HEADER LYASE 16-JUL-19 6KHP TITLE CRYSTAL STRUCTURE OF ORYZA SATIVA TDC WITH PLP AND TRYPTAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPTOPHAN DECARBOXYLASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TDC; COMPND 5 EC: 4.1.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA SUBSP. JAPONICA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 39947; SOURCE 5 GENE: TDC1, OS08G0140300, LOC_OS08G04540, OJ1368_G08.14, OSJ_25993; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS AMINO ACID DECARBOXYLASE, TRANSFERASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.Z.ZHOU,L.J.LIAO,X.K.LIU,Y.GUO,Y.C.ZHAO,Z.X.ZENG REVDAT 1 15-JUL-20 6KHP 0 JRNL AUTH Y.ZHOU,L.LIAO,X.LIU,B.LIU,X.CHEN,Y.GUO,C.HUANG,Y.ZHAO,Z.ZENG JRNL TITL CRYSTAL STRUCTURE OFORYZA SATIVATDC REVEALS THE SUBSTRATE JRNL TITL 2 SPECIFICITY FOR TDC-MEDIATED MELATONIN BIOSYNTHESIS. JRNL REF J ADV RES V. 24 501 2020 JRNL REFN ISSN 2090-1232 JRNL PMID 32595985 JRNL DOI 10.1016/J.JARE.2020.06.004 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 63528 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 3160 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 28.1390 - 6.5119 0.99 2748 151 0.1398 0.1469 REMARK 3 2 6.5119 - 5.1792 1.00 2670 145 0.1605 0.1945 REMARK 3 3 5.1792 - 4.5276 1.00 2672 137 0.1298 0.1483 REMARK 3 4 4.5276 - 4.1150 1.00 2655 138 0.1278 0.1558 REMARK 3 5 4.1150 - 3.8208 1.00 2628 150 0.1418 0.1873 REMARK 3 6 3.8208 - 3.5960 1.00 2635 129 0.1486 0.1845 REMARK 3 7 3.5960 - 3.4163 1.00 2627 142 0.1744 0.2180 REMARK 3 8 3.4163 - 3.2678 1.00 2628 129 0.1815 0.2071 REMARK 3 9 3.2678 - 3.1422 1.00 2618 157 0.1787 0.2092 REMARK 3 10 3.1422 - 3.0339 0.99 2603 128 0.1823 0.2263 REMARK 3 11 3.0339 - 2.9391 0.99 2588 159 0.1766 0.2162 REMARK 3 12 2.9391 - 2.8552 1.00 2595 149 0.1838 0.2510 REMARK 3 13 2.8552 - 2.7801 1.00 2575 149 0.1794 0.2293 REMARK 3 14 2.7801 - 2.7123 1.00 2648 137 0.1754 0.2131 REMARK 3 15 2.7123 - 2.6507 1.00 2633 109 0.1713 0.1979 REMARK 3 16 2.6507 - 2.5943 1.00 2591 147 0.1798 0.2049 REMARK 3 17 2.5943 - 2.5425 1.00 2575 145 0.1801 0.2266 REMARK 3 18 2.5425 - 2.4945 1.00 2640 139 0.1901 0.2191 REMARK 3 19 2.4945 - 2.4500 1.00 2605 111 0.1939 0.2528 REMARK 3 20 2.4500 - 2.4085 1.00 2630 145 0.1895 0.2478 REMARK 3 21 2.4085 - 2.3697 1.00 2597 118 0.1930 0.2493 REMARK 3 22 2.3697 - 2.3332 1.00 2603 111 0.2018 0.2644 REMARK 3 23 2.3332 - 2.2990 0.99 2604 135 0.2278 0.2770 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.75 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6KHP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300013024. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2-8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91905 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 R CDTE 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63568 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 28.139 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 15.90 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : 0.11600 REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 13.30 REMARK 200 R MERGE FOR SHELL (I) : 0.71700 REMARK 200 R SYM FOR SHELL (I) : 0.71700 REMARK 200 FOR SHELL : 2.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1000, IMIDAZOLE/HYDROCHLORIC ACID, REMARK 280 CALCIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 34.03133 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 68.06267 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 68.06267 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 34.03133 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: 33300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 58920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -269.0 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -68.06267 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 GLY A 2 REMARK 465 SER A 3 REMARK 465 LEU A 4 REMARK 465 ASP A 5 REMARK 465 THR A 6 REMARK 465 ASN A 7 REMARK 465 PRO A 8 REMARK 465 THR A 9 REMARK 465 ALA A 10 REMARK 465 PHE A 11 REMARK 465 SER A 12 REMARK 465 ALA A 13 REMARK 465 PHE A 14 REMARK 465 PRO A 15 REMARK 465 ALA A 16 REMARK 465 GLY A 17 REMARK 465 GLU A 18 REMARK 465 GLY A 19 REMARK 465 GLU A 20 REMARK 465 ARG A 159 REMARK 465 THR A 160 REMARK 465 GLY A 161 REMARK 465 GLU A 162 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 SER B 3 REMARK 465 LEU B 4 REMARK 465 ASP B 5 REMARK 465 THR B 6 REMARK 465 ASN B 7 REMARK 465 PRO B 8 REMARK 465 THR B 9 REMARK 465 ALA B 10 REMARK 465 PHE B 11 REMARK 465 SER B 12 REMARK 465 ALA B 13 REMARK 465 PHE B 14 REMARK 465 PRO B 15 REMARK 465 ALA B 16 REMARK 465 GLY B 17 REMARK 465 GLU B 18 REMARK 465 GLY B 19 REMARK 465 GLU B 20 REMARK 465 THR B 350 REMARK 465 GLY B 351 REMARK 465 SER B 352 REMARK 465 LEU B 353 REMARK 465 GLU B 354 REMARK 465 THR B 355 REMARK 465 ASN B 356 REMARK 465 PRO B 357 REMARK 465 GLU B 358 REMARK 465 TYR B 359 REMARK 465 LEU B 360 REMARK 465 LYS B 361 REMARK 465 ASN B 362 REMARK 465 HIS B 363 REMARK 465 ALA B 364 REMARK 465 SER B 365 REMARK 465 ASP B 366 REMARK 465 SER B 367 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 OD1 ASP A 64 O HOH A 701 2.07 REMARK 500 CZ TYR A 359 N1 TSS A 602 2.19 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 103 -126.45 55.33 REMARK 500 SER A 132 96.30 -178.56 REMARK 500 LYS A 330 -73.74 -97.88 REMARK 500 CYS A 338 102.83 -163.45 REMARK 500 ASN A 356 55.27 -143.13 