PDB Short entry for 1JG1 HEADER TRANSFERASE 22-JUN-01 1JG1 TITLE CRYSTAL STRUCTURE OF L-ISOASPARTYL (D-ASPARTYL) O- TITLE 2 METHYLTRANSFERASE WITH S-ADENOSYL-L-HOMOCYSTEINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN-BETA-ASPARTATE METHYLTRANSFERASE; PIMT; COMPND 5 PROTEIN L-ISOASPARTYL METHYLTRANSFERASE; L-ISOASPARTYL COMPND 6 PROTEIN CARBOXYL METHYLTRANSFERASE; COMPND 7 EC: 2.1.1.77; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ROSSMANN METHYLTRANSFERASE, PROTEIN REPAIR ISOMERIZATION EXPDTA X-RAY DIFFRACTION AUTHOR S.C.GRIFFITH,M.R.SAWAYA,D.BOUTZ,N.THAPAR,J.KATZ,S.CLARKE, AUTHOR 2 T.O.YEATES REVDAT 3 24-FEB-09 1JG1 1 VERSN REVDAT 2 01-APR-03 1JG1 1 JRNL REVDAT 1 16-NOV-01 1JG1 0 JRNL AUTH S.C.GRIFFITH,M.R.SAWAYA,D.R.BOUTZ,N.THAPAR, JRNL AUTH 2 J.E.KATZ,S.CLARKE,T.O.YEATES JRNL TITL CRYSTAL STRUCTURE OF A PROTEIN REPAIR JRNL TITL 2 METHYLTRANSFERASE FROM PYROCOCCUS FURIOSUS WITH JRNL TITL 3 ITS L-ISOASPARTYL PEPTIDE SUBSTRATE. JRNL REF J.MOL.BIOL. V. 313 1103 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11700066 JRNL DOI 10.1006/JMBI.2001.5095 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 500.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.150 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.147 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3127 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 58666 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1675 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 256 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 2.500 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JG1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-01. REMARK 100 THE RCSB ID CODE IS RCSB013726. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-00 REMARK 200 TEMPERATURE (KELVIN) : 118 REMARK 200 PH : 4.5 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) : 1.000 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 : 61904 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 500.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : 0.04500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.38500 REMARK 200 R SYM FOR SHELL (I) : 0.38500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 2000, 15% GLYCEROL, 0.2 M REMARK 280 AMMONIUM ACETATE PH 4.5, VAPOR DIFFUSION, HANGING DROP AT 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 19.58000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.31800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.26100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.31800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.58000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.26100 REMARK 290 SMTRY3 4 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 MET A 1 REMARK 465 HIS A 2 REMARK 465 LEU A 3 REMARK 465 TYR A 4 REMARK 465 SER A 5 REMARK 465 SER A 6 REMARK 465 ASP A 7 REMARK 465 PHE A 8 REMARK 465 PRO A 9 REMARK 465 LEU A 10 REMARK 465 MET A 11 REMARK 465 MET A 12 REMARK 465 ASP A 13 REMARK 465 GLU A 229 REMARK 465 HIS A 230 REMARK 465 HIS A 231 REMARK 465 HIS A 232 REMARK 465 HIS A 233 REMARK 465 HIS A 234 REMARK 465 HIS A 235 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 GLU A 14 CG CD OE1 OE2 REMARK 470 LYS A 15 CG CD CE NZ REMARK 470 GLU A 16 OE1 OE2 REMARK 470 ARG A 23 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 35 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 132 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ASN A 212 OD1 - CG - ND2 ANGL. DEV. = -14.1 DEGREES 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 PHE A 153 81.62 -153.