HEADER LYASE 10-FEB-21 7NHE TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PDX1K166R-I333 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRIDOXAL 5'-PHOSPHATE SYNTHASE SUBUNIT PDX1.3; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: PLP SYNTHASE SUBUNIT PDX1.3; COMPND 5 EC: 4.3.3.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: PDX13, GIP2, PDX1L3, RSR4, AT5G01410, T10O8.120; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VITAMIN B6 BIOSYTHESIS, PLP SYNTHASE, PDX1, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.J.RODRIGUES,Y.ZHANG,R.BOLTON,G.EVANS,N.GIRI,A.ROYANT,T.BEGLEY, AUTHOR 2 S.E.EALICK,I.TEWS REVDAT 3 31-JAN-24 7NHE 1 REMARK REVDAT 2 13-APR-22 7NHE 1 JRNL REVDAT 1 22-DEC-21 7NHE 0 JRNL AUTH M.J.RODRIGUES,N.GIRI,A.ROYANT,Y.ZHANG,R.BOLTON,G.EVANS, JRNL AUTH 2 S.E.EALICK,T.BEGLEY,I.TEWS JRNL TITL TRAPPING AND STRUCTURAL CHARACTERISATION OF A COVALENT JRNL TITL 2 INTERMEDIATE IN VITAMIN B 6 BIOSYNTHESIS CATALYSED BY THE JRNL TITL 3 PDX1 PLP SYNTHASE. JRNL REF RSC CHEM BIOL V. 3 227 2022 JRNL REFN ESSN 2633-0679 JRNL PMID 35360887 JRNL DOI 10.1039/D1CB00160D REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 92.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.940 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 66314 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3316 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 92.2300 - 6.4200 0.99 2600 131 0.1398 0.1829 REMARK 3 2 6.4200 - 5.1000 1.00 2637 147 0.1769 0.2130 REMARK 3 3 5.0900 - 4.4500 0.99 2642 126 0.1447 0.1649 REMARK 3 4 4.4500 - 4.0400 1.00 2610 147 0.1353 0.1745 REMARK 3 5 4.0400 - 3.7500 1.00 2654 145 0.1488 0.1971 REMARK 3 6 3.7500 - 3.5300 0.99 2605 150 0.1638 0.2138 REMARK 3 7 3.5300 - 3.3600 1.00 2642 127 0.1708 0.2212 REMARK 3 8 3.3500 - 3.2100 1.00 2622 129 0.1789 0.2391 REMARK 3 9 3.2100 - 3.0900 1.00 2661 143 0.1882 0.2498 REMARK 3 10 3.0900 - 2.9800 1.00 2623 123 0.1923 0.2263 REMARK 3 11 2.9800 - 2.8900 1.00 2637 135 0.1876 0.2547 REMARK 3 12 2.8900 - 2.8000 0.99 2636 139 0.1884 0.2474 REMARK 3 13 2.8000 - 2.7300 0.99 2640 128 0.1848 0.2643 REMARK 3 14 2.7300 - 2.6600 0.99 2601 134 0.1869 0.2212 REMARK 3 15 2.6600 - 2.6000 0.99 2645 143 0.1946 0.2658 REMARK 3 16 2.6000 - 2.5500 0.99 2580 149 0.2042 0.2459 REMARK 3 17 2.5500 - 2.5000 0.99 2610 138 0.2092 0.2410 REMARK 3 18 2.5000 - 2.4500 1.00 2660 147 0.2101 0.2415 REMARK 3 19 2.4500 - 2.4100 0.99 2608 147 0.2159 0.2530 REMARK 3 20 2.4100 - 2.3600 0.99 2630 142 0.2332 0.2546 REMARK 3 21 2.3600 - 2.3300 0.99 2621 127 0.2351 0.2439 REMARK 3 22 2.3300 - 2.2900 0.99 2574 144 0.2532 0.3083 REMARK 3 23 2.2900 - 2.2600 0.99 2666 137 0.2578 0.3264 REMARK 3 24 2.2600 - 2.2300 0.99 2594 138 0.2752 0.3077 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.44 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 : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 21:301) REMARK 3 ORIGIN FOR THE GROUP (A): 14.7798 -35.6248 -16.1760 REMARK 3 T TENSOR REMARK 3 T11: 0.2812 T22: 0.2187 REMARK 3 T33: 0.7616 T12: 0.0008 REMARK 3 T13: -0.0222 T23: 0.0483 REMARK 3 L TENSOR REMARK 3 L11: 1.1116 L22: 0.3067 REMARK 3 L33: 0.6000 L12: -0.0248 REMARK 3 L13: -0.0898 L23: -0.2462 REMARK 3 S TENSOR REMARK 3 S11: -0.0202 S12: -0.1380 S13: -0.1197 REMARK 3 S21: 0.1138 S22: -0.0221 S23: -0.0603 REMARK 3 S31: -0.0668 S32: -0.0181 S33: 0.0412 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESSEQ 22:301) REMARK 3 ORIGIN FOR THE GROUP (A): -23.3027 -30.6973 -16.2605 REMARK 3 T TENSOR REMARK 3 T11: 0.2733 T22: 0.2553 REMARK 3 T33: 0.8201 T12: 0.0163 REMARK 3 T13: 0.0578 T23: 0.0530 REMARK 3 L TENSOR REMARK 3 L11: 0.8028 L22: 0.9119 REMARK 3 L33: 0.5407 L12: -0.4381 REMARK 3 L13: 0.1394 L23: -0.1960 REMARK 3 S TENSOR REMARK 3 S11: -0.0919 S12: -0.1454 S13: -0.1107 REMARK 3 S21: 0.2063 S22: 0.0945 S23: 0.1619 REMARK 3 S31: -0.0127 S32: -0.0608 S33: -0.0002 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN C AND RESSEQ 21:301) REMARK 3 ORIGIN FOR THE GROUP (A): -9.6427 -37.3681 -60.5992 REMARK 3 T TENSOR REMARK 3 T11: 0.2663 T22: 0.3108 REMARK 3 T33: 0.7873 T12: 0.0025 REMARK 3 T13: -0.0077 T23: -0.1196 REMARK 3 L TENSOR REMARK 3 L11: 1.6620 L22: 0.5510 REMARK 3 L33: 0.9498 L12: -0.0401 REMARK 3 L13: 0.4944 L23: 0.0197 REMARK 3 S TENSOR REMARK 3 S11: -0.0038 S12: 0.3288 S13: -0.1963 REMARK 3 S21: -0.1295 S22: -0.0049 S23: 0.0286 REMARK 3 S31: 0.0697 S32: 0.0655 S33: 0.0104 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN D AND RESSEQ 23:301) REMARK 3 ORIGIN FOR THE GROUP (A): 27.5168 -26.8479 -60.6487 REMARK 3 T TENSOR REMARK 3 T11: 0.2822 T22: 0.2968 REMARK 3 T33: 0.7482 T12: 0.0311 REMARK 3 T13: 0.0670 T23: -0.0491 REMARK 3 L TENSOR REMARK 3 L11: 0.5310 L22: 0.9578 REMARK 3 L33: 0.4268 L12: 0.4575 REMARK 3 L13: -0.1839 L23: 0.2244 REMARK 3 S TENSOR REMARK 3 S11: -0.0727 S12: 0.1730 S13: -0.0914 REMARK 3 S21: -0.2243 S22: 0.0465 S23: -0.1228 REMARK 3 S31: -0.0480 S32: -0.0240 S33: 0.0250 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 7NHE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292108985. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980023 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66508 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 92.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.88600 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5LNU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28.1% PEG 1000 (W/V) AND 100 MM HEPES REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 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 1.000000 0.000000 0.000000 88.98650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 51.37638 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.37367 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 88.98650 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 51.37638 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 38.37367 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 88.98650 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 51.37638 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.37367 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 102.75276 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 76.74733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 102.75276 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 76.74733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 102.75276 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 76.74733 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 2 REMARK 465 GLU A 3 REMARK 465 GLY A 4 REMARK 465 THR A 5 REMARK 465 GLY A 6 REMARK 465 VAL A 7 REMARK 465 VAL A 8 REMARK 465 ALA A 9 REMARK 465 VAL A 10 REMARK 465 TYR A 11 REMARK 465 GLY A 12 REMARK 465 ASN A 13 REMARK 465 GLY A 14 REMARK 465 ALA A 15 REMARK 465 ILE A 16 REMARK 465 THR A 17 REMARK 465 GLU A 18 REMARK 465 ALA A 19 REMARK 465 LYS A 20 REMARK 465 MET B 2 REMARK 465 GLU B 3 REMARK 465 GLY B 4 REMARK 465 THR B 5 REMARK 465 GLY B 6 REMARK 465 VAL B 7 REMARK 465 VAL B 8 REMARK 465 ALA B 9 REMARK 465 VAL B 10 REMARK 465 TYR B 11 REMARK 465 GLY B 12 REMARK 465 ASN B 13 REMARK 465 GLY B 14 REMARK 465 ALA B 15 REMARK 465 ILE B 16 REMARK 465 THR B 17 REMARK 465 GLU B 18 REMARK 465 ALA B 19 REMARK 465 LYS B 20 REMARK 465 LYS B 21 REMARK 465 MET C 2 REMARK 465 GLU C 3 REMARK 465 GLY C 4 REMARK 465 THR C 5 REMARK 465 GLY C 6 REMARK 465 VAL C 7 REMARK 