REMARK 500 VAL A 380 -65.90 -92.40 REMARK 500 ARG A 382 144.25 -170.93 REMARK 500 PHE A 433 -115.84 -134.71 REMARK 500 ASN B 56 57.22 -101.39 REMARK 500 PHE B 103 -121.27 54.71 REMARK 500 SER B 132 93.28 -176.63 REMARK 500 LYS B 330 -76.87 -93.09 REMARK 500 CYS B 338 98.69 -160.54 REMARK 500 THR B 346 -7.63 -58.93 REMARK 500 PHE B 433 -125.56 -130.73 REMARK 500 MET B 513 9.81 -67.97 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 CA A 603 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 408 OD1 REMARK 620 2 HOH A 715 O 81.0 REMARK 620 3 HOH A 727 O 80.2 76.8 REMARK 620 4 HOH A 738 O 96.3 163.8 87.0 REMARK 620 5 HOH A 746 O 121.6 128.5 146.2 66.5 REMARK 620 6 HOH A 791 O 87.9 81.0 156.2 114.9 57.1 REMARK 620 7 HOH A 853 O 153.5 85.5 74.7 90.4 84.6 112.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 602 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 408 OD1 REMARK 620 2 HOH B 803 O 120.0 REMARK 620 3 HOH B 768 O 83.3 53.1 REMARK 620 4 HOH B 791 O 159.6 80.4 113.4 REMARK 620 5 HOH B 747 O 91.5 74.7 113.1 92.4 REMARK 620 6 HOH B 708 O 80.1 123.6 82.2 90.2 161.7 REMARK 620 7 HOH B 761 O 78.7 153.3 153.6 81.6 86.6 75.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 604 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 876 O REMARK 620 2 HOH A 871 O 107.8 REMARK 620 3 HOH A 892 O 121.0 110.6 REMARK 620 4 HOH B 895 O 65.6 130.8 55.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 603 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 701 O REMARK 620 2 HOH B 703 O 131.0 REMARK 620 3 HOH A 885 O 90.8 126.3 REMARK 620 4 HOH B 882 O 108.7 72.1 62.0 REMARK 620 5 HOH A 737 O 72.4 59.9 151.0 100.5 REMARK 620 N 1 2 3 4 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TSS A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP B 601 and LYS B REMARK 800 330 DBREF 6KHP A 1 514 UNP Q6ZJK7 TDC1_ORYSJ 1 514 DBREF 6KHP B 1 514 UNP Q6ZJK7 TDC1_ORYSJ 1 514 SEQRES 1 A 514 MET GLY SER LEU ASP THR ASN PRO THR ALA PHE SER ALA SEQRES 2 A 514 PHE PRO ALA GLY GLU GLY GLU THR PHE GLN PRO LEU ASN SEQRES 3 A 514 ALA ASP ASP VAL ARG SER TYR LEU HIS LYS ALA VAL ASP SEQRES 4 A 514 PHE ILE SER ASP TYR TYR LYS SER VAL GLU SER MET PRO SEQRES 5 A 514 VAL LEU PRO ASN VAL LYS PRO GLY TYR LEU GLN ASP GLU SEQRES 6 A 514 LEU ARG ALA SER PRO PRO THR TYR SER ALA PRO PHE ASP SEQRES 7 A 514 VAL THR MET LYS GLU LEU ARG SER SER VAL VAL PRO GLY SEQRES 8 A 514 MET THR HIS TRP ALA SER PRO ASN PHE PHE ALA PHE PHE SEQRES 9 A 514 PRO SER THR ASN SER ALA ALA ALA ILE ALA GLY ASP LEU SEQRES 10 A 514 ILE ALA SER ALA MET ASN THR VAL GLY PHE THR TRP GLN SEQRES 11 A 514 ALA SER PRO ALA ALA THR GLU MET GLU VAL LEU ALA LEU SEQRES 12 A 514 ASP TRP LEU ALA GLN MET LEU ASN LEU PRO