HEADER CYTOSOLIC PROTEIN 02-NOV-22 8BIZ TITLE CYSTATHIONINE GAMMA-LYASE FROM TOXOPLASMA GONDII IN COMPLEX WITH TITLE 2 CYSTEINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTATHIONINE BETA-LYASE, PUTATIVE; COMPND 3 CHAIN: E, A; COMPND 4 SYNONYM: PUTATIVE CYSTATHIONE GAMMA LYASE; COMPND 5 EC: 4.4.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOXOPLASMA GONDII; SOURCE 3 ORGANISM_TAXID: 5811; SOURCE 4 GENE: BN1205_096960, TGVEG_312930; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSSULFURATION PATHWAY, HYDROGEN SULFIDE, CYSTEINE, TOXOPLASMA, KEYWDS 2 CYTOSOLIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.FERNANDEZ-RODRIGUEZ,C.CONTER,I.OYENARTE,F.FAVRETTO,I.QUINTANA, AUTHOR 2 M.L.MARTINEZ-CHANTAR,A.ASTEGNO,L.A.MARTINEZ-CRUZ REVDAT 2 07-FEB-24 8BIZ 1 REMARK REVDAT 1 12-APR-23 8BIZ 0 JRNL AUTH C.FERNANDEZ-RODRIGUEZ,C.CONTER,I.OYENARTE,F.FAVRETTO, JRNL AUTH 2 I.QUINTANA,M.L.MARTINEZ-CHANTAR,A.ASTEGNO,L.A.MARTINEZ-CRUZ JRNL TITL STRUCTURAL BASIS OF THE INHIBITION OF CYSTATHIONINE JRNL TITL 2 GAMMA-LYASE FROM TOXOPLASMA GONDII BY PROPARGYLGLYCINE AND JRNL TITL 3 CYSTEINE. JRNL REF PROTEIN SCI. V. 32 E4619 2023 JRNL REFN ESSN 1469-896X JRNL PMID 36883335 JRNL DOI 10.1002/PRO.4619 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 108472 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5530 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.4120 - 5.8714 1.00 3611 210 0.1641 0.1706 REMARK 3 2 5.8714 - 4.6618 1.00 3538 155 0.1627 0.1840 REMARK 3 3 4.6618 - 4.0729 1.00 3471 196 0.1447 0.1577 REMARK 3 4 4.0729 - 3.7007 1.00 3487 164 0.1549 0.1735 REMARK 3 5 3.7007 - 3.4356 1.00 3470 164 0.1516 0.1512 REMARK 3 6 3.4356 - 3.2331 1.00 3408 205 0.1642 0.1840 REMARK 3 7 3.2331 - 3.0712 1.00 3489 169 0.1713 0.1899 REMARK 3 8 3.0712 - 2.9375 1.00 3410 181 0.1789 0.1925 REMARK 3 9 2.9375 - 2.8245 1.00 3429 202 0.1711 0.1884 REMARK 3 10 2.8245 - 2.7270 1.00 3445 188 0.1803 0.1859 REMARK 3 11 2.7270 - 2.6418 1.00 3420 181 0.1845 0.2161 REMARK 3 12 2.6418 - 2.5663 1.00 3418 201 0.1841 0.1974 REMARK 3 13 2.5663 - 2.4987 1.00 3419 199 0.1787 0.1858 REMARK 3 14 2.4987 - 2.4377 1.00 3405 177 0.1821 0.1991 REMARK 3 15 2.4377 - 2.3823 1.00 3453 167 0.1857 0.2021 REMARK 3 16 2.3823 - 2.3316 1.00 3387 178 0.1774 0.2012 REMARK 3 17 2.3316 - 2.2850 1.00 3424 184 0.1812 0.2135 REMARK 3 18 2.2850 - 2.2419 1.00 3444 166 0.1749 0.1876 REMARK 3 19 2.2419 - 2.2018 1.00 3413 175 0.1787 0.2062 REMARK 3 20 2.2018 - 2.1645 1.00 3404 174 0.1809 0.1834 REMARK 3 21 