HEADER TRANSFERASE 10-APR-17 5VG9 TITLE STRUCTURE OF THE EUKARYOTIC INTRAMEMBRANE RAS METHYLTRANSFERASE ICMT TITLE 2 (ISOPRENYLCYSTEINE CARBOXYL METHYLTRANSFERASE) WITHOUT A MONOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-S-ISOPRENYLCYSTEINE O-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.1.100; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRIBOLIUM CASTANEUM; SOURCE 3 ORGANISM_COMMON: RED FLOUR BEETLE; SOURCE 4 ORGANISM_TAXID: 7070; SOURCE 5 GENE: TCASGA2_TC013078; SOURCE 6 EXPRESSION_SYSTEM: PICHIA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4919 KEYWDS MEMBRANE PROTEIN, MEMBRANE ENZYME, METHYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.B.LONG,M.M.DIVER,L.PEDI,A.KOIDE,S.KOIDE REVDAT 4 13-MAR-24 5VG9 1 REMARK REVDAT 3 07-FEB-18 5VG9 1 JRNL REVDAT 2 31-JAN-18 5VG9 1 JRNL REVDAT 1 17-JAN-18 5VG9 0 JRNL AUTH M.M.DIVER,L.PEDI,A.KOIDE,S.KOIDE,S.B.LONG JRNL TITL ATOMIC STRUCTURE OF THE EUKARYOTIC INTRAMEMBRANE RAS JRNL TITL 2 METHYLTRANSFERASE ICMT. JRNL REF NATURE V. 553 526 2018 JRNL REFN ESSN 1476-4687 JRNL PMID 29342140 JRNL DOI 10.1038/NATURE25439 REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 6119 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.371 REMARK 3 R VALUE (WORKING SET) : 0.370 REMARK 3 FREE R VALUE : 0.389 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.650 REMARK 3 FREE R VALUE TEST SET COUNT : 346 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 33.1995 - 5.0372 0.96 3111 186 0.3529 0.3705 REMARK 3 2 5.0372 - 4.0004 0.86 2662 160 0.4297 0.4450 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.980 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 53.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 209.0 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 2353 REMARK 3 ANGLE : 0.453 3209 REMARK 3 CHIRALITY : 0.040 356 REMARK 3 PLANARITY : 0.003 391 REMARK 3 DIHEDRAL : 18.173 794 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 5VG9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6119 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.000 REMARK 200 RESOLUTION RANGE LOW (A) : 33.198 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 34.60 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 85.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 35.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 78.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG400 200 MM CACL2 50 MM NA REMARK 280 ACETATE, PH 5.5, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 118.06000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 118.06000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 25.82000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.82500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.82000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.82500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 118.06000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.82000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.82500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 118.06000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.82000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.82500 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 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 ILE A 281 REMARK 465 ALA A 282 REMARK 465 ALA A 283 REMARK 465 GLU A 284 REMARK 465 GLY A 285 REMARK 465 GLU A 286 REMARK 465 GLU A 287 REMARK 465 PHE A 288 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 