PDB Short entry for 1LT7 HEADER TRANSFERASE 20-MAY-02 1LT7 TITLE OXIDIZED HOMO SAPIENS BETAINE-HOMOCYSTEINE S-METHYLTRANSFERASE IN TITLE 2 COMPLEX WITH FOUR SM(III) IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETAINE-HOMOCYSTEINE METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BETAINE-HOMOCYSTEINE S-METHYLTRANSFERASE; COMPND 5 EC: 2.1.1.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTYB4 KEYWDS TRANSFERASE, HOMOCYSTEINE METABOLISM, HOMOCYSTEINEMIA, THIOL ALKYL KEYWDS 2 TRANSFER EXPDTA X-RAY DIFFRACTION AUTHOR J.C.EVANS,D.P.HUDDLER,J.JIRACEK,C.CASTRO,N.S.MILLIAN,T.A.GARROW, AUTHOR 2 M.L.LUDWIG REVDAT 4 27-OCT-21 1LT7 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1LT7 1 VERSN REVDAT 2 24-FEB-09 1LT7 1 VERSN REVDAT 1 11-SEP-02 1LT7 0 JRNL AUTH J.C.EVANS,D.P.HUDDLER,J.JIRACEK,C.CASTRO,N.S.MILLIAN, JRNL AUTH 2 T.A.GARROW,M.L.LUDWIG JRNL TITL BETAINE-HOMOCYSTEINE METHYLTRANSFERASE: ZINC IN A DISTORTED JRNL TITL 2 BARREL. JRNL REF STRUCTURE V. 10 1159 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 12220488 JRNL DOI 10.1016/S0969-2126(02)00796-7 REMARK 2 REMARK 2 RESOLUTION. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 75110 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) : 0.203 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 7403 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7887 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 869 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4818 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 298 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.19000 REMARK 3 B22 (A**2) : -2.63000 REMARK 3 B33 (A**2) : 4.82000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.07000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.460 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.290 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.250 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.170 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.49 REMARK 3 BSOL : 100.3 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 : MY_ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : CITRATE.CNS.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : MY_ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CITRATE.CNS.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LT7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016255. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.845, 1.746 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78638 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 1.880 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : 0.04600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.82 REMARK 200 R MERGE FOR SHELL (I) : 0.21300 REMARK 200 R SYM FOR SHELL (I) : 0.21300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.410 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 200, SODIUM CITRATE, N,N REMARK 