HEADER TRANSFERASE 06-MAR-23 8GDU TITLE CRYSTAL STRUCTURE OF A MUTANT METHYL TRANSFERASE FROM METHANOSARCINA TITLE 2 ACETIVORANS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET TITLE 3 MVR53-11M COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLTRANSFERASE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA ACETIVORANS C2A; SOURCE 3 ORGANISM_TAXID: 188937; SOURCE 4 GENE: MA_2137; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SAM-BINDING PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.FOROUHAR,N.E.BANAYAN,B.L.LOUGHLIN,S.SINGH,V.WONG,H.S.HUNT, AUTHOR 2 S.K.HANDELMAN,N.PRICE,J.F.HUNT REVDAT 2 20-MAR-24 8GDU 1 JRNL REVDAT 1 24-JAN-24 8GDU 0 JRNL AUTH N.E.BANAYAN,B.J.LOUGHLIN,S.SINGH,F.FOROUHAR,G.LU,K.H.WONG, JRNL AUTH 2 M.NEKY,H.S.HUNT,L.B.BATEMAN JR.,A.TAMEZ,S.K.HANDELMAN, JRNL AUTH 3 W.N.PRICE,J.F.HUNT JRNL TITL SYSTEMATIC ENHANCEMENT OF PROTEIN CRYSTALLIZATION EFFICIENCY JRNL TITL 2 BY BULK LYSINE-TO-ARGININE (KR) SUBSTITUTION. JRNL REF PROTEIN SCI. V. 33 E4898 2024 JRNL REFN ESSN 1469-896X JRNL PMID 38358135 JRNL DOI 10.1002/PRO.4898 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16541 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1642 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 77.7500 - 4.6000 1.00 1368 146 0.1986 0.2149 REMARK 3 2 4.6000 - 3.6500 1.00 1292 121 0.1756 0.1874 REMARK 3 3 3.6500 - 3.1900 1.00 1257 145 0.1743 0.2026 REMARK 3 4 3.1900 - 2.9000 1.00 1210 160 0.1745 0.2165 REMARK 3 5 2.9000 - 2.6900 1.00 1248 131 0.1700 0.1973 REMARK 3 6 2.6900 - 2.5300 1.00 1233 134 0.1745 0.2355 REMARK 3 7 2.5300 - 2.4100 1.00 1220 135 0.1815 0.2079 REMARK 3 8 2.4100 - 2.3000 1.00 1204 138 0.1746 0.2060 REMARK 3 9 2.3000 - 2.2100 1.00 1222 135 0.1767 0.2331 REMARK 3 10 2.2100 - 2.1400 1.00 1226 132 0.1868 0.2230 REMARK 3 11 2.1400 - 2.0700 1.00 1200 131 0.1932 0.2569 REMARK 3 12 2.0700 - 2.0100 1.00 1219 134 0.2215 0.2436 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.530 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 : 0.007 1544 REMARK 3 ANGLE : 1.035 2087 REMARK 3 CHIRALITY : 0.067 227 REMARK 3 PLANARITY : 0.006 272 REMARK 3 DIHEDRAL : 34.247 580 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): -9.2734 33.6148 0.4888 REMARK 3 T TENSOR REMARK 3 T11: 0.2714 T22: 0.2718 REMARK 3 T33: 0.2534 T12: -0.0229 REMARK 3 T13: -0.0046 T23: 0.0145 REMARK 3 L TENSOR REMARK 3 L11: 1.8291 L22: 1.7145 REMARK 3 L33: 1.8186 L12: 1.0592 REMARK 3 L13: -0.3136 L23: 0.3423 REMARK 3 S TENSOR REMARK 3 S11: -0.0492 S12: -0.0266 S13: -0.1062 REMARK 3 S21: 0.0575 S22: -0.0342 S23: -0.0639 REMARK 3 S31: 0.2016 S32: -0.1559 S33: -0.0013 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 8GDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000272806. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19350 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 109.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 25.40 REMARK 200 R MERGE (I) : 0.13500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.82800 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES AND 30% (W/V) PEG 1K, PH REMARK 280 7.5, MICROBATCH, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 SMTRY1 3 0.000000 -1.000000 0.000000 54.97500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 54.97500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.56200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 54.97500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 54.97500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.56200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 54.97500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.97500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 19.56200 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 54.97500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.97500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.56200 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 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 433 LIES ON A SPECIAL POSITION. 