2.1645 - 2.1296 1.00 3476 165 0.1841 0.2119 REMARK 3 22 2.1296 - 2.0968 1.00 3353 188 0.1822 0.2097 REMARK 3 23 2.0968 - 2.0660 1.00 3428 188 0.1883 0.1818 REMARK 3 24 2.0660 - 2.0369 1.00 3405 196 0.1893 0.2246 REMARK 3 25 2.0369 - 2.0094 1.00 3415 168 0.1845 0.1999 REMARK 3 26 2.0094 - 1.9833 1.00 3385 169 0.1891 0.2133 REMARK 3 27 1.9833 - 1.9585 1.00 3369 209 0.1867 0.1917 REMARK 3 28 1.9585 - 1.9349 1.00 3384 217 0.1858 0.1912 REMARK 3 29 1.9349 - 1.9124 1.00 3431 165 0.1926 0.2278 REMARK 3 30 1.9124 - 1.8910 1.00 3351 229 0.2073 0.2307 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.280 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 6250 REMARK 3 ANGLE : 0.919 8494 REMARK 3 CHIRALITY : 0.058 939 REMARK 3 PLANARITY : 0.006 1091 REMARK 3 DIHEDRAL : 6.447 5114 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -75.0840 -1.2631 29.1133 REMARK 3 T TENSOR REMARK 3 T11: 0.1120 T22: 0.0809 REMARK 3 T33: 0.0820 T12: 0.0074 REMARK 3 T13: 0.0047 T23: 0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.0641 L22: 0.6523 REMARK 3 L33: 0.1632 L12: 0.0874 REMARK 3 L13: 0.0246 L23: 0.0312 REMARK 3 S TENSOR REMARK 3 S11: 0.0099 S12: 0.0210 S13: -0.0130 REMARK 3 S21: -0.1207 S22: 0.0024 S23: 0.0043 REMARK 3 S31: -0.0119 S32: 0.0081 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8BIZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126443. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 108481 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 45.412 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 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 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: PHASER REMARK 200 STARTING MODEL: 2NMP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% (W/V) PEG 3350, 0.1M SODIUM REMARK 280 CITRATE PH 4.6, CYMAL-3, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 25510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -162.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 94.21300 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 746 LIES ON A SPECIAL POSITION. 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 E 1 REMARK 465 ALA E 2 REMARK 465 SER E 3 REMARK 465 LYS E 4 REMARK 465 GLN E 5 REMARK 465 ASN E 6 REMARK 465 ASP E 7 REMARK 465 LYS E 8 REMARK 465 ASP E 9 REMARK 465 GLY E 10 REMARK 465 ALA E 11 REMARK 465 VAL E 12 REMARK 465 ARG E 13 REMARK 465 ARG E 14 REMARK 465 ASP E 15 REMARK 465 ALA E 16 REMARK 465 SER E 17 REMARK 465 PHE E 18 REMARK 465 GLU E 19 REMARK 465 