465 VAL C 8 REMARK 465 ALA C 9 REMARK 465 VAL C 10 REMARK 465 TYR C 11 REMARK 465 GLY C 12 REMARK 465 ASN C 13 REMARK 465 GLY C 14 REMARK 465 ALA C 15 REMARK 465 ILE C 16 REMARK 465 THR C 17 REMARK 465 GLU C 18 REMARK 465 ALA C 19 REMARK 465 LYS C 20 REMARK 465 MET C 292 REMARK 465 MET D 2 REMARK 465 GLU D 3 REMARK 465 GLY D 4 REMARK 465 THR D 5 REMARK 465 GLY D 6 REMARK 465 VAL D 7 REMARK 465 VAL D 8 REMARK 465 ALA D 9 REMARK 465 VAL D 10 REMARK 465 TYR D 11 REMARK 465 GLY D 12 REMARK 465 ASN D 13 REMARK 465 GLY D 14 REMARK 465 ALA D 15 REMARK 465 ILE D 16 REMARK 465 THR D 17 REMARK 465 GLU D 18 REMARK 465 ALA D 19 REMARK 465 LYS D 20 REMARK 465 LYS D 21 REMARK 465 SER D 22 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 A 21 CG CD CE NZ REMARK 470 SER B 22 OG REMARK 470 GLU B 46 CG CD OE1 OE2 REMARK 470 GLN B 218 CG CD OE1 NE2 REMARK 470 GLU B 279 CG CD OE1 OE2 REMARK 470 LYS C 21 CG CD CE NZ REMARK 470 LYS C 257 CG CD CE NZ REMARK 470 GLU C 290 CG CD OE1 OE2 REMARK 470 GLU D 46 CG CD OE1 OE2 REMARK 470 GLU D 283 CG CD OE1 OE2 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 LYS A 257 35.92 -88.44 REMARK 500 ILE B 255 -60.38 -91.90 REMARK 500 HIS B 274 51.28 -119.04 REMARK 500 ILE C 255 -60.98 -102.05 REMARK 500 HIS C 274 54.57 -116.59 REMARK 500 PRO D 223 0.52 -68.90 REMARK 500 ILE D 255 -63.27 -93.01 REMARK 500 REMARK 500 REMARK: NULL DBREF 7NHE A 2 292 UNP Q8L940 PDX13_ARATH 1 291 DBREF 7NHE B 2 292 UNP Q8L940 PDX13_ARATH 1 291 DBREF 7NHE C 2 292 UNP Q8L940 PDX13_ARATH 1 291 DBREF 7NHE D 2 292 UNP Q8L940 PDX13_ARATH 1 291 SEQADV 7NHE ARG A 166 UNP Q8L940 LYS 165 ENGINEERED MUTATION SEQADV 7NHE ARG B 166 UNP Q8L940 LYS 165 ENGINEERED MUTATION SEQADV 7NHE ARG C 166 UNP Q8L940 LYS 165 ENGINEERED MUTATION SEQADV 7NHE ARG D 166 UNP Q8L940 LYS 165 ENGINEERED MUTATION SEQRES 1 A 291 MET GLU GLY THR GLY VAL VAL ALA VAL TYR GLY ASN GLY SEQRES 2 A 291 ALA ILE THR GLU ALA LYS LYS SER PRO PHE SER VAL LYS SEQRES 3 A 291 VAL GLY LEU ALA GLN MET LEU ARG GLY GLY VAL ILE MET SEQRES 4 A 291 ASP VAL VAL ASN ALA GLU GLN ALA ARG ILE ALA GLU GLU SEQRES 5 A 291 ALA GLY ALA CYS ALA VAL MET ALA LEU GLU ARG VAL PRO SEQRES 6 A 291 ALA ASP ILE ARG ALA GLN GLY GLY VAL ALA ARG MET SER SEQRES 7 A 291 ASP PRO GLN MET ILE LYS GLU ILE LYS GLN ALA VAL THR SEQRES 8 A 291 ILE PRO VAL MET ALA LYS ALA ARG ILE GLY HIS PHE VAL SEQRES 9 A 291 GLU ALA GLN ILE LEU GLU ALA ILE GLY ILE ASP TYR ILE SEQRES 10 A 291 ASP GLU SER GLU VAL LEU THR LEU ALA