THR SER PHE SEQRES 13 A 514 MET ASN ARG THR GLY GLU GLY ARG GLY THR GLY GLY GLY SEQRES 14 A 514 VAL ILE LEU GLY THR THR SER GLU ALA MET LEU VAL THR SEQRES 15 A 514 LEU VAL ALA ALA ARG ASP ALA ALA LEU ARG ARG SER GLY SEQRES 16 A 514 SER ASP GLY VAL ALA GLY LEU HIS ARG LEU ALA VAL TYR SEQRES 17 A 514 ALA ALA ASP GLN THR HIS SER THR PHE PHE LYS ALA CYS SEQRES 18 A 514 ARG LEU ALA GLY PHE ASP PRO ALA ASN ILE ARG SER ILE SEQRES 19 A 514 PRO THR GLY ALA GLU THR ASP TYR GLY LEU ASP PRO ALA SEQRES 20 A 514 ARG LEU LEU GLU ALA MET GLN ALA ASP ALA ASP ALA GLY SEQRES 21 A 514 LEU VAL PRO THR TYR VAL CYS ALA THR VAL GLY THR THR SEQRES 22 A 514 SER SER ASN ALA VAL ASP PRO VAL GLY ALA VAL ALA ASP SEQRES 23 A 514 VAL ALA ALA ARG PHE ALA ALA TRP VAL HIS VAL ASP ALA SEQRES 24 A 514 ALA TYR ALA GLY SER ALA CYS ILE CYS PRO GLU PHE ARG SEQRES 25 A 514 HIS HIS LEU ASP GLY VAL GLU ARG VAL ASP SER ILE SER SEQRES 26 A 514 MET SER PRO HIS LYS TRP LEU MET THR CYS LEU ASP CYS SEQRES 27 A 514 THR CYS LEU TYR VAL ARG ASP THR HIS ARG LEU THR GLY SEQRES 28 A 514 SER LEU GLU THR ASN PRO GLU TYR LEU LYS ASN HIS ALA SEQRES 29 A 514 SER ASP SER GLY GLU VAL THR ASP LEU LYS ASP MET GLN SEQRES 30 A 514 VAL GLY VAL GLY ARG ARG PHE ARG GLY LEU LYS LEU TRP SEQRES 31 A 514 MET VAL MET ARG THR TYR GLY VAL ALA LYS LEU GLN GLU SEQRES 32 A 514 HIS ILE ARG SER ASP VAL ALA MET ALA LYS VAL PHE GLU SEQRES 33 A 514 ASP LEU VAL ARG GLY ASP ASP ARG PHE GLU VAL VAL VAL SEQRES 34 A 514 PRO ARG ASN PHE ALA LEU VAL CYS PHE ARG ILE ARG ALA SEQRES 35 A 514 GLY ALA GLY ALA ALA ALA ALA THR GLU GLU ASP ALA ASP SEQRES 36 A 514 GLU ALA ASN ARG GLU LEU MET GLU ARG LEU ASN LYS THR SEQRES 37 A 514 GLY LYS ALA TYR VAL ALA HIS THR VAL VAL GLY GLY ARG SEQRES 38 A 514 PHE VAL LEU ARG PHE ALA VAL GLY SER SER LEU GLN GLU SEQRES 39 A 514 GLU HIS HIS VAL ARG SER ALA TRP GLU LEU ILE LYS LYS SEQRES 40 A 514 THR THR THR GLU MET MET ASN SEQRES 1 B 514 MET GLY SER LEU ASP THR ASN PRO THR ALA PHE SER ALA SEQRES 2 B 514 PHE PRO ALA GLY GLU GLY GLU THR PHE GLN PRO LEU ASN SEQRES 3 B 514 ALA ASP ASP VAL ARG SER TYR LEU HIS LYS ALA VAL ASP SEQRES 4 B 514 PHE ILE SER ASP TYR TYR LYS SER VAL GLU SER MET PRO SEQRES 5 B 514 VAL LEU PRO ASN VAL LYS PRO GLY TYR LEU GLN ASP GLU SEQRES 6 B 514 LEU ARG ALA SER PRO PRO THR TYR SER ALA PRO PHE ASP SEQRES 7 B 514 VAL THR MET LYS GLU LEU ARG SER SER VAL VAL PRO GLY SEQRES 8 B 514 MET THR HIS TRP ALA SER PRO ASN PHE PHE ALA PHE PHE SEQRES 9 B 514 PRO SER THR ASN SER ALA ALA ALA ILE ALA GLY ASP LEU SEQRES 10 B 514 ILE ALA SER ALA MET ASN THR VAL GLY PHE THR TRP GLN SEQRES 11 B 514 ALA SER PRO ALA ALA THR GLU MET GLU VAL LEU ALA LEU SEQRES 12 B 514 ASP TRP LEU ALA GLN MET LEU ASN LEU PRO THR SER PHE SEQRES 