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 ASP A 141 REMARK 465 ARG A 142 REMARK 465 GLU A 143 REMARK 465 PRO A 144 REMARK 465 GLY A 145 REMARK 465 GLU A 146 REMARK 465 TYR A 147 REMARK 465 GLU A 148 REMARK 465 LEU A 149 REMARK 465 PRO A 150 REMARK 465 LEU A 195 REMARK 465 GLU A 196 REMARK 465 HIS A 197 REMARK 465 HIS A 198 REMARK 465 HIS A 199 REMARK 465 HIS A 200 REMARK 465 HIS A 201 REMARK 465 HIS A 202 DBREF 8GDU A 1 194 UNP Q8TNZ0 Q8TNZ0_METAC 1 194 SEQADV 8GDU ARG A 8 UNP Q8TNZ0 LYS 8 ENGINEERED MUTATION SEQADV 8GDU ARG A 52 UNP Q8TNZ0 LYS 52 ENGINEERED MUTATION SEQADV 8GDU ARG A 64 UNP Q8TNZ0 LYS 64 ENGINEERED MUTATION SEQADV 8GDU ARG A 65 UNP Q8TNZ0 ASP 65 ENGINEERED MUTATION SEQADV 8GDU ARG A 71 UNP Q8TNZ0 LYS 71 ENGINEERED MUTATION SEQADV 8GDU ARG A 126 UNP Q8TNZ0 LYS 126 ENGINEERED MUTATION SEQADV 8GDU ARG A 129 UNP Q8TNZ0 LYS 129 ENGINEERED MUTATION SEQADV 8GDU ARG A 133 UNP Q8TNZ0 LYS 133 ENGINEERED MUTATION SEQADV 8GDU ARG A 142 UNP Q8TNZ0 LYS 142 ENGINEERED MUTATION SEQADV 8GDU ARG A 155 UNP Q8TNZ0 LYS 155 ENGINEERED MUTATION SEQADV 8GDU ARG A 172 UNP Q8TNZ0 LYS 172 ENGINEERED MUTATION SEQADV 8GDU ARG A 194 UNP Q8TNZ0 LYS 194 ENGINEERED MUTATION SEQADV 8GDU LEU A 195 UNP Q8TNZ0 EXPRESSION TAG SEQADV 8GDU GLU A 196 UNP Q8TNZ0 EXPRESSION TAG SEQADV 8GDU HIS A 197 UNP Q8TNZ0 EXPRESSION TAG SEQADV 8GDU HIS A 198 UNP Q8TNZ0 EXPRESSION TAG SEQADV 8GDU HIS A 199 UNP Q8TNZ0 EXPRESSION TAG SEQADV 8GDU HIS A 200 UNP Q8TNZ0 EXPRESSION TAG SEQADV 8GDU HIS A 201 UNP Q8TNZ0 EXPRESSION TAG SEQADV 8GDU HIS A 202 UNP Q8TNZ0 EXPRESSION TAG SEQRES 1 A 202 MET PHE TRP ASP GLU VAL TYR ARG GLY THR PRO PRO TRP SEQRES 2 A 202 ASP ILE ASP HIS PRO GLN PRO ALA PHE GLN ALA LEU ILE SEQRES 3 A 202 GLU SER GLY GLU ILE ARG PRO GLY ARG ALA LEU ASP ILE SEQRES 4 A 202 GLY CYS GLY ARG GLY GLU ASN ALA ILE MET LEU ALA ARG SEQRES 5 A 202 ASN GLY CYS ASP VAL THR GLY ILE ASP LEU ALA ARG ARG SEQRES 6 A 202 ALA ILE SER ASP ALA ARG ALA LYS ALA ILE GLU ARG HIS SEQRES 7 A 202 VAL LYS VAL ASN PHE ILE VAL GLY ASN VAL LEU GLU MET SEQRES 8 A 202 ASP GLN LEU PHE THR GLU ASP GLU PHE ASP ILE VAL ILE SEQRES 9 A 202 ASP SER GLY LEU PHE HIS VAL ILE THR ASP GLU GLU ARG SEQRES 10 A 202 LEU LEU PHE THR ARG HIS VAL HIS ARG VAL LEU ARG GLU SEQRES 11 A 202 GLY GLY ARG TYR PHE MET LEU CYS PHE SER ASP ARG GLU SEQRES 12 A 202 PRO GLY GLU TYR GLU LEU PRO ARG ARG ALA SER ARG ALA SEQRES 13 A 202 GLU ILE GLU SER THR PHE SER PRO LEU PHE ASN ILE ILE SEQRES 14 A 202 TYR ILE ARG ASP VAL ILE PHE ASP SER LEU LEU ASN PRO SEQRES 15 A 202 GLY ARG ARG GLN ALA TYR LEU LEU SER ALA THR ARG LEU SEQRES 16 A 202 GLU HIS HIS HIS HIS HIS HIS HET SAH A 301 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 HOH *89(H2 O) HELIX 1 AA1 MET A 1 TYR A 7 1 7 HELIX 2 AA2 GLN A 19 SER A 28 1 10 HELIX 3 AA3 GLY A 44 ASN A 53 1 10 HELIX 4 AA4 ALA A 63 ARG A 77 1 15 HELIX 5 AA5 ASN A 87 LEU A 94 5 8 HELIX 6 AA6 LEU A 108 ILE A 112 5 5 HELIX 7 AA7 THR A 113 GLU A 115 5 3 HELIX 8 AA8 GLU A 116 VAL A 127 1 12 HELIX 9 AA9 ARG A 152 SER A 163 1 12 SHEET 1 AA1 7 ASN A 82 VAL A 85 0 SHEET 2 AA1 7 ASP A 56 ASP A 61 1 N GLY A 59 O ASN A 82 SHEET 3 AA1 7 ARG A 35 ILE A 39 1 N ASP A 38 O THR A 58 SHEET 4 AA1 7 PHE A 100 SER A 106 1 O ILE A 104 N LEU A 37 SHEET 5 AA1 7 LEU A 128 PHE A 139 1 O LEU A 137 N ASP A 105 SHEET 6 AA1 7 ARG A 184 THR A 193 -1 O TYR A 188 N CYS A 138 SHEET 7 AA1 7 ASN A 167 ASP A 177 -1 N ASN A 167 O THR A 193 CRYST1 109.950 109.950 39.124 90.00 90.00 90.00 P 42 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 0.009095 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009095 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025560 0.00000