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1229 DISTANCE = 5.16 ANGSTROMS 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 500 DBREF 1JG1 A 11 229 UNP Q8TZR3 PIMT_PYRFU 1 219 SEQRES 1 A 235 MET HIS LEU TYR SER SER ASP PHE PRO LEU MET MET ASP SEQRES 2 A 235 GLU LYS GLU LEU TYR GLU LYS TRP MET ARG THR VAL GLU SEQRES 3 A 235 MET LEU LYS ALA GLU GLY ILE ILE ARG SER LYS GLU VAL SEQRES 4 A 235 GLU ARG ALA PHE LEU LYS TYR PRO ARG TYR LEU SER VAL SEQRES 5 A 235 GLU ASP LYS TYR LYS LYS TYR ALA HIS ILE ASP GLU PRO SEQRES 6 A 235 LEU PRO ILE PRO ALA GLY GLN THR VAL SER ALA PRO HIS SEQRES 7 A 235 MET VAL ALA ILE MET LEU GLU ILE ALA ASN LEU LYS PRO SEQRES 8 A 235 GLY MET ASN ILE LEU GLU VAL GLY THR GLY SER GLY TRP SEQRES 9 A 235 ASN ALA ALA LEU ILE SER GLU ILE VAL LYS THR ASP VAL SEQRES 10 A 235 TYR THR ILE GLU ARG ILE PRO GLU LEU VAL GLU PHE ALA SEQRES 11 A 235 LYS ARG ASN LEU GLU ARG ALA GLY VAL LYS ASN VAL HIS SEQRES 12 A 235 VAL ILE LEU GLY ASP GLY SER LYS GLY PHE PRO PRO LYS SEQRES 13 A 235 ALA PRO TYR ASP VAL ILE ILE VAL THR ALA GLY ALA PRO SEQRES 14 A 235 LYS ILE PRO GLU PRO LEU ILE GLU GLN LEU LYS ILE GLY SEQRES 15 A 235 GLY LYS LEU ILE ILE PRO VAL GLY SER TYR HIS LEU TRP SEQRES 16 A 235 GLN GLU LEU LEU GLU VAL ARG LYS THR LYS ASP GLY ILE SEQRES 17 A 235 LYS ILE LYS ASN HIS GLY GLY VAL ALA PHE VAL PRO LEU SEQRES 18 A 235 ILE GLY GLU TYR GLY TRP LYS GLU HIS HIS HIS HIS HIS SEQRES 19 A 235 HIS HET SAH A 500 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 HOH *256(H2 O) HELIX 1 1 GLU A 14 GLU A 31 1 18 HELIX 2 2 SER A 36 TYR A 46 1 11 HELIX 3 3 PRO A 47 VAL A 52 5 6 HELIX 4 4 GLU A 53 ALA A 60 5 8 HELIX 5 5 ALA A 76 ASN A 88 1 13 HELIX 6 6 GLY A 103 LYS A 114 1 12 HELIX 7 7 ILE A 123 ALA A 137 1 15 HELIX 8 8 ASP A 148 GLY A 152 5 5 HELIX 9 9 PHE A 153 ALA A 157 5 5 HELIX 10 10 PRO A 172 GLN A 178 1 7 SHEET 1 A 2 LEU A 66 PRO A 67 0 SHEET 2 A 2 THR A 73 VAL A 74 -1 N VAL A 74 O LEU A 66 SHEET 1 B 7 VAL A 142 LEU A 146 0 SHEET 2 B 7 VAL A 117 GLU A 121 1 O VAL A 117 N HIS A 143 SHEET 3 B 7 ILE A 95 VAL A 98 1 O ILE A 95 N TYR A 118 SHEET 4 B 7 TYR A 159 VAL A 164 1 O VAL A 161 N LEU A 96 SHEET 5 B 7 LEU A 179 VAL A 189 1 N LYS A 180 O TYR A 159 SHEET 6 B 7 GLN A 196 THR A 204 -1 O GLU A 197 N VAL A 189 SHEET 7 B 7 GLY A 207 VAL A 216 -1 N GLY A 207 O THR A 204 CISPEP 1 ALA A 157 PRO A 158 0 -3.25 SITE 1 AC1 24 GLN A 72 THR A 73 GLU A 97 GLY A 99 SITE 2 AC1 24 THR A 100 GLY A 101 SER A 102 TRP A 104 SITE 3 AC1 24 ASN A 105 ILE A 120 GLU A 121 ARG A 122 SITE 4 AC1 24 ILE A 123 LEU A 126 GLY A 147 ASP A 148 SITE 5 AC1 24 GLY A 149 THR A 165 PRO A 220 LEU A 221 SITE 6 AC1 24 ILE A 222 HOH A1014 HOH A1028 HOH A1067 CRYST1 39.160 52.522 96.636 90.00 90.00 90.00 P 21 21 21 4 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 0.025536 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010348 0.00000