ASP GLU ASP HIS SEQRES 11 A 291 HIS ILE ASN LYS HIS ASN PHE ARG ILE PRO PHE VAL CYS SEQRES 12 A 291 GLY CYS ARG ASN LEU GLY GLU ALA LEU ARG ARG ILE ARG SEQRES 13 A 291 GLU GLY ALA ALA MET ILE ARG THR ARG GLY GLU ALA GLY SEQRES 14 A 291 THR GLY ASN ILE ILE GLU ALA VAL ARG HIS VAL ARG SER SEQRES 15 A 291 VAL ASN GLY ASP ILE ARG VAL LEU ARG ASN MET ASP ASP SEQRES 16 A 291 ASP GLU VAL PHE THR PHE ALA LYS LYS LEU ALA ALA PRO SEQRES 17 A 291 TYR ASP LEU VAL MET GLN THR LYS GLN LEU GLY ARG LEU SEQRES 18 A 291 PRO VAL VAL GLN PHE ALA ALA GLY GLY VAL ALA THR PRO SEQRES 19 A 291 ALA ASP ALA ALA LEU MET MET GLN LEU GLY CYS ASP GLY SEQRES 20 A 291 VAL PHE VAL GLY SER GLY ILE PHE LYS SER GLY ASP PRO SEQRES 21 A 291 ALA ARG ARG ALA ARG ALA ILE VAL GLN ALA VAL THR HIS SEQRES 22 A 291 TYR SER ASP PRO GLU MET LEU VAL GLU VAL SER CYS GLY SEQRES 23 A 291 LEU GLY GLU ALA MET SEQRES 1 B 291 MET GLU GLY THR GLY VAL VAL ALA VAL TYR GLY ASN GLY SEQRES 2 B 291 ALA ILE THR GLU ALA LYS LYS SER PRO PHE SER VAL LYS SEQRES 3 B 291 VAL GLY LEU ALA GLN MET LEU ARG GLY GLY VAL ILE MET SEQRES 4 B 291 ASP VAL VAL ASN ALA GLU GLN ALA ARG ILE ALA GLU GLU SEQRES 5 B 291 ALA GLY ALA CYS ALA VAL MET ALA LEU GLU ARG VAL PRO SEQRES 6 B 291 ALA ASP ILE ARG ALA GLN GLY GLY VAL ALA ARG MET SER SEQRES 7 B 291 ASP PRO GLN MET ILE LYS GLU ILE LYS GLN ALA VAL THR SEQRES 8 B 291 ILE PRO VAL MET ALA LYS ALA ARG ILE GLY HIS PHE VAL SEQRES 9 B 291 GLU ALA GLN ILE LEU GLU ALA ILE GLY ILE ASP TYR ILE SEQRES 10 B 291 ASP GLU SER GLU VAL LEU THR LEU ALA ASP GLU ASP HIS SEQRES 11 B 291 HIS ILE ASN LYS HIS ASN PHE ARG ILE PRO PHE VAL CYS SEQRES 12 B 291 GLY CYS ARG ASN LEU GLY GLU ALA LEU ARG ARG ILE ARG SEQRES 13 B 291 GLU GLY ALA ALA MET ILE ARG THR ARG GLY GLU ALA GLY SEQRES 14 B 291 THR GLY ASN ILE ILE GLU ALA VAL ARG HIS VAL ARG SER SEQRES 15 B 291 VAL ASN GLY ASP ILE ARG VAL LEU ARG ASN MET ASP ASP SEQRES 16 B 291 ASP GLU VAL PHE THR PHE ALA LYS LYS LEU ALA ALA PRO SEQRES 17 B 291 TYR ASP LEU VAL MET GLN THR LYS GLN LEU GLY ARG LEU SEQRES 18 B 291 PRO VAL VAL GLN PHE ALA ALA GLY GLY VAL ALA THR PRO SEQRES 19 B 291 ALA ASP ALA ALA LEU MET MET GLN LEU GLY CYS ASP GLY SEQRES 20 B 291 VAL PHE VAL GLY SER GLY ILE PHE LYS SER GLY ASP PRO SEQRES 21 B 291 ALA ARG ARG ALA ARG ALA ILE VAL GLN ALA VAL THR HIS SEQRES 22 B 291 TYR SER ASP PRO GLU MET LEU VAL GLU VAL SER CYS GLY SEQRES 23 B 291 LEU GLY GLU ALA MET SEQRES 1 C 291 MET GLU GLY THR GLY VAL VAL ALA VAL TYR GLY ASN GLY SEQRES 