HEADER TRANSFERASE 08-JAN-02 1KR5 TITLE CRYSTAL STRUCTURE OF HUMAN L-ISOASPARTYL METHYLTRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.1.77; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PDM2X KEYWDS ROSSMANN-FOLD DOUBLY-WOUND-ALPHA-BETA-ALPHA-SANDWICH, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.RYTTERSGAARD,S.C.GRIFFITH,M.R.SAWAYA,D.C.MACLAREN,S.CLARKE, AUTHOR 2 T.O.YEATES REVDAT 5 20-SEP-23 1KR5 1 REMARK REVDAT 4 21-DEC-22 1KR5 1 REMARK SEQADV REVDAT 3 24-FEB-09 1KR5 1 VERSN REVDAT 2 27-MAR-02 1KR5 1 JRNL REVDAT 1 08-FEB-02 1KR5 0 JRNL AUTH C.RYTTERSGAARD,S.C.GRIFFITH,M.R.SAWAYA,D.C.MACLAREN, JRNL AUTH 2 S.CLARKE,T.O.YEATES JRNL TITL CRYSTAL STRUCTURE OF HUMAN L-ISOASPARTYL METHYLTRANSFERASE. JRNL REF J.BIOL.CHEM. V. 277 10642 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11792715 JRNL DOI 10.1074/JBC.M200229200 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 641174.090 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 11959 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.100 REMARK 3 FREE R VALUE TEST SET COUNT : 731 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1334 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 97 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1634 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.54000 REMARK 3 B22 (A**2) : -17.41000 REMARK 3 B33 (A**2) : 14.87000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.86000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.37 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.950 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.290 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.010 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.020 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.840 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 63.45 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : SAH.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : SAH.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015256. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 118 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.100 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12501 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07400 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) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.25600 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: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1JG1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MAGNESIUM ACETATE, REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.84900 REMARK 290 SMTRY3 2 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 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 ALA A 1 REMARK 465 TRP A 2 REMARK 465 LYS A 3 REMARK 465 SER A 4 REMARK 465 GLY A 5 REMARK 465 GLY A 6 REMARK 465 TRP A 225 REMARK 465 LYS A 226 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 18 CG CD CE NZ REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 LYS A 220 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 LYS A 23 10.96 -141.09 REMARK 500 THR A 34 79.12 -111.92 REMARK 500 LEU A 75 42.49 -104.37 REMARK 500 TYR A 146 75.20 -153.40 REMARK 500 LEU A 207 -71.48 -103.92 REMARK 500 THR A 216 -161.41 -129.85 REMARK 500 SER A 223 -71.63 -104.14 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 300 DBREF 1KR5 A 1 226 UNP P22061 PIMT_HUMAN 1 226 SEQADV 1KR5 VAL A 119 UNP P22061 ILE 119 VARIANT SEQRES 1 A 226 ALA TRP LYS SER GLY GLY ALA SER HIS SER GLU LEU ILE SEQRES 2 A 226 HIS ASN LEU ARG LYS ASN GLY ILE ILE LYS THR ASP LYS SEQRES 3 A 226 VAL PHE GLU VAL MET LEU ALA THR ASP ARG SER HIS TYR SEQRES 4 A 226 ALA LYS CYS ASN PRO TYR MET ASP SER PRO GLN SER ILE SEQRES 5 A 226 GLY PHE GLN ALA THR ILE SER ALA PRO HIS MET HIS ALA SEQRES 6 A 226 TYR ALA LEU GLU LEU LEU PHE ASP GLN LEU HIS GLU GLY SEQRES 7 A 226 ALA LYS ALA LEU ASP VAL GLY SER GLY SER GLY ILE LEU SEQRES 8 A 226 THR ALA CYS PHE ALA ARG MET VAL GLY CYS THR GLY LYS SEQRES 9 A 226 VAL ILE GLY ILE ASP HIS ILE LYS GLU LEU VAL ASP ASP SEQRES 10 A 226 SER VAL ASN ASN VAL ARG LYS ASP ASP PRO THR LEU LEU SEQRES 11 A 226 SER SER GLY ARG VAL GLN LEU VAL VAL GLY ASP GLY ARG SEQRES 12 A 226 MET GLY TYR ALA GLU GLU ALA PRO TYR ASP ALA ILE HIS SEQRES 13 A 226 VAL GLY ALA ALA ALA PRO VAL VAL PRO GLN ALA LEU ILE SEQRES 14 A 226 ASP GLN LEU LYS PRO GLY GLY ARG LEU ILE LEU PRO VAL SEQRES 15 A 226 GLY PRO ALA GLY GLY ASN GLN MET LEU GLU GLN TYR ASP SEQRES 16 A 226 LYS LEU GLN ASP GLY SER ILE LYS MET LYS PRO LEU MET SEQRES 17 A 226 GLY VAL ILE TYR VAL PRO LEU THR ASP LYS GLU LYS GLN SEQRES 18 A 226 TRP SER ARG TRP LYS HET SAH A 300 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 HOH *64(H2 O) HELIX 1 1 SER A 8 ASN A 19 1 12 HELIX 2 2 THR A 24 THR A 34 1 11 HELIX 3 3 ASP A 35 TYR A 39 5 5 HELIX 4 4 ALA A 60 LEU A 71 1 12 HELIX 5 5 PHE A 72 HIS A 76 5 5 HELIX 6 6 GLY A 89 VAL A 99 1 11 HELIX 7 7 ILE A 111 ASP A 126 1 16 HELIX 8 8 PRO A 127 SER A 132 1 6 HELIX 9 9 ASP A 141 GLY A 145 5 5 HELIX 10 10 TYR A 146 ALA A 150 5 5 HELIX 11 11 PRO A 165 GLN A 171 1 7 HELIX 12 12 ASP A 217 TRP A 222 1 6 SHEET 1 A 2 GLN A 50 SER A 51 0 SHEET 2 A 2 THR A 57 ILE A 58 -1 O ILE A 58 N GLN A 50 SHEET 1 B 7 VAL A 135 VAL A 139 0 SHEET 2 B 7 LYS A 104 ASP A 109 1 N GLY A 107 O GLN A 136 SHEET 3 B 7 LYS A 80 VAL A 84 1 N ASP A 83 O ILE A 106 SHEET 4 B 7 TYR A 152 VAL A 157 1 O HIS A 156 N VAL A 84 SHEET 5 B 7 LEU A 172 VAL A 182 1 O LYS A 173 N TYR A 152 SHEET 6 B 7 GLN A 189 LYS A 196 -1 O TYR A 194 N LEU A 178 SHEET 7 B 7 ILE A 202 VAL A 210 -1 O VAL A 210 N GLN A 189 CISPEP 1 ALA A 150 PRO A 151 0 -0.79 SITE 1 AC1 23 ALA A 56 THR A 57 ILE A 58 SER A 59 SITE 2 AC1 23 HIS A 64 GLY A 85 SER A 86 GLY A 87 SITE 3 AC1 23 SER A 88 ASP A 109 HIS A 110 LEU A 114 SITE 4 AC1 23 GLY A 140 ASP A 141 GLY A 142 ARG A 143 SITE 5 AC1 23 GLY A 158 PRO A 214 LEU A 215 THR A 216 SITE 6 AC1 23 GLN A 221 HOH A 301 HOH A 304 CRYST1 48.007 53.698 49.003 90.00 115.60 90.00 P 1 21 1 2 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 0.020830 0.000000 0.009980 0.00000 SCALE2 0.000000 0.018623 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022628 0.00000