HEADER LYASE 09-NOV-09 3A9Z TITLE CRYSTAL STRUCTURE OF RAS SELENOCYSTEINE LYASE IN COMPLEX WITH TITLE 2 SELENOPROPIONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SELENOCYSTEINE LYASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.4.1.16; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: SCLY; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A(+) KEYWDS SELENOCYSTEINE, PLP, LYASE, PYRIDOXAL PHOSPHATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.OMI,K.HIROTSU REVDAT 2 30-OCT-13 3A9Z 1 JRNL VERSN REVDAT 1 16-MAR-10 3A9Z 0 JRNL AUTH R.OMI,S.KUROKAWA,H.MIHARA,H.HAYASHI,M.GOTO,I.MIYAHARA, JRNL AUTH 2 T.KURIHARA,K.HIROTSU,N.ESAKI JRNL TITL REACTION MECHANISM AND MOLECULAR BASIS FOR SELENIUM/SULFUR JRNL TITL 2 DISCRIMINATION OF SELENOCYSTEINE LYASE. JRNL REF J.BIOL.CHEM. V. 285 12133 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20164179 JRNL DOI 10.1074/JBC.M109.084475 REMARK 2 REMARK 2 RESOLUTION. 1.55 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 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) (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 159477 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) : 0.187 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 15884 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.65 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 2516 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.005 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6139 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 527 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.11 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) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.029 REMARK 3 BOND ANGLES (DEGREES) : 2.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.76 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3A9Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-NOV-09. REMARK 100 THE RCSB ID CODE IS RCSB028997. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 159678 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M AMMONIUM DIHYDROGEN PHOSPHATE, PH REMARK 280 4.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 27.70800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 98.67800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.60300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 98.67800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.70800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.60300 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 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 ASP A 2 REMARK 465 VAL A 3 REMARK 465 ALA A 4 REMARK 465 ARG A 5 REMARK 465 ASN A 6 REMARK 465 GLY A 7 REMARK 465 ALA A 8 REMARK 465 ARG A 9 REMARK 465 GLY A 10 REMARK 465 SER A 11 REMARK 465 VAL A 12 REMARK 465 GLU A 13 REMARK 465 SER A 14 REMARK 465 PRO A 15 REMARK 465 PRO A 16 REMARK 465 ASN A 17 REMARK 465 GLY A 110 REMARK 465 ARG A 111 REMARK 465 THR A 112 REMARK 465 VAL A 113 REMARK 465 ASP A 114 REMARK 465 GLN A 115 REMARK 465 ILE A 116 REMARK 465 SER A 117 REMARK 465 PRO A 118 REMARK 465 GLU A 119 REMARK 465 GLU A 120 REMARK 465 GLY A 121 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 VAL B 3 REMARK 465 ALA B 4 REMARK 465 ARG B 5 REMARK 465 ASN B 6 