2 C 291 ALA ILE THR GLU ALA LYS LYS SER PRO PHE SER VAL LYS SEQRES 3 C 291 VAL GLY LEU ALA GLN MET LEU ARG GLY GLY VAL ILE MET SEQRES 4 C 291 ASP VAL VAL ASN ALA GLU GLN ALA ARG ILE ALA GLU GLU SEQRES 5 C 291 ALA GLY ALA CYS ALA VAL MET ALA LEU GLU ARG VAL PRO SEQRES 6 C 291 ALA ASP ILE ARG ALA GLN GLY GLY VAL ALA ARG MET SER SEQRES 7 C 291 ASP PRO GLN MET ILE LYS GLU ILE LYS GLN ALA VAL THR SEQRES 8 C 291 ILE PRO VAL MET ALA LYS ALA ARG ILE GLY HIS PHE VAL SEQRES 9 C 291 GLU ALA GLN ILE LEU GLU ALA ILE GLY ILE ASP TYR ILE SEQRES 10 C 291 ASP GLU SER GLU VAL LEU THR LEU ALA ASP GLU ASP HIS SEQRES 11 C 291 HIS ILE ASN LYS HIS ASN PHE ARG ILE PRO PHE VAL CYS SEQRES 12 C 291 GLY CYS ARG ASN LEU GLY GLU ALA LEU ARG ARG ILE ARG SEQRES 13 C 291 GLU GLY ALA ALA MET ILE ARG THR ARG GLY GLU ALA GLY SEQRES 14 C 291 THR GLY ASN ILE ILE GLU ALA VAL ARG HIS VAL ARG SER SEQRES 15 C 291 VAL ASN GLY ASP ILE ARG VAL LEU ARG ASN MET ASP ASP SEQRES 16 C 291 ASP GLU VAL PHE THR PHE ALA LYS LYS LEU ALA ALA PRO SEQRES 17 C 291 TYR ASP LEU VAL MET GLN THR LYS GLN LEU GLY ARG LEU SEQRES 18 C 291 PRO VAL VAL GLN PHE ALA ALA GLY GLY VAL ALA THR PRO SEQRES 19 C 291 ALA ASP ALA ALA LEU MET MET GLN LEU GLY CYS ASP GLY SEQRES 20 C 291 VAL PHE VAL GLY SER GLY ILE PHE LYS SER GLY ASP PRO SEQRES 21 C 291 ALA ARG ARG ALA ARG ALA ILE VAL GLN ALA VAL THR HIS SEQRES 22 C 291 TYR SER ASP PRO GLU MET LEU VAL GLU VAL SER CYS GLY SEQRES 23 C 291 LEU GLY GLU ALA MET SEQRES 1 D 291 MET GLU GLY THR GLY VAL VAL ALA VAL TYR GLY ASN GLY SEQRES 2 D 291 ALA ILE THR GLU ALA LYS LYS SER PRO PHE SER VAL LYS SEQRES 3 D 291 VAL GLY LEU ALA GLN MET LEU ARG GLY GLY VAL ILE MET SEQRES 4 D 291 ASP VAL VAL ASN ALA GLU GLN ALA ARG ILE ALA GLU GLU SEQRES 5 D 291 ALA GLY ALA CYS ALA VAL MET ALA LEU GLU ARG VAL PRO SEQRES 6 D 291 ALA ASP ILE ARG ALA GLN GLY GLY VAL ALA ARG MET SER SEQRES 7 D 291 ASP PRO GLN MET ILE LYS GLU ILE LYS GLN ALA VAL THR SEQRES 8 D 291 ILE PRO VAL MET ALA LYS ALA ARG ILE GLY HIS PHE VAL SEQRES 9 D 291 GLU ALA GLN ILE LEU GLU ALA ILE GLY ILE ASP TYR ILE SEQRES 10 D 291 ASP GLU SER GLU VAL LEU THR LEU ALA ASP GLU ASP HIS SEQRES 11 D 291 HIS ILE ASN LYS HIS ASN PHE ARG ILE PRO PHE VAL CYS SEQRES 12 D 291 GLY CYS ARG ASN LEU GLY GLU ALA LEU ARG ARG ILE ARG SEQRES 13 D 291 GLU GLY ALA ALA MET ILE ARG THR ARG GLY GLU ALA GLY SEQRES 14 D 291 THR GLY ASN ILE ILE GLU ALA VAL ARG HIS VAL ARG SER SEQRES 15 D 291 VAL ASN GLY ASP ILE ARG VAL LEU ARG ASN MET ASP ASP SEQRES 