PDB Short entry for 1I1N HEADER TRANSFERASE 02-FEB-01 1I1N TITLE HUMAN PROTEIN L-ISOASPARTATE O-METHYLTRANSFERASE WITH S-ADENOSYL TITLE 2 HOMOCYSTEINE 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 ORGAN: FETAL BRAIN; SOURCE 6 GENE: PIMT_HUMAN; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21C KEYWDS METHYLTRANSFERASE, S-ADENOSYL HOMOCYSTEINE, PROTEIN REPAIR, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.D.SMITH,D.CHATTOPADHYAY,M.CARSON,A.M.FRIEDMAN,M.M.SKINNER REVDAT 3 09-AUG-23 1I1N 1 REMARK REVDAT 2 24-FEB-09 1I1N 1 VERSN REVDAT 1 13-MAR-02 1I1N 0 JRNL AUTH C.D.SMITH,M.CARSON,A.M.FRIEDMAN,M.M.SKINNER,L.DELUCAS, JRNL AUTH 2 L.CHANTALAT,L.WEISE,T.SHIRASAWA,D.CHATTOPADHYAY JRNL TITL CRYSTAL STRUCTURE OF HUMAN JRNL TITL 2 L-ISOASPARTYL-O-METHYL-TRANSFERASE WITH S-ADENOSYL JRNL TITL 3 HOMOCYSTEINE AT 1.6-A RESOLUTION AND MODELING OF AN JRNL TITL 4 ISOASPARTYL-CONTAINING PEPTIDE AT THE ACTIVE SITE. JRNL REF PROTEIN SCI. V. 11 625 2002 JRNL REFN ISSN 0961-8368 JRNL PMID 11847284 JRNL DOI 10.1110/PS.37802 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 944740.240 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.6 REMARK 3 NUMBER OF REFLECTIONS : 30470 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) : 0.183 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1513 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 40.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2310 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 118 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1705 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 279 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.54000 REMARK 3 B22 (A**2) : -3.24000 REMARK 3 B33 (A**2) : -0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.73000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.10 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.830 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) : 1.030 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.580 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.880 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.740 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 56.88 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 : RNA-BONDS-ETC.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : RNA-DIHE.PARAM REMARK 3 PARAMETER FILE 5 : SAH.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : SAH.TOPOL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED. REMARK 3 THE SAH TOPOLOGY/PARAMETER FILES FOR CNS WERE CREATED REMARK 3 BY COMBINING THE STANDARD MET AND ADE ENTRIES. REMARK 3 THE DEFAULT CNS DNA-RNA_REP.PARAM FOR RNA/DNA WAS MODIFIED REMARK 3 IN THE LATER STAGES OF REFINEMENT. REMARK 3 THE RIBOSE RING DIHEDRAL FORCE CONSTANTS WERE SET TO 0.0 REMARK 3 TO ALLOW THE RIBOSE RING PUCKER TO FIT THE ELECTRON DENSITY. REMARK 4 REMARK 4 1I1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000012791. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-97 REMARK 200 TEMPERATURE (KELVIN) : 93.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NICKEL FILTER REMARK 200 OPTICS : MSC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31332 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.8 REMARK 200 DATA REDUNDANCY : 3.470 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 34.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.16 REMARK 200 R MERGE FOR SHELL (I) : 0.20500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: CNS REMARK 200 STARTING MODEL: 1DL5.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, SODIUM CACODYLATE, MAGNESIUM REMARK 280 ACETATE, DTT, BIS-TRIS ACETATE, S-ADENOSYL HOMOCYSTEINE, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 26.95850 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 LYS A 226 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 LEU A 75 49.95 -93.03 REMARK 500 TYR A 146 82.66 -151.82 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 1300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DL5 RELATED DB: PDB REMARK 900 PROTEIN L-ISOASPARTATE O-METHYLTRANSFERASE FROM THERMOTOGA MARITIMA DBREF 1I1N A 1 226 UNP P22061 PIMT_HUMAN 1 226 SEQADV 1I1N VAL A 119 UNP P22061 ILE 119 SEE REMARK 999 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 A1300 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 HOH *279(H2 O) HELIX 1 1 SER A 8 ASN A 19 1 12 HELIX 2 2 THR A 24 ALA A 33 1 10 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 GLY A 89 GLY A 100 1 12 HELIX 6 6 ILE A 111 ASP A 126 1 16 HELIX 7 7 PRO A 127 SER A 132 1 6 HELIX 8 8 ASP A 141 GLY A 145 5 5 HELIX 9 9 TYR A 146 ALA A 150 5 5 HELIX 10 10 PRO A 165 GLN A 171 1 7 HELIX 11 11 ASP A 217 TRP A 222 1 6 SHEET 1 A 2 GLN A 50 GLY A 53 0 SHEET 2 A 2 ALA A 56 ILE A 58 -1 N ALA A 56 O GLY A 53 SHEET 1 B 7 VAL A 135 VAL A 139 0 SHEET 2 B 7 LYS A 104 ASP A 109 1 O VAL A 105 N GLN A 136 SHEET 3 B 7 LYS A 80 VAL A 84 1 N ALA A 81 O LYS A 104 SHEET 4 B 7 TYR A 152 VAL A 157 1 N ASP A 153 O LYS A 80 SHEET 5 B 7 LEU A 172 VAL A 182 1 N LYS A 173 O TYR A 152 SHEET 6 B 7 GLN A 189 LYS A 196 -1 N MET A 190 O VAL A 182 SHEET 7 B 7 ILE A 202 VAL A 210 -1 O LYS A 203 N ASP A 195 CISPEP 1 ALA A 150 PRO A 151 0 0.11 SITE 1 AC1 26 ALA A 56 THR A 57 ILE A 58 SER A 59 SITE 2 AC1 26 HIS A 64 GLY A 85 SER A 86 GLY A 87 SITE 3 AC1 26 SER A 88 ASP A 109 HIS A 110 ILE A 111 SITE 4 AC1 26 LEU A 114 GLY A 140 ASP A 141 GLY A 142 SITE 5 AC1 26 ARG A 143 GLY A 158 VAL A 213 PRO A 214 SITE 6 AC1 26 LEU A 215 THR A 216 GLN A 221 HOH A 307 SITE 7 AC1 26 HOH A 308 HOH A 316 CRYST1 48.105 53.917 48.814 90.00 116.15 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 0.020788 0.000000 0.010207 0.00000 SCALE2 0.000000 0.018547 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022822 0.00000