HEADER TRANSFERASE 27-MAR-14 4PYI TITLE HUMAN APO COMT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATECHOL O-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SOLUBLE FORM, UNP RESIDEUS 51-271; COMPND 5 EC: 2.1.1.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: COMT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METHYLTRANSFERASE, NEUROTRANSMITTER DEGRADATION, CONFORMATIONAL KEYWDS 2 CHANGE, CATECHOLAMINE METABOLISM, CELL MEMBRANE, MEMBRANE, METAL- KEYWDS 3 BINDING, SIGNAL-ANCHOR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.EHLER,J.BENZ,D.SCHLATTER,M.G.RUDOLPH REVDAT 5 03-APR-24 4PYI 1 REMARK REVDAT 4 28-FEB-24 4PYI 1 REMARK LINK REVDAT 3 23-AUG-17 4PYI 1 REMARK REVDAT 2 27-AUG-14 4PYI 1 JRNL REVDAT 1 11-JUN-14 4PYI 0 JRNL AUTH A.EHLER,J.BENZ,D.SCHLATTER,M.G.RUDOLPH JRNL TITL MAPPING THE CONFORMATIONAL SPACE ACCESSIBLE TO JRNL TITL 2 CATECHOL-O-METHYLTRANSFERASE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 2163 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 25084335 JRNL DOI 10.1107/S1399004714012917 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1491) 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 38318 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1921 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 28.7802 - 3.2523 0.85 2400 124 0.1615 0.1853 REMARK 3 2 3.2523 - 2.5820 0.98 2718 150 0.1517 0.2000 REMARK 3 3 2.5820 - 2.2557 0.97 2725 144 0.1414 0.1824 REMARK 3 4 2.2557 - 2.0495 0.95 2678 144 0.1422 0.1792 REMARK 3 5 2.0495 - 1.9027 0.95 2670 133 0.1456 0.2235 REMARK 3 6 1.9027 - 1.7905 0.96 2671 143 0.1392 0.1955 REMARK 3 7 1.7905 - 1.7009 0.95 2675 140 0.1452 0.1984 REMARK 3 8 1.7009 - 1.6268 0.95 2689 138 0.1461 0.2318 REMARK 3 9 1.6268 - 1.5642 0.95 2648 126 0.1581 0.2133 REMARK 3 10 1.5642 - 1.5102 0.93 2584 130 0.1932 0.2944 REMARK 3 11 1.5102 - 1.4630 0.93 2644 144 0.2209 0.2937 REMARK 3 12 1.4630 - 1.4212 0.92 2544 152 0.2387 0.3148 REMARK 3 13 1.4212 - 1.3838 0.92 2559 139 0.2563 0.3207 REMARK 3 14 1.3838 - 1.3500 0.78 2192 114 0.3346 0.3600 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.650 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 : 0.009 1704 REMARK 3 ANGLE : 1.233 2320 REMARK 3 CHIRALITY : 0.070 268 REMARK 3 PLANARITY : 0.006 300 REMARK 3 DIHEDRAL : 13.870 655 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 4PYI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000085378. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38358 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 28.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.01000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.202 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: INHOUSE MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 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 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 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 51 REMARK 465 GLY A 52 REMARK 465 ASP A 53 REMARK 465 GLU A 87 REMARK 465 TRP A 88 REMARK 465 ALA A 89 REMARK 465 MET A 90 REMARK 465 ASN A 91 REMARK 465 VAL A 92 REMARK 465 SER A 267 REMARK 465 GLU A 268 REMARK 465 ALA A 269 REMARK 465 GLY A 270 REMARK 465 PRO A 271 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 O HOH A 414 O HOH A 465 2.05 REMARK 500 O HOH A 410 O HOH A 430 2.12 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 TYR A 118 -111.34 53.19 REMARK 500 ASP A 183 -74.14 -97.68 REMARK 500 ASP A 191 29.91 -152.77 REMARK 500 HIS A 192 -153.20 -103.