280 -DIMETHYLGLYCINE, SAMARIUM (III) ACETATE, PH 5.2, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 54.99500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.04250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.99500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.04250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 109.99000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ALA A 2 REMARK 465 PRO A 3 REMARK 465 VAL A 4 REMARK 465 GLY A 5 REMARK 465 GLY A 6 REMARK 465 LYS A 7 REMARK 465 LYS A 8 REMARK 465 ALA A 9 REMARK 465 LYS A 10 REMARK 465 VAL A 39 REMARK 465 LYS A 40 REMARK 465 ALA A 41 REMARK 465 GLY A 42 REMARK 465 PRO A 43 REMARK 465 TRP A 44 REMARK 465 THR A 45 REMARK 465 PRO A 46 REMARK 465 GLU A 47 REMARK 465 ALA A 48 REMARK 465 ALA A 49 REMARK 465 VAL A 50 REMARK 465 GLU A 51 REMARK 465 PHE A 76 REMARK 465 TYR A 77 REMARK 465 ALA A 78 REMARK 465 SER A 79 REMARK 465 GLU A 80 REMARK 465 ASP A 81 REMARK 465 LYS A 82 REMARK 465 LEU A 83 REMARK 465 GLU A 84 REMARK 465 ASN A 85 REMARK 465 ARG A 86 REMARK 465 GLY A 87 REMARK 465 ASN A 88 REMARK 465 TYR A 89 REMARK 465 VAL A 90 REMARK 465 LEU A 91 REMARK 465 GLU A 92 REMARK 465 LYS A 93 REMARK 465 ILE A 94 REMARK 465 SER A 95 REMARK 465 GLY A 96 REMARK 465 GLN A 97 REMARK 465 GLU A 98 REMARK 465 ALA A 324 REMARK 465 SER A 325 REMARK 465 GLU A 326 REMARK 465 LYS A 327 REMARK 465 HIS A 328 REMARK 465 GLY A 329 REMARK 465 SER A 330 REMARK 465 TRP A 331 REMARK 465 GLY A 332 REMARK 465 SER A 333 REMARK 465 GLY A 334 REMARK 465 LEU A 335 REMARK 465 ASP A 336 REMARK 465 MET A 337 REMARK 465 HIS A 338 REMARK 465 THR A 339 REMARK 465 LYS A 340 REMARK 465 PRO A 341 REMARK 465 TRP A 342 REMARK 465 VAL A 343 REMARK 465 GLY A 372 REMARK 465 TRP A 373 REMARK 465 GLY A 374 REMARK 465 VAL A 375 REMARK 465 THR A 376 REMARK 465 LYS A 377 REMARK 465 GLY A 378 REMARK 465 THR A 379 REMARK 465 ALA A 380 REMARK 465 GLU A 381 REMARK 465 LEU A 382 REMARK 465 MET A 383 REMARK 465 GLN A 384 REMARK 465 GLN A 385 REMARK 465 LYS A 386 REMARK 465 GLU A 387 REMARK 465 ALA A 388 REMARK 465 THR A 389 REMARK 465 THR A 390 REMARK 465 GLU A 391 REMARK 465 GLN A 392 REMARK 465 GLN A 393 REMARK 465 LEU A 394 REMARK 465 LYS A 395 REMARK 465 GLU A 396 REMARK 465 LEU A 397 REMARK 465 PHE A 398 REMARK 465 GLU A 399 REMARK 465 LYS A 400 REMARK 465 GLN A 401 REMARK 465 LYS A 402 REMARK 465 PHE A 403 REMARK 465 LYS A 404 REMARK 465 SER A 405 REMARK 465 GLN A 406 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 PRO B 3 REMARK 465 VAL B 4 REMARK 465 GLY B 5 REMARK 465 GLY B 6 REMARK 465 LYS B 7 REMARK 465 LYS B 8 REMARK 465 ALA B 9 REMARK 465 LYS B 10 REMARK 465 VAL B 39 REMARK 465 LYS B 40 REMARK 465 ALA B 41 REMARK 465 GLY B 42 REMARK 465 PRO B 43 REMARK 465 TRP B 44 REMARK 465 THR B 45 REMARK 465 PRO B 46 REMARK 465 GLU B 47 REMARK 465 ALA B 48 REMARK 465 ALA B 49 REMARK 465 VAL B 50 REMARK 465 GLU B 51 REMARK 465 PHE B 76 