CYS E 20 REMARK 465 GLY E 21 REMARK 465 VAL E 22 REMARK 465 THR E 375 REMARK 465 HIS E 376 REMARK 465 ALA E 377 REMARK 465 ASN E 378 REMARK 465 MET E 379 REMARK 465 LEU E 380 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 GLN A 5 REMARK 465 ASN A 6 REMARK 465 ASP A 7 REMARK 465 LYS A 8 REMARK 465 ASP A 9 REMARK 465 GLY A 10 REMARK 465 ALA A 11 REMARK 465 VAL A 12 REMARK 465 ARG A 13 REMARK 465 ARG A 14 REMARK 465 ASP A 15 REMARK 465 ALA A 16 REMARK 465 SER A 17 REMARK 465 PHE A 18 REMARK 465 GLU A 19 REMARK 465 CYS A 20 REMARK 465 GLY A 21 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 E 23 CG CD CE NZ REMARK 470 LYS E 164 CG CD CE NZ REMARK 470 GLN E 193 CG CD OE1 NE2 REMARK 470 GLU E 249 CD OE1 OE2 REMARK 470 LYS E 300 CE NZ REMARK 470 GLU E 342 CG CD OE1 OE2 REMARK 470 CYS E 370 SG REMARK 470 VAL E 373 CG1 CG2 REMARK 470 GLU E 382 CG CD OE1 OE2 REMARK 470 ASP E 383 CG OD1 OD2 REMARK 470 LYS E 386 CG CD CE NZ REMARK 470 LYS A 23 CG CD CE NZ REMARK 470 GLU A 45 CD OE1 OE2 REMARK 470 GLU A 249 CG CD OE1 OE2 REMARK 470 GLU A 342 CG CD OE1 OE2 REMARK 470 GLU A 382 CG CD OE1 OE2 REMARK 470 LYS A 386 CG CD CE NZ 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 NH2 ARG A 346 O HOH A 601 1.82 REMARK 500 O HOH A 607 O HOH A 636 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O GLY A 30 O HOH A 601 3445 2.17 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 LEU E 275 CA - CB - CG ANGL. DEV. = 13.8 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 ASN E 70 43.51 -89.82 REMARK 500 SER E 77 -39.41 -142.89 REMARK 500 THR E 210 155.08 65.31 REMARK 500 LYS E 230 -82.83 -84.47 REMARK 500 GLN E 317 45.64 -100.79 REMARK 500 ASN E 327 -51.21 72.39 REMARK 500 SER E 360 -177.15 77.20 REMARK 500 ASN A 70 41.70 -107.18 REMARK 500 SER A 77 -40.87 -138.77 REMARK 500 THR A 210 153.70 65.77 REMARK 500 LYS A 230 -80.32 -88.95 REMARK 500 ASN A 327 -49.21 74.87 REMARK 500 SER A 360 -176.60 73.51 REMARK 500 THR A 375 -50.06 -123.42 REMARK 500 HIS A 376 48.98 -97.56 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 E 868 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A 852 DISTANCE = 6.32 ANGSTROMS DBREF 8BIZ E 1 417 UNP B6K8Y1 B6K8Y1_TOXGV 1 417 DBREF 8BIZ A 1 417 UNP B6K8Y1 B6K8Y1_TOXGV 1 417 SEQADV 8BIZ SER E 360 UNP B6K8Y1 ASN 360 ENGINEERED MUTATION SEQADV 8BIZ SER A 360 UNP B6K8Y1 ASN 360 ENGINEERED MUTATION SEQRES 1 E 417 MET ALA SER LYS GLN ASN ASP LYS ASP GLY ALA VAL ARG SEQRES 2 E 417 ARG ASP ALA SER PHE GLU CYS GLY VAL LYS ALA GLY