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 301 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 233 O REMARK 620 2 ARG A 234 O 84.3 REMARK 620 3 SER A 236 O 97.7 105.0 REMARK 620 4 PHE A 239 O 97.9 162.9 91.6 REMARK 620 5 HOH A 401 O 172.2 88.8 80.7 89.8 REMARK 620 6 HOH A 449 O 108.8 83.0 153.1 80.2 73.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4P7K RELATED DB: PDB REMARK 900 RELATED ID: 4P7F RELATED DB: PDB REMARK 900 RELATED ID: 4P7G RELATED DB: PDB REMARK 900 RELATED ID: 4P7J RELATED DB: PDB REMARK 900 RELATED ID: 4PYJ RELATED DB: PDB REMARK 900 RELATED ID: 4PYK RELATED DB: PDB REMARK 900 RELATED ID: 4PYL RELATED DB: PDB REMARK 900 RELATED ID: 4PYM RELATED DB: PDB REMARK 900 RELATED ID: 4PYN RELATED DB: PDB REMARK 900 RELATED ID: 4PYO RELATED DB: PDB REMARK 900 RELATED ID: 4PYQ RELATED DB: PDB DBREF 4PYI A 51 271 UNP P21964 COMT_HUMAN 51 271 SEQRES 1 A 221 MET GLY ASP THR LYS GLU GLN ARG ILE LEU ASN HIS VAL SEQRES 2 A 221 LEU GLN HIS ALA GLU PRO GLY ASN ALA GLN SER VAL LEU SEQRES 3 A 221 GLU ALA ILE ASP THR TYR CYS GLU GLN LYS GLU TRP ALA SEQRES 4 A 221 MET ASN VAL GLY ASP LYS LYS GLY LYS ILE VAL ASP ALA SEQRES 5 A 221 VAL ILE GLN GLU HIS GLN PRO SER VAL LEU LEU GLU LEU SEQRES 6 A 221 GLY ALA TYR CYS GLY TYR SER ALA VAL ARG MET ALA ARG SEQRES 7 A 221 LEU LEU SER PRO GLY ALA ARG LEU ILE THR ILE GLU ILE SEQRES 8 A 221 ASN PRO ASP CYS ALA ALA ILE THR GLN ARG MET VAL ASP SEQRES 9 A 221 PHE ALA GLY VAL LYS ASP LYS VAL THR LEU VAL VAL GLY SEQRES 10 A 221 ALA SER GLN ASP ILE ILE PRO GLN LEU LYS LYS LYS TYR SEQRES 11 A 221 ASP VAL ASP THR LEU ASP MET VAL PHE LEU ASP HIS TRP SEQRES 12 A 221 LYS ASP ARG TYR LEU PRO ASP THR LEU LEU LEU GLU GLU SEQRES 13 A 221 CYS GLY LEU LEU ARG LYS GLY THR VAL LEU LEU ALA ASP SEQRES 14 A 221 ASN VAL ILE CYS PRO GLY ALA PRO ASP PHE LEU ALA HIS SEQRES 15 A 221 VAL ARG GLY SER SER CYS PHE GLU CYS THR HIS TYR GLN SEQRES 16 A 221 SER PHE LEU GLU TYR ARG GLU VAL VAL ASP GLY LEU GLU SEQRES 17 A 221 LYS ALA ILE TYR LYS GLY PRO GLY SER GLU ALA GLY PRO HET NA A 301 1 HETNAM NA SODIUM ION FORMUL 2 NA NA 1+ FORMUL 3 HOH *133(H2 O) HELIX 1 1 THR A 54 ALA A 67 1 14 HELIX 2 2 ASN A 71 GLN A 85 1 15 HELIX 3 3 ASP A 94 GLN A 108 1 15 HELIX 4 4 GLY A 120 ARG A 128 1 9 HELIX 5 5 ASN A 142 ALA A 156 1 15 HELIX 6 6 VAL A 158 ASP A 160 5 3 HELIX 7 7 ALA A 168 ILE A 173 1 6 HELIX 8 8 GLN A 175 ASP A 181 1 7 HELIX 9 9 TRP A 193 ASP A 195 5 3 HELIX 10 10 ARG A 196 CYS A 207 1 12 HELIX 11 11 ALA A 226 SER A 236 1 11 SHEET 1 A 7 VAL A 162 VAL A 166 0 SHEET 2 A 7 ARG A 135 GLU A 140 1 N THR A 138 O VAL A 165 SHEET 3 A 7 VAL A 111 LEU A 115 1 N GLU A 114 O ILE A 137 SHEET 4 A 7 LEU A 185 LEU A 190 1 O PHE A 189 N LEU A 115 SHEET 5 A 7 LEU A 210 ALA A 218 1 O VAL A 215 N VAL A 188 SHEET 6 A 7 GLU A 252 TYR A 262 -1 O TYR A 262 N GLY A 213 SHEET 7 A 7 PHE A 239 LEU A 248 -1 N TYR A 244 O LEU A 257 LINK O VAL A 233 NA NA A 301 1555 1555 2.42 LINK O ARG A 234 NA NA A 301 1555 1555 2.52 LINK O SER A 236 NA NA A 301 1555 1555 2.28 LINK O PHE A 239 NA NA A 301 1555 1555 2.37 LINK NA NA A 301 O HOH A 401 1555 1555 2.43 LINK NA NA A 301 O HOH A 449 1555 1555 2.72 CISPEP 1 CYS A 223 PRO A 224 0 3.90 SITE 1 AC1 6 VAL A 233 ARG A 234 SER A 236 PHE A 239 SITE 2 AC1 6 HOH A 401 HOH A 449 CRYST1 31.596 42.638 43.663 115.03 95.35 108.98 P 1 1 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 0.031650 0.010885 0.009364 0.00000 SCALE2 0.000000 0.024802 0.013629 0.00000 SCALE3 0.000000 0.000000 0.026247 0.00000