REMARK 465 TYR B 77 REMARK 465 ALA B 78 REMARK 465 SER B 79 REMARK 465 GLU B 80 REMARK 465 ASP B 81 REMARK 465 LYS B 82 REMARK 465 LEU B 83 REMARK 465 GLU B 84 REMARK 465 ASN B 85 REMARK 465 ARG B 86 REMARK 465 GLY B 87 REMARK 465 ASN B 88 REMARK 465 TYR B 89 REMARK 465 VAL B 90 REMARK 465 LEU B 91 REMARK 465 GLU B 92 REMARK 465 LYS B 93 REMARK 465 ILE B 94 REMARK 465 SER B 95 REMARK 465 GLY B 96 REMARK 465 GLN B 97 REMARK 465 GLU B 98 REMARK 465 ALA B 324 REMARK 465 SER B 325 REMARK 465 GLU B 326 REMARK 465 LYS B 327 REMARK 465 HIS B 328 REMARK 465 GLY B 329 REMARK 465 SER B 330 REMARK 465 TRP B 331 REMARK 465 GLY B 332 REMARK 465 SER B 333 REMARK 465 GLY B 372 REMARK 465 TRP B 373 REMARK 465 GLY B 374 REMARK 465 VAL B 375 REMARK 465 THR B 376 REMARK 465 LYS B 377 REMARK 465 GLY B 378 REMARK 465 THR B 379 REMARK 465 ALA B 380 REMARK 465 GLU B 381 REMARK 465 LEU B 382 REMARK 465 MET B 383 REMARK 465 GLN B 384 REMARK 465 GLN B 385 REMARK 465 LYS B 386 REMARK 465 GLU B 387 REMARK 465 ALA B 388 REMARK 465 THR B 389 REMARK 465 THR B 390 REMARK 465 GLU B 391 REMARK 465 GLN B 392 REMARK 465 GLN B 393 REMARK 465 LEU B 394 REMARK 465 LYS B 395 REMARK 465 GLU B 396 REMARK 465 LEU B 397 REMARK 465 PHE B 398 REMARK 465 GLU B 399 REMARK 465 LYS B 400 REMARK 465 GLN B 401 REMARK 465 LYS B 402 REMARK 465 PHE B 403 REMARK 465 LYS B 404 REMARK 465 SER B 405 REMARK 465 GLN B 406 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 NH1 ARG A 16 O HOH A 747 2.16 REMARK 500 O ASP A 371 O HOH A 668 2.18 REMARK 500 NH2 ARG A 356 C2 CIT A 601 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 CYS A 217 N - CA - C ANGL. DEV. = 16.2 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 ASP A 26 49.99 -100.97 REMARK 500 ASP A 115 69.30 -100.23 REMARK 500 SER A 133 -163.24 33.71 REMARK 500 GLU A 134 -129.42 34.22 REMARK 500 TYR A 160 80.72 70.26 REMARK 500 CYS A 217 13.13 49.88 REMARK 500 THR A 253 48.67 -140.95 REMARK 500 CYS A 299 -135.74 -127.27 REMARK 500 ASP B 26 62.37 -104.15 REMARK 500 ALA B 131 -46.02 62.51 REMARK 500 GLU B 134 -108.16 141.82 REMARK 500 TYR B 160 88.18 34.67 REMARK 500 LEU B 193 -7.79 -55.13 REMARK 500 CYS B 217 13.05 55.57 REMARK 500 CYS B 299 -135.07 -124.47 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 SM A 501 SM REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CIT A 601 O4 REMARK 620 2 CIT A 601 O6 81.2 REMARK 620 3 CIT A 601 O7 70.1 64.1 REMARK 620 4 HOH A 618 O 141.7 90.4 72.6 REMARK 620 5 HOH A 646 O 135.2 67.6 118.5 72.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SM B 502 SM REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 694 O REMARK 620 2 HOH B 702 O 72.