ASP SEQRES 3 E 417 TRP LEU PRO GLY PHE THR PRO ARG GLU GLU THR VAL TYR SEQRES 4 E 417 VAL HIS GLY GLY VAL GLU PRO ASP PRO LEU THR GLY ALA SEQRES 5 E 417 ILE LEU PRO PRO ILE TYR GLN ASN THR THR PHE VAL GLN SEQRES 6 E 417 GLU SER VAL GLU ASN TYR LEU SER LYS GLY PHE SER TYR SEQRES 7 E 417 SER ARG THR SER ASN PRO THR VAL LEU SER LEU GLU LYS SEQRES 8 E 417 LYS ILE ALA GLU ILE GLU GLY GLY PHE GLY ALA CYS CYS SEQRES 9 E 417 PHE ALA THR GLY MET ALA ALA THR VAL THR ILE PHE SER SEQRES 10 E 417 ALA PHE LEU ALA PRO GLY ASP HIS CYS LEU VAL THR ASN SEQRES 11 E 417 CYS SER TYR GLY GLY THR ASN ARG CYS ALA ARG LEU HIS SEQRES 12 E 417 PHE SER LYS TYR ASN ILE ASP PHE GLU PHE ILE ASP PHE SEQRES 13 E 417 ARG ASP PRO THR ASN VAL GLU LYS ALA ILE ARG PRO GLN SEQRES 14 E 417 THR LYS VAL VAL PHE SER GLU SER PRO CYS ASN PRO THR SEQRES 15 E 417 LEU TYR LEU ALA ASP ILE GLU ALA ILE SER GLN ILE CYS SEQRES 16 E 417 LYS GLU LYS LYS VAL LEU HIS VAL CYS ASP SER THR PHE SEQRES 17 E 417 ALA THR PRO TYR MET MET ARG PRO LEU ASP LEU GLY ALA SEQRES 18 E 417 ASP ILE VAL VAL GLN SER THR THR LYS TYR TYR ASP GLY SEQRES 19 E 417 HIS ASN CYS THR LEU GLY GLY ALA VAL ILE SER SER THR SEQRES 20 E 417 LYS GLU ILE HIS ASP LYS VAL PHE PHE LEU ARG ASN VAL SEQRES 21 E 417 MET GLY ASN ILE MET SER ALA GLN THR ALA PHE TYR THR SEQRES 22 E 417 LEU LEU THR LEU LYS THR LEU PRO ILE ARG VAL GLU LYS SEQRES 23 E 417 GLN SER ALA ASN ALA GLN LYS ILE ALA GLU PHE LEU SER SEQRES 24 E 417 LYS HIS HIS LYS VAL GLU HIS VAL ILE TYR PRO GLY ILE SEQRES 25 E 417 PRO SER PHE PRO GLN LYS GLU LEU ALA LEU LYS GLN HIS SEQRES 26 E 417 LYS ASN VAL HIS GLY GLY MET LEU ALA PHE GLU VAL LYS SEQRES 27 E 417 GLY GLY THR GLU ALA GLY ILE ARG MET MET ASN HIS VAL SEQRES 28 E 417 PRO ARG PRO TRP SER LEU CYS GLU SER LEU GLY ALA CYS SEQRES 29 E 417 GLU SER ILE ILE THR CYS PRO ALA VAL PHE THR HIS ALA SEQRES 30 E 417 ASN MET LEU ARG GLU ASP ARG LEU LYS VAL GLY ILE THR SEQRES 31 E 417 ASP GLY PHE ILE ARG VAL SER VAL GLY ILE GLU ASP VAL SEQRES 32 E 417 ASN ASP LEU ILE ASP GLY LEU ASP TYR ALA LEU SER LYS SEQRES 33 E 417 ALA SEQRES 1 A 417 MET ALA SER LYS GLN ASN ASP LYS ASP GLY ALA VAL ARG SEQRES 2 A 417 ARG ASP ALA SER PHE GLU CYS GLY VAL LYS ALA GLY ASP SEQRES 3 A 417 TRP LEU PRO GLY PHE THR PRO ARG GLU GLU THR VAL TYR SEQRES 4 A 417 VAL HIS GLY GLY VAL GLU PRO ASP PRO LEU THR GLY ALA SEQRES 5 A 417 ILE LEU PRO PRO ILE TYR GLN ASN THR THR PHE VAL GLN SEQRES 6 A 417 GLU SER VAL GLU ASN TYR LEU SER LYS GLY PHE SER TYR SEQRES 7 A 417 SER ARG THR SER ASN PRO THR