REMARK 465 GLY B 7 REMARK 465 ALA B 8 REMARK 465 ARG B 9 REMARK 465 GLY B 10 REMARK 465 SER B 11 REMARK 465 VAL B 12 REMARK 465 GLU B 13 REMARK 465 SER B 14 REMARK 465 PRO B 15 REMARK 465 PRO B 16 REMARK 465 ASN B 17 REMARK 465 GLN B 106 REMARK 465 THR B 107 REMARK 465 LEU B 108 REMARK 465 GLN B 109 REMARK 465 GLY B 110 REMARK 465 ARG B 111 REMARK 465 THR B 112 REMARK 465 VAL B 113 REMARK 465 ASP B 114 REMARK 465 GLN B 115 REMARK 465 ILE B 116 REMARK 465 SER B 117 REMARK 465 PRO B 118 REMARK 465 GLU B 119 REMARK 465 GLU B 120 REMARK 465 GLY B 121 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 ARG A 18 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 109 CG CD OE1 NE2 REMARK 470 GLN A 427 CG CD OE1 NE2 REMARK 470 VAL A 432 CG1 CG2 REMARK 470 ARG B 18 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 36 CG CD OE1 NE2 REMARK 470 GLU B 164 CG CD OE1 OE2 REMARK 470 LYS B 263 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 33 CG GLU A 33 CD 0.111 REMARK 500 GLU A 33 CD GLU A 33 OE1 0.068 REMARK 500 CYS A 177 CB CYS A 177 SG -0.221 REMARK 500 GLU A 302 CD GLU A 302 OE1 0.077 REMARK 500 GLU A 302 CD GLU A 302 OE2 0.084 REMARK 500 GLU A 305 CD GLU A 305 OE1 0.075 REMARK 500 GLU B 44 CD GLU B 44 OE1 0.086 REMARK 500 GLU B 44 CD GLU B 44 OE2 0.078 REMARK 500 GLU B 166 CD GLU B 166 OE2 0.073 REMARK 500 CYS B 177 CB CYS B 177 SG -0.124 REMARK 500 GLN B 206 CG GLN B 206 CD 0.146 REMARK 500 LYS B 263 CA LYS B 263 CB -0.151 REMARK 500 GLU B 305 CD GLU B 305 OE2 0.087 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 GLU A 44 OE1 - CD - OE2 ANGL. DEV. = -8.4 DEGREES REMARK 500 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 123 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 199 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 199 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 215 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 230 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 252 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 298 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 321 CG - CD - NE ANGL. DEV. = -13.2 DEGREES REMARK 500 ARG A 329 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 335 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 335 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG A 356 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 356 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 GLY A 372 C - N - CA ANGL. DEV. = -13.7 DEGREES REMARK 500 ARG A 402 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP B 61 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 67 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 67 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 123 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 GLU B 196 OE1 - CD - OE2 ANGL. DEV. = -9.9 DEGREES REMARK 500 ARG B 199 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 199 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 230 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 252 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 MET B 270 CG - SD - CE ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG B 315 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 321 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP B 378 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP B 381 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 395 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP B 395 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG B 398 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG B 398 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 LYS B 422 CD - CE - NZ ANGL. DEV. = 15.6 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 ARG A 252 42.17 -77.28 REMARK 500 LYS A 263 -41.09 -130.00 REMARK 500 ARG A 281 80.56 -155.28 REMARK 500 ARG A 335 59.18 -117.94 REMARK 500 HIS A 379 51.08 -143.74 REMARK 500 ARG B 252 39.16 -76.22 REMARK 500 ARG B 335 63.97 -103.24 REMARK 500 LEU B 355 44.22 -108.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 268 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ARG B 18 23.9 L L OUTSIDE RANGE REMARK 500 VAL B 54 23.9 L L OUTSIDE RANGE 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 PLP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SLP A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SLP B 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A9X RELATED DB: PDB REMARK 900 UNLIGANDED FORM REMARK 900 RELATED ID: 3A9Y RELATED DB: PDB DBREF 3A9Z A 1 432 UNP Q68FT9 SCLY_RAT 1 432 DBREF 3A9Z B 1 432 UNP Q68FT9 SCLY_RAT 1 432 SEQRES 1 A 432 MET ASP VAL ALA ARG ASN GLY ALA ARG GLY SER VAL GLU SEQRES 2 A 432 SER PRO PRO ASN ARG LYS VAL TYR MET ASP TYR ASN ALA SEQRES 3 A 432 THR THR PRO LEU GLU PRO GLU VAL ILE GLN ALA VAL THR SEQRES 4 A 432 GLU ALA MET LYS GLU ALA TRP GLY ASN PRO SER SER SER SEQRES 5 A 432 TYR VAL ALA GLY ARG LYS ALA LYS ASP ILE ILE ASN THR SEQRES 6 A 432 ALA ARG ALA SER LEU ALA LYS MET ILE GLY GLY LYS PRO SEQRES 7 A 432 GLN ASP ILE ILE PHE THR SER GLY GLY THR GLU SER ASN SEQRES 8 A 432 ASN LEU VAL ILE HIS SER THR VAL ARG CYS PHE HIS GLU SEQRES 9 A 432 GLN GLN THR LEU GLN GLY ARG THR VAL ASP GLN ILE SER SEQRES 10 A 432 PRO GLU GLU GLY THR ARG PRO HIS PHE ILE THR CYS THR SEQRES 11 A 432 VAL GLU HIS ASP SER ILE ARG LEU PRO LEU GLU HIS LEU SEQRES 12 A 432 VAL GLU ASP GLN VAL ALA GLU VAL THR PHE VAL PRO VAL SEQRES 13 A 432 SER LYS VAL ASN GLY GLN VAL GLU VAL GLU ASP ILE LEU SEQRES 14 A 432 ALA ALA VAL ARG PRO THR THR CYS LEU VAL THR ILE MET SEQRES 15 A 432 LEU ALA ASN ASN GLU THR GLY VAL ILE MET PRO ILE SER SEQRES 16 A 432 GLU ILE SER ARG ARG ILE LYS ALA LEU ASN GLN ILE ARG SEQRES 17 A 432 ALA ALA SER GLY LEU PRO ARG VAL LEU VAL HIS THR ASP SEQRES 18 A 432 ALA ALA GLN ALA LEU GLY LYS ARG ARG VAL ASP VAL GLU SEQRES 19 A 432 ASP LEU GLY VAL ASP PHE LEU THR ILE VAL GLY HIS LYS SEQRES 20 A 432 PHE TYR GLY PRO ARG ILE GLY ALA LEU TYR VAL ARG GLY SEQRES 21 A 432 VAL GLY LYS LEU THR PRO LEU TYR PRO MET LEU PHE GLY SEQRES 22 A 432 GLY GLY GLN GLU ARG ASN PHE ARG PRO GLY THR GLU ASN SEQRES 23 A 432 THR PRO MET ILE ALA GLY LEU GLY LYS ALA ALA ASP LEU SEQRES 24 A 432 VAL SER GLU ASN CYS GLU THR TYR GLU ALA HIS MET ARG SEQRES 25 A 432 ASP ILE ARG ASP TYR LEU GLU GLU ARG LEU GLU ALA GLU SEQRES 26 A 432 PHE GLY LYS ARG ILE HIS LEU ASN SER ARG PHE PRO GLY SEQRES 27 A 432 VAL GLU ARG LEU PRO ASN THR CYS ASN PHE SER ILE GLN SEQRES 28 A 432 GLY SER GLN LEU ARG GLY TYR MET VAL LEU ALA GLN CYS SEQRES 29 A 432 GLN THR LEU