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SM B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SM A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SM B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT B 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LT8 RELATED DB: PDB REMARK 900 1LT8 IS REDUCED HOMO SAPIENS BETAINE-HOMOCYSTEINE S- REMARK 900 METHYLTRANSFERASE IN COMPLEX WITH S-(DELTA-CARBOXYBUTYL)-L- REMARK 900 HOMOCYSTEINE DBREF 1LT7 A 1 406 UNP Q93088 BHMT_HUMAN 1 406 DBREF 1LT7 B 1 406 UNP Q93088 BHMT_HUMAN 1 406 SEQADV 1LT7 ALA A 2 UNP Q93088 PRO 2 ENGINEERED MUTATION SEQADV 1LT7 ALA A 104 UNP Q93088 CYS 104 ENGINEERED MUTATION SEQADV 1LT7 ALA A 131 UNP Q93088 CYS 131 ENGINEERED MUTATION SEQADV 1LT7 ALA A 186 UNP Q93088 CYS 186 ENGINEERED MUTATION SEQADV 1LT7 ALA A 201 UNP Q93088 CYS 201 ENGINEERED MUTATION SEQADV 1LT7 GLN A 239 UNP Q93088 ARG 239 SEE REMARK 999 SEQADV 1LT7 ALA A 256 UNP Q93088 CYS 256 ENGINEERED MUTATION SEQADV 1LT7 ALA B 2 UNP Q93088 PRO 2 ENGINEERED MUTATION SEQADV 1LT7 ALA B 104 UNP Q93088 CYS 104 ENGINEERED MUTATION SEQADV 1LT7 ALA B 131 UNP Q93088 CYS 131 ENGINEERED MUTATION SEQADV 1LT7 ALA B 186 UNP Q93088 CYS 186 ENGINEERED MUTATION SEQADV 1LT7 ALA B 201 UNP Q93088 CYS 201 ENGINEERED MUTATION SEQADV 1LT7 GLN B 239 UNP Q93088 ARG 239 SEE REMARK 999 SEQADV 1LT7 ALA B 256 UNP Q93088 CYS 256 ENGINEERED MUTATION SEQRES 1 A 406 MET ALA PRO VAL GLY GLY LYS LYS ALA LYS LYS GLY ILE SEQRES 2 A 406 LEU GLU ARG LEU ASN ALA GLY GLU ILE VAL ILE GLY ASP SEQRES 3 A 406 GLY GLY PHE VAL PHE ALA LEU GLU LYS ARG GLY TYR VAL SEQRES 4 A 406 LYS ALA GLY PRO TRP THR PRO GLU ALA ALA VAL GLU HIS SEQRES 5 A 406 PRO GLU ALA VAL ARG GLN LEU HIS ARG GLU PHE LEU ARG SEQRES 6 A 406 ALA GLY SER ASN VAL MET GLN THR PHE THR PHE TYR ALA SEQRES 7 A 406 SER GLU ASP LYS LEU GLU ASN ARG GLY ASN TYR VAL LEU SEQRES 8 A 406 GLU LYS ILE SER GLY GLN GLU VAL ASN GLU ALA ALA ALA SEQRES 9 A 406 ASP ILE ALA ARG GLN VAL ALA ASP GLU GLY ASP ALA LEU SEQRES 10 A 406 VAL ALA GLY GLY VAL SER GLN THR PRO SER TYR LEU SER SEQRES 11 A 406 ALA LYS SER GLU THR GLU VAL LYS LYS VAL PHE LEU GLN SEQRES 12 A 406 GLN LEU GLU VAL PHE MET LYS LYS ASN VAL ASP PHE LEU SEQRES 13 A 406 ILE ALA GLU TYR PHE GLU HIS VAL GLU GLU ALA VAL TRP SEQRES 14 A 406 ALA VAL GLU THR LEU ILE ALA SER GLY LYS PRO VAL ALA SEQRES 15 A 406 ALA THR MET ALA ILE GLY PRO GLU GLY ASP LEU HIS GLY SEQRES 16 A 406 VAL PRO PRO GLY GLU ALA ALA VAL ARG LEU VAL LYS ALA SEQRES 17 A 406 GLY ALA SER ILE ILE GLY VAL ASN CYS HIS PHE ASP PRO SEQRES 18 A 406 THR ILE SER LEU LYS THR VAL LYS LEU MET LYS GLU GLY SEQRES 19 A 406 LEU GLU ALA ALA GLN LEU LYS ALA HIS LEU MET SER GLN SEQRES 20 A 406 PRO LEU ALA TYR HIS THR PRO ASP ALA ASN LYS GLN GLY SEQRES 21 A 406 PHE ILE ASP LEU PRO GLU PHE PRO PHE GLY LEU GLU PRO SEQRES 22 A 406 ARG VAL ALA THR ARG TRP ASP ILE GLN LYS TYR ALA ARG SEQRES 23 A 406 GLU ALA TYR ASN LEU GLY VAL ARG TYR ILE GLY GLY CYS SEQRES 24 A 406 CYS GLY PHE GLU PRO TYR HIS ILE ARG ALA ILE ALA GLU SEQRES 25 A 406 GLU LEU ALA PRO GLU ARG GLY PHE LEU PRO PRO ALA SER SEQRES 26 A 406 GLU LYS HIS GLY SER TRP GLY SER GLY LEU ASP MET HIS SEQRES 27 A 406 THR LYS PRO TRP VAL ARG ALA