASN VAL LEU THR ILE PHE PRO GLN MET SEQRES 2 A 218 PHE PRO GLY PRO LEU GLY VAL SER ASN LEU GLY SER ALA SEQRES 3 A 218 LEU LYS LYS GLY LEU TRP THR LEU ASN VAL PHE ASP ILE SEQRES 4 A 218 ARG ALA PHE ALA ASN ASN LYS HIS ASN THR VAL ASP ASP SEQRES 5 A 218 THR PRO TYR GLY GLY GLY PRO GLY MET LEU LEU ARG ALA SEQRES 6 A 218 ASP VAL LEU GLY ARG CYS ILE ASP GLU VAL LEU SER LEU SEQRES 7 A 218 HIS PRO ASN THR LYS LEU MET PHE THR SER PRO ARG GLY SEQRES 8 A 218 VAL SER PHE THR GLN ASP ILE ALA ARG GLN THR MET ASN SEQRES 9 A 218 PHE ASP ASN ILE THR LEU LEU CYS GLY ARG PHE GLU GLY SEQRES 10 A 218 ILE ASP GLU ARG VAL VAL ASP PHE TYR LYS LEU GLN GLU SEQRES 11 A 218 VAL SER ILE GLY ASP TYR VAL LEU SER GLY GLY GLU LEU SEQRES 12 A 218 ALA ALA MET VAL ILE ILE ASP THR CYS VAL ARG MET VAL SEQRES 13 A 218 PRO GLY VAL ILE GLY ASN ALA GLU SER LEU LYS GLN GLU SEQRES 14 A 218 SER MET GLU GLY SER LEU GLU TYR PRO GLN TYR THR ARG SEQRES 15 A 218 PRO ALA SER TRP LYS GLY MET GLU VAL PRO GLU VAL LEU SEQRES 16 A 218 LEU THR GLY ASN HIS GLY GLU ILE GLU LYS TRP ARG ARG SEQRES 17 A 218 ASN ALA SER LEU SER ILE THR ALA ALA ARG HET GOL A 301 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *24(H2 O) HELIX 1 AA1 PHE A 9 PHE A 13 5 5 HELIX 2 AA2 PRO A 14 GLY A 18 5 5 HELIX 3 AA3 VAL A 19 GLY A 29 1 11 HELIX 4 AA4 ARG A 39 ALA A 42 5 4 HELIX 5 AA5 ARG A 63 HIS A 78 1 16 HELIX 6 AA6 THR A 94 ASN A 103 1 10 HELIX 7 AA7 ASP A 118 LYS A 126 1 9 HELIX 8 AA8 GLY A 140 ARG A 153 1 14 HELIX 9 AA9 GLY A 160 LYS A 166 1 7 HELIX 10 AB1 PRO A 191 GLY A 197 5 7 HELIX 11 AB2 ASN A 198 SER A 212 1 15 SHEET 1 AA1 6 THR A 32 ASP A 37 0 SHEET 2 AA1 6 ILE A 2 THR A 7 1 N VAL A 5 O ASN A 34 SHEET 3 AA1 6 ASN A 106 CYS A 111 1 O LEU A 109 N ASN A 4 SHEET 4 AA1 6 LYS A 82 THR A 86 1 N LYS A 82 O THR A 108 SHEET 5 AA1 6 GLN A 128 SER A 131 1 O VAL A 130 N PHE A 85 SHEET 6 AA1 6 VAL A 91 SER A 92 1 N VAL A 91 O SER A 131 SHEET 1 AA2 2 SER A 184 TRP A 185 0 SHEET 2 AA2 2 MET A 188 GLU A 189 -1 O MET A 188 N TRP A 185 CISPEP 1 PHE A 13 PRO A 14 0 0.98 CISPEP 2 ARG A 181 PRO A 182 0 -10.72 CRYST1 104.730 104.730 91.230 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009548 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009548 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010961 0.00000