13 B 514 MET ASN ARG THR GLY GLU GLY ARG GLY THR GLY GLY GLY SEQRES 14 B 514 VAL ILE LEU GLY THR THR SER GLU ALA MET LEU VAL THR SEQRES 15 B 514 LEU VAL ALA ALA ARG ASP ALA ALA LEU ARG ARG SER GLY SEQRES 16 B 514 SER ASP GLY VAL ALA GLY LEU HIS ARG LEU ALA VAL TYR SEQRES 17 B 514 ALA ALA ASP GLN THR HIS SER THR PHE PHE LYS ALA CYS SEQRES 18 B 514 ARG LEU ALA GLY PHE ASP PRO ALA ASN ILE ARG SER ILE SEQRES 19 B 514 PRO THR GLY ALA GLU THR ASP TYR GLY LEU ASP PRO ALA SEQRES 20 B 514 ARG LEU LEU GLU ALA MET GLN ALA ASP ALA ASP ALA GLY SEQRES 21 B 514 LEU VAL PRO THR TYR VAL CYS ALA THR VAL GLY THR THR SEQRES 22 B 514 SER SER ASN ALA VAL ASP PRO VAL GLY ALA VAL ALA ASP SEQRES 23 B 514 VAL ALA ALA ARG PHE ALA ALA TRP VAL HIS VAL ASP ALA SEQRES 24 B 514 ALA TYR ALA GLY SER ALA CYS ILE CYS PRO GLU PHE ARG SEQRES 25 B 514 HIS HIS LEU ASP GLY VAL GLU ARG VAL ASP SER ILE SER SEQRES 26 B 514 MET SER PRO HIS LYS TRP LEU MET THR CYS LEU ASP CYS SEQRES 27 B 514 THR CYS LEU TYR VAL ARG ASP THR HIS ARG LEU THR GLY SEQRES 28 B 514 SER LEU GLU THR ASN PRO GLU TYR LEU LYS ASN HIS ALA SEQRES 29 B 514 SER ASP SER GLY GLU VAL THR ASP LEU LYS ASP MET GLN SEQRES 30 B 514 VAL GLY VAL GLY ARG ARG PHE ARG GLY LEU LYS LEU TRP SEQRES 31 B 514 MET VAL MET ARG THR TYR GLY VAL ALA LYS LEU GLN GLU SEQRES 32 B 514 HIS ILE ARG SER ASP VAL ALA MET ALA LYS VAL PHE GLU SEQRES 33 B 514 ASP LEU VAL ARG GLY ASP ASP ARG PHE GLU VAL VAL VAL SEQRES 34 B 514 PRO ARG ASN PHE ALA LEU VAL CYS PHE ARG ILE ARG ALA SEQRES 35 B 514 GLY ALA GLY ALA ALA ALA ALA THR GLU GLU ASP ALA ASP SEQRES 36 B 514 GLU ALA ASN ARG GLU LEU MET GLU ARG LEU ASN LYS THR SEQRES 37 B 514 GLY LYS ALA TYR VAL ALA HIS THR VAL VAL GLY GLY ARG SEQRES 38 B 514 PHE VAL LEU ARG PHE ALA VAL GLY SER SER LEU GLN GLU SEQRES 39 B 514 GLU HIS HIS VAL ARG SER ALA TRP GLU LEU ILE LYS LYS SEQRES 40 B 514 THR THR THR GLU MET MET ASN HET PLP A 601 15 HET TSS A 602 12 HET CA A 603 1 HET CA A 604 1 HET ACT A 605 4 HET ACT A 606 4 HET PEG A 607 7 HET PLP B 601 15 HET CA B 602 1 HET CA B 603 1 HET PEG B 604 7 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM TSS 2-(1H-INDOL-3-YL)ETHANAMINE HETNAM CA CALCIUM ION HETNAM ACT ACETATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN TSS TRYPTAMINE FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 4 TSS C10 H12 N2 FORMUL 5 CA 4(CA 2+) FORMUL 7 ACT 2(C2 H3 O2 1-) FORMUL 9 PEG 2(C4 H10 O3) FORMUL 14 HOH *409(H2 O) HELIX 1 AA1 ASN A 26 VAL A 48 1 23 HELIX 2 AA2 GLU A 49 MET A 51 5 3 HELIX 3 AA3 GLY A 60 LEU A 66 1 7 HELIX 4 AA4 PRO A 76 VAL A 88 1 13 HELIX 5 AA5 VAL A 89 MET A 92 5 4 HELIX 6 AA6 SER A 109 ASN A 123 1 15 HELIX 7 AA7 SER A 132 LEU A 150 1 19 HELIX 8 AA8 PRO A 153 MET A 157 5 5 