ARG ALA ARG LYS GLU TYR SEQRES 28 A 406 TRP GLU ASN LEU ARG ILE ALA SER GLY ARG PRO TYR ASN SEQRES 29 A 406 PRO SER MET SER LYS PRO ASP GLY TRP GLY VAL THR LYS SEQRES 30 A 406 GLY THR ALA GLU LEU MET GLN GLN LYS GLU ALA THR THR SEQRES 31 A 406 GLU GLN GLN LEU LYS GLU LEU PHE GLU LYS GLN LYS PHE SEQRES 32 A 406 LYS SER GLN SEQRES 1 B 406 MET ALA PRO VAL GLY GLY LYS LYS ALA LYS LYS GLY ILE SEQRES 2 B 406 LEU GLU ARG LEU ASN ALA GLY GLU ILE VAL ILE GLY ASP SEQRES 3 B 406 GLY GLY PHE VAL PHE ALA LEU GLU LYS ARG GLY TYR VAL SEQRES 4 B 406 LYS ALA GLY PRO TRP THR PRO GLU ALA ALA VAL GLU HIS SEQRES 5 B 406 PRO GLU ALA VAL ARG GLN LEU HIS ARG GLU PHE LEU ARG SEQRES 6 B 406 ALA GLY SER ASN VAL MET GLN THR PHE THR PHE TYR ALA SEQRES 7 B 406 SER GLU ASP LYS LEU GLU ASN ARG GLY ASN TYR VAL LEU SEQRES 8 B 406 GLU LYS ILE SER GLY GLN GLU VAL ASN GLU ALA ALA ALA SEQRES 9 B 406 ASP ILE ALA ARG GLN VAL ALA ASP GLU GLY ASP ALA LEU SEQRES 10 B 406 VAL ALA GLY GLY VAL SER GLN THR PRO SER TYR LEU SER SEQRES 11 B 406 ALA LYS SER GLU THR GLU VAL LYS LYS VAL PHE LEU GLN SEQRES 12 B 406 GLN LEU GLU VAL PHE MET LYS LYS ASN VAL ASP PHE LEU SEQRES 13 B 406 ILE ALA GLU TYR PHE GLU HIS VAL GLU GLU ALA VAL TRP SEQRES 14 B 406 ALA VAL GLU THR LEU ILE ALA SER GLY LYS PRO VAL ALA SEQRES 15 B 406 ALA THR MET ALA ILE GLY PRO GLU GLY ASP LEU HIS GLY SEQRES 16 B 406 VAL PRO PRO GLY GLU ALA ALA VAL ARG LEU VAL LYS ALA SEQRES 17 B 406 GLY ALA SER ILE ILE GLY VAL ASN CYS HIS PHE ASP PRO SEQRES 18 B 406 THR ILE SER LEU LYS THR VAL LYS LEU MET LYS GLU GLY SEQRES 19 B 406 LEU GLU ALA ALA GLN LEU LYS ALA HIS LEU MET SER GLN SEQRES 20 B 406 PRO LEU ALA TYR HIS THR PRO ASP ALA ASN LYS GLN GLY SEQRES 21 B 406 PHE ILE ASP LEU PRO GLU PHE PRO PHE GLY LEU GLU PRO SEQRES 22 B 406 ARG VAL ALA THR ARG TRP ASP ILE GLN LYS TYR ALA ARG SEQRES 23 B 406 GLU ALA TYR ASN LEU GLY VAL ARG TYR ILE GLY GLY CYS SEQRES 24 B 406 CYS GLY PHE GLU PRO TYR HIS ILE ARG ALA ILE ALA GLU SEQRES 25 B 406 GLU LEU ALA PRO GLU ARG GLY PHE LEU PRO PRO ALA SER SEQRES 26 B 406 GLU LYS HIS GLY SER TRP GLY SER GLY LEU ASP MET HIS SEQRES 27 B 406 THR LYS PRO TRP VAL ARG ALA ARG ALA ARG LYS GLU TYR SEQRES 28 B 406 TRP GLU ASN LEU ARG ILE ALA SER GLY ARG PRO TYR ASN SEQRES 29 B 406 PRO SER MET SER LYS PRO ASP GLY TRP GLY VAL THR LYS SEQRES 30 B 406 GLY THR ALA GLU LEU MET GLN GLN LYS GLU ALA THR THR SEQRES 31 B 406 GLU GLN GLN LEU LYS GLU LEU PHE GLU LYS GLN LYS PHE SEQRES 32 B 406 LYS SER GLN HET SM A 501 1 HET SM A 503 1 HET CIT A 601 13 HET SM B 502 1 HET SM B 504 1 HET CIT B 602 13 HETNAM SM SAMARIUM (III) ION HETNAM CIT CITRIC ACID FORMUL 3 SM 4(SM 3+) FORMUL 5 CIT 2(C6 H8 O7) FORMUL 9 HOH *298(H2 O) HELIX 1 1 GLY A 12 ALA A 19 1 8 HELIX 2 2 GLY A 28 GLY A 37 1 10 HELIX 3 3 HIS A 52 GLY A 67 1 16 HELIX 4 4 VAL A 99 GLU A 113 1 15 HELIX 5 5 THR A 125 SER A 130 1 6 HELIX 6 6 SER A 133 LYS A 151 1 19 HELIX 7 7 HIS A 163 ILE A 175 1 13 HELIX 8 8 ALA A 