VAL LEU SER LEU GLU LYS SEQRES 8 A 417 LYS ILE ALA GLU ILE GLU GLY GLY PHE GLY ALA CYS CYS SEQRES 9 A 417 PHE ALA THR GLY MET ALA ALA THR VAL THR ILE PHE SER SEQRES 10 A 417 ALA PHE LEU ALA PRO GLY ASP HIS CYS LEU VAL THR ASN SEQRES 11 A 417 CYS SER TYR GLY GLY THR ASN ARG CYS ALA ARG LEU HIS SEQRES 12 A 417 PHE SER LYS TYR ASN ILE ASP PHE GLU PHE ILE ASP PHE SEQRES 13 A 417 ARG ASP PRO THR ASN VAL GLU LYS ALA ILE ARG PRO GLN SEQRES 14 A 417 THR LYS VAL VAL PHE SER GLU SER PRO CYS ASN PRO THR SEQRES 15 A 417 LEU TYR LEU ALA ASP ILE GLU ALA ILE SER GLN ILE CYS SEQRES 16 A 417 LYS GLU LYS LYS VAL LEU HIS VAL CYS ASP SER THR PHE SEQRES 17 A 417 ALA THR PRO TYR MET MET ARG PRO LEU ASP LEU GLY ALA SEQRES 18 A 417 ASP ILE VAL VAL GLN SER THR THR LYS TYR TYR ASP GLY SEQRES 19 A 417 HIS ASN CYS THR LEU GLY GLY ALA VAL ILE SER SER THR SEQRES 20 A 417 LYS GLU ILE HIS ASP LYS VAL PHE PHE LEU ARG ASN VAL SEQRES 21 A 417 MET GLY ASN ILE MET SER ALA GLN THR ALA PHE TYR THR SEQRES 22 A 417 LEU LEU THR LEU LYS THR LEU PRO ILE ARG VAL GLU LYS SEQRES 23 A 417 GLN SER ALA ASN ALA GLN LYS ILE ALA GLU PHE LEU SER SEQRES 24 A 417 LYS HIS HIS LYS VAL GLU HIS VAL ILE TYR PRO GLY ILE SEQRES 25 A 417 PRO SER PHE PRO GLN LYS GLU LEU ALA LEU LYS GLN HIS SEQRES 26 A 417 LYS ASN VAL HIS GLY GLY MET LEU ALA PHE GLU VAL LYS SEQRES 27 A 417 GLY GLY THR GLU ALA GLY ILE ARG MET MET ASN HIS VAL SEQRES 28 A 417 PRO ARG PRO TRP SER LEU CYS GLU SER LEU GLY ALA CYS SEQRES 29 A 417 GLU SER ILE ILE THR CYS PRO ALA VAL PHE THR HIS ALA SEQRES 30 A 417 ASN MET LEU ARG GLU ASP ARG LEU LYS VAL GLY ILE THR SEQRES 31 A 417 ASP GLY PHE ILE ARG VAL SER VAL GLY ILE GLU ASP VAL SEQRES 32 A 417 ASN ASP LEU ILE ASP GLY LEU ASP TYR ALA LEU SER LYS SEQRES 33 A 417 ALA HET PLP E 501 15 HET CYS E 502 7 HET PLP A 501 15 HET CYS A 502 7 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM CYS CYSTEINE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 4 CYS 2(C3 H7 N O2 S) FORMUL 7 HOH *520(H2 O) HELIX 1 AA1 ARG E 34 GLY E 42 1 9 HELIX 2 AA2 ASN E 83 GLY E 98 1 16 HELIX 3 AA3 THR E 107 LEU E 120 1 14 HELIX 4 AA4 TYR E 133 HIS E 143 1 11 HELIX 5 AA5 PHE E 144 ASN E 148 5 5 HELIX 6 AA6 ASP E 158 ILE E 166 1 9 HELIX 7 AA7 ASP E 187 LYS E 199 1 13 HELIX 8 AA8 ARG E 215 GLY E 220 5 6 HELIX 9 AA9 THR E 247 GLY E 262 1 16 HELIX 10 AB1 SER E 266 LEU E 277 1 12 HELIX 11 AB2 THR E 279 HIS E 301 1 23 HELIX 12 AB3 GLN E 317 HIS E 325 1 9 HELIX 13 AB4 GLY E 340 HIS E 350 1 11 HELIX 14 AB5 GLU E 382 GLY E 388 1 7 HELIX 15 