HELIX 9 AA9 THR A 174 SER A 194 1 21 HELIX 10 AB1 GLY A 201 HIS A 203 5 3 HELIX 11 AB2 HIS A 214 ALA A 224 1 11 HELIX 12 AB3 ASP A 227 ALA A 229 5 3 HELIX 13 AB4 GLY A 237 ASP A 241 5 5 HELIX 14 AB5 ASP A 245 ALA A 259 1 15 HELIX 15 AB6 PRO A 280 ARG A 290 1 11 HELIX 16 AB7 TYR A 301 CYS A 308 5 8 HELIX 17 AB8 PHE A 311 ASP A 316 5 6 HELIX 18 AB9 GLY A 317 VAL A 321 5 5 HELIX 19 AC1 SER A 327 LEU A 332 1 6 HELIX 20 AC2 ASP A 345 GLU A 354 1 10 HELIX 21 AC3 PRO A 357 LYS A 361 5 5 HELIX 22 AC4 ASN A 362 SER A 367 1 6 HELIX 23 AC5 ASP A 372 GLN A 377 5 6 HELIX 24 AC6 ARG A 385 GLY A 421 1 37 HELIX 25 AC7 THR A 450 THR A 468 1 19 HELIX 26 AC8 GLU A 494 ASN A 514 1 21 HELIX 27 AC9 ASN B 26 VAL B 48 1 23 HELIX 28 AD1 GLU B 49 MET B 51 5 3 HELIX 29 AD2 GLY B 60 GLU B 65 5 6 HELIX 30 AD3 PRO B 76 VAL B 88 1 13 HELIX 31 AD4 VAL B 89 MET B 92 5 4 HELIX 32 AD5 SER B 109 ASN B 123 1 15 HELIX 33 AD6 SER B 132 LEU B 150 1 19 HELIX 34 AD7 PRO B 153 MET B 157 5 5 HELIX 35 AD8 THR B 174 SER B 194 1 21 HELIX 36 AD9 GLY B 201 HIS B 203 5 3 HELIX 37 AE1 HIS B 214 ALA B 224 1 11 HELIX 38 AE2 ASP B 227 ALA B 229 5 3 HELIX 39 AE3 GLY B 237 ASP B 241 5 5 HELIX 40 AE4 ASP B 245 ALA B 259 1 15 HELIX 41 AE5 PRO B 280 ARG B 290 1 11 HELIX 42 AE6 TYR B 301 CYS B 308 5 8 HELIX 43 AE7 PHE B 311 ASP B 316 5 6 HELIX 44 AE8 GLY B 317 VAL B 321 5 5 HELIX 45 AE9 SER B 327 LEU B 332 1 6 HELIX 46 AF1 ASP B 345 LEU B 349 5 5 HELIX 47 AF2 ARG B 385 GLY B 421 1 37 HELIX 48 AF3 GLY B 445 ALA B 449 5 5 HELIX 49 AF4 THR B 450 THR B 468 1 19 HELIX 50 AF5 GLU B 494 MET B 513 1 20 SHEET 1 AA1 7 GLY A 168 LEU A 172 0 SHEET 2 AA1 7 THR A 339 VAL A 343 -1 O THR A 339 N LEU A 172 SHEET 3 AA1 7 SER A 323 MET A 326 -1 N ILE A 324 O TYR A 342 SHEET 4 AA1 7 TRP A 294 ASP A 298 1 N VAL A 297 O SER A 325 SHEET 5 AA1 7 VAL A 262 THR A 269 1 N ALA A 268 O ASP A 298 SHEET 6 AA1 7 LEU A 205 ALA A 210 1 N ALA A 206 O THR A 264 SHEET 7 AA1 7 ILE A 231 ILE A 234 1 O ARG A 232 N VAL A 207 SHEET 1 AA2 4 PHE A 425 VAL A 427 0 SHEET 2 AA2 4 LEU A 435 ILE A 440 -1 O ARG A 439 N GLU A 426 SHEET 3 AA2 4 ARG A 481 ALA A 487 -1 O LEU A 484 N PHE A 438 SHEET 4 AA2 4 HIS A 475 VAL A 478 -1 N THR A 476 O VAL A 483 SHEET 1 AA3 7 GLY B 168 LEU B 172 0 SHEET 2 AA3 7 THR B 339 VAL B 343 -1 O THR B 339 N LEU B 172 SHEET 3 AA3 7 SER B 323 MET B 326 -1 N ILE B 324 O TYR B 342 SHEET 4 AA3 7 TRP B 294 ASP B 298 1 N VAL B 297 O SER B 325 SHEET 5 AA3 7 VAL B 262 THR B 269 1 N ALA B 268 O ASP B 298 SHEET 6 AA3 7 LEU B 205 ALA B 210 1 N ALA B 206 O THR B 264 SHEET 7 AA3 7 ILE B 231 ILE B 234 1 O ILE B 234 N ALA B 209 SHEET 1 AA4 4 PHE B 425 VAL B 427 0 SHEET 2 AA4 4 LEU B 435 ILE B 440 -1 O ARG B 439 N GLU B 426 SHEET 3 AA4 4 ARG B 481 ALA B 