176 GLY A 178 5 3 HELIX 9 9 PRO A 197 ALA A 208 1 12 HELIX 10 10 ASP A 220 ALA A 238 1 19 HELIX 11 11 GLY A 260 LEU A 264 5 5 HELIX 12 12 LEU A 271 VAL A 275 5 5 HELIX 13 13 THR A 277 GLY A 292 1 16 HELIX 14 14 GLU A 303 LEU A 314 1 12 HELIX 15 15 LEU A 314 GLY A 319 1 6 HELIX 16 16 ARG A 348 LEU A 355 1 8 HELIX 17 17 GLY B 12 ALA B 19 1 8 HELIX 18 18 GLY B 28 ARG B 36 1 9 HELIX 19 19 HIS B 52 GLY B 67 1 16 HELIX 20 20 VAL B 99 ASP B 112 1 14 HELIX 21 21 THR B 125 LEU B 129 5 5 HELIX 22 22 GLU B 134 LYS B 151 1 18 HELIX 23 23 HIS B 163 ALA B 176 1 14 HELIX 24 24 PRO B 197 ALA B 208 1 12 HELIX 25 25 ASP B 220 ALA B 238 1 19 HELIX 26 26 GLY B 260 LEU B 264 5 5 HELIX 27 27 LEU B 271 VAL B 275 5 5 HELIX 28 28 THR B 277 GLY B 292 1 16 HELIX 29 29 GLU B 303 LEU B 314 1 12 HELIX 30 30 LEU B 314 GLY B 319 1 6 HELIX 31 31 GLY B 334 HIS B 338 5 5 HELIX 32 32 LYS B 340 ALA B 345 1 6 HELIX 33 33 ARG B 348 LEU B 355 1 8 SHEET 1 A 8 VAL A 23 ILE A 24 0 SHEET 2 A 8 TYR A 295 ILE A 296 1 O ILE A 296 N VAL A 23 SHEET 3 A 8 HIS A 243 GLN A 247 1 N SER A 246 O TYR A 295 SHEET 4 A 8 ILE A 212 ASN A 216 1 N VAL A 215 O GLN A 247 SHEET 5 A 8 VAL A 181 MET A 185 1 N ALA A 183 O ILE A 212 SHEET 6 A 8 PHE A 155 ALA A 158 1 N ALA A 158 O ALA A 182 SHEET 7 A 8 LEU A 117 VAL A 122 1 N VAL A 122 O ILE A 157 SHEET 8 A 8 VAL A 70 PHE A 74 1 N THR A 73 O GLY A 121 SHEET 1 B 8 VAL B 23 ILE B 24 0 SHEET 2 B 8 TYR B 295 ILE B 296 1 O ILE B 296 N VAL B 23 SHEET 3 B 8 HIS B 243 GLN B 247 1 N SER B 246 O TYR B 295 SHEET 4 B 8 ILE B 212 ASN B 216 1 N ILE B 213 O HIS B 243 SHEET 5 B 8 VAL B 181 MET B 185 1 N ALA B 183 O ILE B 212 SHEET 6 B 8 PHE B 155 ALA B 158 1 N ALA B 158 O ALA B 182 SHEET 7 B 8 LEU B 117 VAL B 122 1 N GLY B 120 O ILE B 157 SHEET 8 B 8 VAL B 70 PHE B 74 1 N MET B 71 O LEU B 117 SSBOND 1 CYS A 217 CYS A 299 1555 1555 2.29 SSBOND 2 CYS B 217 CYS B 299 1555 1555 2.36 LINK SM SM A 501 O4 CIT A 601 1555 1555 2.51 LINK SM SM A 501 O6 CIT A 601 1555 1555 2.31 LINK SM SM A 501 O7 CIT A 601 1555 1555 2.62 LINK SM SM A 501 O HOH A 618 1555 1555 2.77 LINK SM SM A 501 O HOH A 646 1555 1555 2.63 LINK SM SM A 503 O HOH A 749 1555 1555 2.62 LINK O HOH A 694 SM SM B 502 1555 1555 2.73 LINK SM SM B 502 O HOH B 702 1555 1555 2.14 CISPEP 1 PHE A 267 PRO A 268 0 -0.41 CISPEP 2 PHE B 267 PRO B 268 0 -0.05 SITE 1 AC1 3 CIT A 601 HOH A 618 HOH A 646 SITE 1 AC2 2 HOH A 694 HOH B 702 SITE 1 AC3 1 HOH A 749 SITE 1 AC4 1 CIT B 602 SITE 1 AC5 9 HIS A 252 LYS A 283 ARG A 356 SM A 501 SITE 2 AC5 9 HOH A 615 HOH A 641 HOH A 646 TYR B 363 SITE 3 AC5 9 LYS B 369 SITE 1 AC6 9 GLY A 360 PRO A 362 TYR A 363 ASP B 220 SITE 2 AC6 9 HIS B 252 ARG B 356 SM B 504 HOH B 606 SITE 3 AC6 9 HOH B 639 CRYST1 109.990 90.085 89.085 90.00 122.10 90.00 C 1 2 1 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 0.009092 0.000000 0.005703 0.00000 SCALE2 0.000000 0.011101 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013251 0.00000