AB6 ASP E 402 ALA E 417 1 16 HELIX 16 AB7 ARG A 34 GLY A 42 1 9 HELIX 17 AB8 ASN A 83 GLY A 98 1 16 HELIX 18 AB9 THR A 107 LEU A 120 1 14 HELIX 19 AC1 TYR A 133 HIS A 143 1 11 HELIX 20 AC2 PHE A 144 ASN A 148 5 5 HELIX 21 AC3 ASP A 158 ILE A 166 1 9 HELIX 22 AC4 ASP A 187 LYS A 199 1 13 HELIX 23 AC5 THR A 247 GLY A 262 1 16 HELIX 24 AC6 SER A 266 LYS A 278 1 13 HELIX 25 AC7 THR A 279 HIS A 301 1 23 HELIX 26 AC8 GLN A 317 HIS A 325 1 9 HELIX 27 AC9 GLY A 339 HIS A 350 1 12 HELIX 28 AD1 CYS A 370 THR A 375 1 6 HELIX 29 AD2 LEU A 380 GLY A 388 1 9 HELIX 30 AD3 ASP A 402 ALA A 417 1 16 SHEET 1 AA1 7 GLY E 101 PHE E 105 0 SHEET 2 AA1 7 GLY E 241 SER E 245 -1 O GLY E 241 N PHE E 105 SHEET 3 AA1 7 ILE E 223 SER E 227 -1 N VAL E 224 O ILE E 244 SHEET 4 AA1 7 LEU E 201 ASP E 205 1 N CYS E 204 O VAL E 225 SHEET 5 AA1 7 THR E 170 GLU E 176 1 N VAL E 173 O LEU E 201 SHEET 6 AA1 7 HIS E 125 THR E 129 1 N LEU E 127 O PHE E 174 SHEET 7 AA1 7 ASP E 150 ILE E 154 1 O ASP E 150 N CYS E 126 SHEET 1 AA2 5 VAL E 304 ILE E 308 0 SHEET 2 AA2 5 MET E 332 VAL E 337 -1 O GLU E 336 N GLU E 305 SHEET 3 AA2 5 PHE E 393 SER E 397 -1 O VAL E 396 N LEU E 333 SHEET 4 AA2 5 ILE E 367 THR E 369 -1 N ILE E 367 O SER E 397 SHEET 5 AA2 5 SER E 356 LEU E 357 1 N SER E 356 O ILE E 368 SHEET 1 AA3 7 GLY A 101 PHE A 105 0 SHEET 2 AA3 7 GLY A 241 SER A 245 -1 O GLY A 241 N PHE A 105 SHEET 3 AA3 7 ILE A 223 SER A 227 -1 N VAL A 224 O ILE A 244 SHEET 4 AA3 7 LEU A 201 ASP A 205 1 N CYS A 204 O VAL A 225 SHEET 5 AA3 7 THR A 170 GLU A 176 1 N VAL A 173 O LEU A 201 SHEET 6 AA3 7 HIS A 125 THR A 129 1 N LEU A 127 O PHE A 174 SHEET 7 AA3 7 ASP A 150 ILE A 154 1 O GLU A 152 N VAL A 128 SHEET 1 AA4 5 VAL A 304 ILE A 308 0 SHEET 2 AA4 5 MET A 332 VAL A 337 -1 O GLU A 336 N GLU A 305 SHEET 3 AA4 5 PHE A 393 SER A 397 -1 O VAL A 396 N LEU A 333 SHEET 4 AA4 5 ILE A 367 THR A 369 -1 N ILE A 367 O SER A 397 SHEET 5 AA4 5 SER A 356 LEU A 357 1 N SER A 356 O ILE A 368 LINK NZ LYS E 230 C4A PLP E 501 1555 1555 1.43 LINK NZ LYS A 230 C4A PLP A 501 1555 1555 1.43 CISPEP 1 SER E 177 PRO E 178 0 -13.05 CISPEP 2 ASN E 180 PRO E 181 0 0.63 CISPEP 3 ARG E 353 PRO E 354 0 12.71 CISPEP 4 SER A 177 PRO A 178 0 -12.53 CISPEP 5 ASN A 180 PRO A 181 0 4.94 CISPEP 6 ARG A 353 PRO A 354 0 13.31 CRYST1 158.346 158.346 94.213 90.00 90.00 120.00 P 3 2 1 12 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 0.006315 0.003646 0.000000 0.00000 SCALE2 0.000000 0.007292 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010614 0.00000