TYR A 29 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 280 CG CD CE NZ 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 ASN A 58 -161.70 -79.63 REMARK 500 GLN A 90 -28.48 -39.94 REMARK 500 GLN A 117 75.01 -108.49 REMARK 500 PHE A 275 10.11 80.77 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 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5V7P RELATED DB: PDB REMARK 900 HIGH RESOLUTION ICMT-MONOBODY COMPLEX DBREF 5VG9 A 1 281 UNP D6WJ77 D6WJ77_TRICA 1 281 SEQADV 5VG9 ALA A 151 UNP D6WJ77 GLY 151 CONFLICT SEQADV 5VG9 ALA A 154 UNP D6WJ77 GLU 154 CONFLICT SEQADV 5VG9 ALA A 282 UNP D6WJ77 EXPRESSION TAG SEQADV 5VG9 ALA A 283 UNP D6WJ77 EXPRESSION TAG SEQADV 5VG9 GLU A 284 UNP D6WJ77 EXPRESSION TAG SEQADV 5VG9 GLY A 285 UNP D6WJ77 EXPRESSION TAG SEQADV 5VG9 GLU A 286 UNP D6WJ77 EXPRESSION TAG SEQADV 5VG9 GLU A 287 UNP D6WJ77 EXPRESSION TAG SEQADV 5VG9 PHE A 288 UNP D6WJ77 EXPRESSION TAG SEQRES 1 A 288 MET LEU SER PRO ALA GLY LYS ILE SER LEU GLN SER PHE SEQRES 2 A 288 THR GLY SER SER LEU VAL PHE PHE VAL ILE CYS MET PHE SEQRES 3 A 288 ASN HIS TYR TYR GLY ILE THR ASN LEU VAL VAL ASN THR SEQRES 4 A 288 LEU ILE VAL PHE PHE TYR ALA VAL ASN VAL TYR PHE PHE SEQRES 5 A 288 LEU LYS PHE PHE TYR ASN GLU PHE ALA PHE ALA ILE ALA SEQRES 6 A 288 ILE ARG ALA ALA PHE LEU GLY LEU VAL LEU VAL LEU GLY SEQRES 7 A 288 LEU TYR ILE LYS LEU VAL ALA PRO PRO ASN ILE GLN ILE SEQRES 8 A 288 PHE GLY GLY TYR MET SER VAL MET ALA LEU PHE HIS TYR SEQRES 9 A 288 SER GLU PHE LEU ALA ILE ALA ILE VAL GLN PRO LYS GLN SEQRES 10 A 288 VAL SER THR ASP SER PHE VAL ILE ASN HIS SER PRO GLN SEQRES 11 A 288 TYR THR ILE ALA ALA VAL SER SER TRP VAL GLU PHE PHE SEQRES 12 A 288 ILE GLU THR TYR PHE PHE PRO ALA LEU LYS ALA ILE HIS SEQRES 13 A 288 TRP LEU SER ASN ILE GLY LEU CYS VAL CYS ILE LEU GLY SEQRES 14 A 288 GLU VAL LEU ARG LYS THR ALA ILE LEU THR ALA GLY SER SEQRES 15 A 288 ASN PHE ASN HIS LEU VAL GLN CYS GLU LYS SER SER ASP SEQRES 16 A 288 HIS VAL LEU VAL THR HIS GLY VAL TYR ALA TRP PHE ARG SEQRES 17 A 288 HIS PRO SER TYR VAL GLY TRP PHE TYR TRP SER ILE GLY SEQRES 18 A 288 THR GLN ILE ILE LEU ILE ASN PRO LEU CYS ILE PRO ALA SEQRES 19 A 288 TYR THR LEU ALA SER TRP MET PHE PHE LYS GLU ARG ILE SEQRES 20 A 288 TYR ILE GLU GLU SER MET LEU LEU SER PHE PHE GLY GLN SEQRES 21 A 288 GLN TYR CYS ASP TYR GLN GLN GLN VAL GLY THR GLY ILE SEQRES 22 A 288 PRO PHE ILE GLU GLY TYR LYS ILE ALA ALA GLU GLY GLU SEQRES 23 A 288 GLU PHE HET SAH A 301 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S HELIX 1 AA1 SER A 3 TYR A 30 1 28 HELIX 2 AA2 ASN A 34 TYR A 57 1 24 HELIX 3 AA3 ASN A 58 ALA A 85 1 28 HELIX 4 AA4 ILE A 89 GLN A 114 1 26 HELIX 5 AA5 PRO A 115 VAL A 118 5 4 HELIX 6 AA6 SER A 119 VAL A 124 1 6 HELIX 7 AA7 SER A 128 PHE A 149 1 22 HELIX 8 AA8 PRO A 150 ALA A 154 5 5 HELIX 9 AA9 ILE A 155 GLY A 181 1 27 HELIX 10 AB1 SER A 182 PHE A 184 5 3 HELIX 11 AB2 GLY A 202 PHE A 207 1 6 HELIX 12 AB3 HIS A 209 ILE A 227 1 19 HELIX 13 AB4 LEU A 230 GLY A 259 1 30 HELIX 14 AB5 GLY A 259 VAL A 269 1 11 SITE 1 AC1 15 ASN A 185 LEU A 187 VAL A 188 GLN A 189 SITE 2 AC1 15 HIS A 196 LEU A 198 VAL A 199 TYR A 204 SITE 3 AC1 15 HIS A 209 PRO A 210 SER A 211 TYR A 212 SITE 4 AC1 15 GLU A 250 LEU A 254 PHE A 257 CRYST1 51.640 123.650 236.120 90.00 90.00 90.00 C 2 2 21 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 0.019365 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008087 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004235 0.00000