LEU ALA SER VAL GLY ALA SER CYS HIS SER SEQRES 30 A 432 ASP HIS GLU ASP ARG PRO SER PRO VAL LEU LEU SER CYS SEQRES 31 A 432 GLY ILE PRO VAL ASP VAL ALA ARG ASN ALA VAL ARG LEU SEQRES 32 A 432 SER VAL GLY ARG SER THR THR ARG ALA GLU VAL ASP LEU SEQRES 33 A 432 ILE VAL GLN ASP LEU LYS GLN ALA VAL ASN GLN LEU GLU SEQRES 34 A 432 GLY PRO VAL SEQRES 1 B 432 MET ASP VAL ALA ARG ASN GLY ALA ARG GLY SER VAL GLU SEQRES 2 B 432 SER PRO PRO ASN ARG LYS VAL TYR MET ASP TYR ASN ALA SEQRES 3 B 432 THR THR PRO LEU GLU PRO GLU VAL ILE GLN ALA VAL THR SEQRES 4 B 432 GLU ALA MET LYS GLU ALA TRP GLY ASN PRO SER SER SER SEQRES 5 B 432 TYR VAL ALA GLY ARG LYS ALA LYS ASP ILE ILE ASN THR SEQRES 6 B 432 ALA ARG ALA SER LEU ALA LYS MET ILE GLY GLY LYS PRO SEQRES 7 B 432 GLN ASP ILE ILE PHE THR SER GLY GLY THR GLU SER ASN SEQRES 8 B 432 ASN LEU VAL ILE HIS SER THR VAL ARG CYS PHE HIS GLU SEQRES 9 B 432 GLN GLN THR LEU GLN GLY ARG THR VAL ASP GLN ILE SER SEQRES 10 B 432 PRO GLU GLU GLY THR ARG PRO HIS PHE ILE THR CYS THR SEQRES 11 B 432 VAL GLU HIS ASP SER ILE ARG LEU PRO LEU GLU HIS LEU SEQRES 12 B 432 VAL GLU ASP GLN VAL ALA GLU VAL THR PHE VAL PRO VAL SEQRES 13 B 432 SER LYS VAL ASN GLY GLN VAL GLU VAL GLU ASP ILE LEU SEQRES 14 B 432 ALA ALA VAL ARG PRO THR THR CYS LEU VAL THR ILE MET SEQRES 15 B 432 LEU ALA ASN ASN GLU THR GLY VAL ILE MET PRO ILE SER SEQRES 16 B 432 GLU ILE SER ARG ARG ILE LYS ALA LEU ASN GLN ILE ARG SEQRES 17 B 432 ALA ALA SER GLY LEU PRO ARG VAL LEU VAL HIS THR ASP SEQRES 18 B 432 ALA ALA GLN ALA LEU GLY LYS ARG ARG VAL ASP VAL GLU SEQRES 19 B 432 ASP LEU GLY VAL ASP PHE LEU THR ILE VAL GLY HIS LYS SEQRES 20 B 432 PHE TYR GLY PRO ARG ILE GLY ALA LEU TYR VAL ARG GLY SEQRES 21 B 432 VAL GLY LYS LEU THR PRO LEU TYR PRO MET LEU PHE GLY SEQRES 22 B 432 GLY GLY GLN GLU ARG ASN PHE ARG PRO GLY THR GLU ASN SEQRES 23 B 432 THR PRO MET ILE ALA GLY LEU GLY LYS ALA ALA ASP LEU SEQRES 24 B 432 VAL SER GLU ASN CYS GLU THR TYR GLU ALA HIS MET ARG SEQRES 25 B 432 ASP ILE ARG ASP TYR LEU GLU GLU ARG LEU GLU ALA GLU SEQRES 26 B 432 PHE GLY LYS ARG ILE HIS LEU ASN SER ARG PHE PRO GLY SEQRES 27 B 432 VAL GLU ARG LEU PRO ASN THR CYS ASN PHE SER ILE GLN SEQRES 28 B 432 GLY SER GLN LEU ARG GLY TYR MET VAL LEU ALA GLN CYS SEQRES 29 B 432 GLN THR LEU LEU ALA SER VAL GLY ALA SER CYS HIS SER SEQRES 30 B 432 ASP HIS GLU ASP ARG PRO SER PRO VAL LEU LEU SER CYS SEQRES 31 B 432 GLY ILE PRO VAL ASP VAL ALA ARG ASN ALA VAL ARG LEU SEQRES 32 B 432 SER VAL GLY ARG SER THR THR ARG ALA GLU VAL ASP LEU SEQRES 33 B 432 ILE VAL GLN ASP LEU LYS GLN ALA VAL ASN GLN LEU GLU SEQRES 34 B 432 GLY PRO VAL HET PLP A 501 15 HET SLP A 502 12 HET PO4 A 504 5 HET PO4 A 505 5 HET PLP B 501 15 HET SLP B 503 12 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM SLP 3-SELANYLPROPANOIC ACID HETNAM PO4 PHOSPHATE ION HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 4 SLP 2(C3 H6 O2 SE) FORMUL 5 PO4 2(O4 P 3-) FORMUL 9 HOH *527(H2 O) HELIX 1 1 GLU A 31 ALA A 45 1 15 HELIX 2 2 TYR A 53 GLY A 75 1 23 HELIX 3 3 LYS A 77 GLN A 79 5 3 HELIX 4 4 GLY A 86 GLN A 109 1 24 HELIX 5 5 HIS A 133 ASP A 146 1 14 HELIX 6 6 GLU A 164 ALA A 171 1 8 HELIX 7 7 PRO A 193 GLY A 212 1 20 HELIX 8 8 ASP A 232 GLY A 237 1 6 HELIX 9 9 HIS A 246 PHE A 248 5 3 HELIX 10 10 GLY