487 -1 O LEU B 484 N PHE B 438 SHEET 4 AA4 4 HIS B 475 VAL B 478 -1 N THR B 476 O VAL B 483 LINK NZ LYS A 330 C4A PLP A 601 1555 1555 1.43 LINK OH TYR A 359 N1 TSS A 602 1555 1555 1.30 LINK OD1 ASP A 408 CA CA A 603 1555 1555 2.29 LINK NZ LYS B 330 C4A PLP B 601 1555 1555 1.43 LINK OD1 ASP B 408 CA CA B 602 1555 1555 2.39 LINK CA CA A 603 O HOH A 715 1555 1555 2.37 LINK CA CA A 603 O HOH A 727 1555 1555 2.43 LINK CA CA A 603 O HOH A 738 1555 1555 2.31 LINK CA CA A 603 O HOH A 746 1555 1555 2.62 LINK CA CA A 603 O HOH A 791 1555 1555 2.43 LINK CA CA A 603 O HOH A 853 1555 1555 2.50 LINK CA CA A 604 O HOH A 876 1555 1555 2.69 LINK CA CA A 604 O HOH A 871 1555 1555 2.59 LINK CA CA A 604 O HOH A 892 1555 1555 2.72 LINK CA CA B 602 O HOH B 803 1555 1555 2.62 LINK CA CA B 602 O HOH B 768 1555 1555 2.40 LINK CA CA B 602 O HOH B 791 1555 1555 2.48 LINK CA CA B 602 O HOH B 747 1555 1555 2.38 LINK CA CA B 602 O HOH B 708 1555 1555 2.40 LINK CA CA B 602 O HOH B 761 1555 1555 2.45 LINK CA CA B 603 O HOH A 701 1555 1555 2.54 LINK CA CA B 603 O HOH B 703 1555 1555 2.55 LINK CA CA B 603 O HOH A 885 1555 1555 2.61 LINK CA CA B 603 O HOH B 882 1555 1555 2.67 LINK CA CA A 604 O HOH B 895 1555 2565 3.09 LINK CA CA B 603 O HOH A 737 1555 6554 2.83 CISPEP 1 LEU A 336 ASP A 337 0 -1.12 CISPEP 2 LEU B 336 ASP B 337 0 -3.25 SITE 1 AC1 12 PHE A 104 THR A 174 THR A 175 SER A 176 SITE 2 AC1 12 HIS A 214 GLY A 271 ASP A 298 ALA A 300 SITE 3 AC1 12 LYS A 330 HOH A 732 VAL B 380 GLY B 381 SITE 1 AC2 9 VAL A 125 PHE A 127 TYR A 359 GLY A 381 SITE 2 AC2 9 PHE B 104 HIS B 214 HIS B 329 LYS B 330 SITE 3 AC2 9 PLP B 601 SITE 1 AC3 7 ASP A 408 HOH A 715 HOH A 727 HOH A 738 SITE 2 AC3 7 HOH A 746 HOH A 791 HOH A 853 SITE 1 AC4 4 HOH A 871 HOH A 876 HOH A 892 HOH B 895 SITE 1 AC5 4 PRO A 357 HIS B 214 SER B 215 HOH B 801 SITE 1 AC6 5 GLN A 23 PRO A 24 LEU A 25 ASN A 26 SITE 2 AC6 5 SER B 491 SITE 1 AC7 7 VAL A 140 LEU A 143 ASP A 144 PHE A 156 SITE 2 AC7 7 MET A 157 GLY A 169 TYR A 342 SITE 1 AC8 7 ASP B 408 HOH B 708 HOH B 747 HOH B 761 SITE 2 AC8 7 HOH B 768 HOH B 791 HOH B 803 SITE 1 AC9 6 ASP A 64 HOH A 701 HOH A 737 HOH A 885 SITE 2 AC9 6 HOH B 703 HOH B 882 SITE 1 AD1 2 GLU B 310 ARG B 406 SITE 1 AD2 20 VAL A 380 GLY A 381 TSS A 602 PHE B 104 SITE 2 AD2 20 PRO B 105 THR B 107 THR B 174 THR B 175 SITE 3 AD2 20 SER B 176 HIS B 214 THR B 273 ASP B 298 SITE 4 AD2 20 SER B 327 PRO B 328 HIS B 329 TRP B 331 SITE 5 AD2 20 LEU B 332 HOH B 753 HOH B 776 HOH B 813 CRYST1 155.769 155.769 102.094 90.00 90.00 120.00 P 31 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 0.006420 0.003706 0.000000 0.00000 SCALE2 0.000000 0.007413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009795 0.00000