A 275 PHE A 280 5 6 HELIX 11 11 ASN A 286 GLY A 327 1 42 HELIX 12 12 ARG A 356 CYS A 364 1 9 HELIX 13 13 ALA A 373 GLU A 380 5 8 HELIX 14 14 SER A 384 CYS A 390 1 7 HELIX 15 15 PRO A 393 ARG A 398 1 6 HELIX 16 16 THR A 410 GLY A 430 1 21 HELIX 17 17 GLU B 31 ALA B 45 1 15 HELIX 18 18 TYR B 53 ILE B 74 1 22 HELIX 19 19 LYS B 77 GLN B 79 5 3 HELIX 20 20 GLY B 86 GLN B 105 1 20 HELIX 21 21 HIS B 133 ASP B 146 1 14 HELIX 22 22 GLU B 164 VAL B 172 1 9 HELIX 23 23 PRO B 193 SER B 211 1 19 HELIX 24 24 ASP B 232 GLY B 237 1 6 HELIX 25 25 HIS B 246 PHE B 248 5 3 HELIX 26 26 GLY B 275 PHE B 280 5 6 HELIX 27 27 ASN B 286 GLY B 327 1 42 HELIX 28 28 ARG B 356 CYS B 364 1 9 HELIX 29 29 ALA B 373 GLU B 380 5 8 HELIX 30 30 SER B 384 CYS B 390 1 7 HELIX 31 31 PRO B 393 ASN B 399 1 7 HELIX 32 32 THR B 410 GLU B 429 1 20 SHEET 1 A 2 VAL A 20 TYR A 21 0 SHEET 2 A 2 LEU A 367 LEU A 368 1 O LEU A 368 N VAL A 20 SHEET 1 B 7 ILE A 81 THR A 84 0 SHEET 2 B 7 GLY A 254 VAL A 258 -1 O GLY A 254 N THR A 84 SHEET 3 B 7 PHE A 240 VAL A 244 -1 N LEU A 241 O TYR A 257 SHEET 4 B 7 LEU A 217 ASP A 221 1 N THR A 220 O THR A 242 SHEET 5 B 7 THR A 176 THR A 180 1 N VAL A 179 O HIS A 219 SHEET 6 B 7 HIS A 125 CYS A 129 1 N HIS A 125 O CYS A 177 SHEET 7 B 7 GLU A 150 VAL A 154 1 O THR A 152 N PHE A 126 SHEET 1 C 3 ILE A 330 LEU A 332 0 SHEET 2 C 3 THR A 345 ILE A 350 -1 O SER A 349 N HIS A 331 SHEET 3 C 3 ALA A 400 SER A 404 -1 O LEU A 403 N CYS A 346 SHEET 1 D 2 VAL B 20 TYR B 21 0 SHEET 2 D 2 LEU B 367 LEU B 368 1 O LEU B 368 N VAL B 20 SHEET 1 E 7 ILE B 81 THR B 84 0 SHEET 2 E 7 GLY B 254 VAL B 258 -1 O LEU B 256 N ILE B 82 SHEET 3 E 7 PHE B 240 VAL B 244 -1 N LEU B 241 O TYR B 257 SHEET 4 E 7 LEU B 217 ASP B 221 1 N THR B 220 O THR B 242 SHEET 5 E 7 THR B 176 THR B 180 1 N VAL B 179 O HIS B 219 SHEET 6 E 7 HIS B 125 CYS B 129 1 N HIS B 125 O CYS B 177 SHEET 7 E 7 GLU B 150 VAL B 154 1 O THR B 152 N PHE B 126 SHEET 1 F 3 ILE B 330 LEU B 332 0 SHEET 2 F 3 THR B 345 ILE B 350 -1 O SER B 349 N HIS B 331 SHEET 3 F 3 ALA B 400 SER B 404 -1 O LEU B 403 N CYS B 346 LINK NZ LYS A 247 C4A PLP A 501 1555 1555 1.52 LINK NZ LYS B 247 C4A PLP B 501 1555 1555 1.37 SITE 1 AC1 16 GLY A 87 THR A 88 HIS A 133 MET A 182 SITE 2 AC1 16 ASP A 221 ALA A 223 GLN A 224 VAL A 244 SITE 3 AC1 16 HIS A 246 LYS A 247 HOH A 463 HOH A 464 SITE 4 AC1 16 HOH A 483 SLP A 502 GLY B 283 THR B 284 SITE 1 AC2 10 ASN A 25 ALA A 26 HIS A 133 ASN A 186 SITE 2 AC2 10 LYS A 247 ALA A 373 SER A 374 CYS A 375 SITE 3 AC2 10 ARG A 402 PLP A 501 SITE 1 AC3 8 ARG A 312 ARG A 315 ARG A 341 GLY A 352 SITE 2 AC3 8 SER A 353 HOH A 540 HOH A 573 HOH A 590 SITE 1 AC4 3 HIS A 310 ASP A 313 HOH A 630 SITE 1 AC5 16 GLY A 283 THR A 284 GLY B 87 THR B 88 SITE 2 AC5 16 HIS B 133 MET B 182 ASP B 221 ALA B 223 SITE 3 AC5 16 GLN B 224 VAL B 244 HIS B 246 LYS B 247 SITE 4 AC5 16 HOH B 442 HOH B 444 HOH B 475 SLP B 503 SITE 1 AC6 10 ASN B 25 ALA B 26 HIS B 133 ASN B 186 SITE 2 AC6 10 LYS B 247 ALA B 373 SER B 374 CYS B 375 SITE 3 AC6 10 ARG B 402 PLP B 501 CRYST1 55.416 101.206 197.356 90.00 90.00 90.00 P 21 21 21 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 0.018045 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009881 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005067 0.00000