16 D 291 ASP GLU VAL PHE THR PHE ALA LYS LYS LEU ALA ALA PRO SEQRES 17 D 291 TYR ASP LEU VAL MET GLN THR LYS GLN LEU GLY ARG LEU SEQRES 18 D 291 PRO VAL VAL GLN PHE ALA ALA GLY GLY VAL ALA THR PRO SEQRES 19 D 291 ALA ASP ALA ALA LEU MET MET GLN LEU GLY CYS ASP GLY SEQRES 20 D 291 VAL PHE VAL GLY SER GLY ILE PHE LYS SER GLY ASP PRO SEQRES 21 D 291 ALA ARG ARG ALA ARG ALA ILE VAL GLN ALA VAL THR HIS SEQRES 22 D 291 TYR SER ASP PRO GLU MET LEU VAL GLU VAL SER CYS GLY SEQRES 23 D 291 LEU GLY GLU ALA MET HET PO4 A 301 5 HET KPR A 302 12 HET PO4 B 301 5 HET KPR B 302 12 HET PO4 C 301 5 HET KPR C 302 12 HET PO4 D 301 5 HET KPR D 302 12 HETNAM PO4 PHOSPHATE ION HETNAM KPR [(~{E},4~{S})-4-AZANYL-3-OXIDANYLIDENE-PENT-1-ENYL] HETNAM 2 KPR DIHYDROGEN PHOSPHATE FORMUL 5 PO4 4(O4 P 3-) FORMUL 6 KPR 4(C5 H10 N O5 P) FORMUL 13 HOH *435(H2 O) HELIX 1 AA1 SER A 22 GLN A 32 1 11 HELIX 2 AA2 MET A 33 ARG A 35 5 3 HELIX 3 AA3 ASN A 44 ALA A 54 1 11 HELIX 4 AA4 VAL A 65 GLY A 73 1 9 HELIX 5 AA5 ASP A 80 VAL A 91 1 12 HELIX 6 AA6 HIS A 103 GLY A 114 1 12 HELIX 7 AA7 ASN A 134 PHE A 138 5 5 HELIX 8 AA8 ASN A 148 GLU A 158 1 11 HELIX 9 AA9 ILE A 174 MET A 194 1 21 HELIX 10 AB1 ASP A 195 ASP A 197 5 3 HELIX 11 AB2 GLU A 198 ALA A 207 1 10 HELIX 12 AB3 PRO A 209 GLY A 220 1 12 HELIX 13 AB4 THR A 234 LEU A 244 1 11 HELIX 14 AB5 GLY A 252 LYS A 257 1 6 HELIX 15 AB6 ASP A 260 HIS A 274 1 15 HELIX 16 AB7 ASP A 277 CYS A 286 1 10 HELIX 17 AB8 PRO B 23 MET B 33 1 11 HELIX 18 AB9 ASN B 44 ALA B 54 1 11 HELIX 19 AC1 VAL B 65 GLY B 73 1 9 HELIX 20 AC2 ASP B 80 VAL B 91 1 12 HELIX 21 AC3 HIS B 103 GLY B 114 1 12 HELIX 22 AC4 ASN B 134 PHE B 138 5 5 HELIX 23 AC5 ASN B 148 GLY B 159 1 12 HELIX 24 AC6 ILE B 174 MET B 194 1 21 HELIX 25 AC7 ASP B 195 ASP B 197 5 3 HELIX 26 AC8 GLU B 198 ALA B 207 1 10 HELIX 27 AC9 PRO B 209 GLY B 220 1 12 HELIX 28 AD1 THR B 234 LEU B 244 1 11 HELIX 29 AD2 GLY B 252 LYS B 257 1 6 HELIX 30 AD3 ASP B 260 HIS B 274 1 15 HELIX 31 AD4 ASP B 277 CYS B 286 1 10 HELIX 32 AD5 SER C 22 MET C 33 1 12 HELIX 33 AD6 ASN C 44 GLY C 55 1 12 HELIX 34 AD7 VAL C 65 GLY C 73 1 9 HELIX 35 AD8 ASP C 80 VAL C 91 1 12 HELIX 36 AD9 HIS C 103 GLY C 114 1 12 HELIX 37 AE1 ASN C 134 PHE C 138 5 5 HELIX 38 AE2 ASN C 148 GLU C 158 1 11 HELIX 39 AE3 ILE C 174 MET C 194 1 21 HELIX 40 AE4 ASP C 195 ASP C 197 5 3 HELIX 41 AE5 GLU C 198 ALA C 207 1 10 HELIX 42 AE6 PRO C 209 GLY C 220 1 12 HELIX 43 AE7 THR C 234 LEU C 244 1 11 HELIX 44 AE8 GLY C 252 LYS C 257 1 6 HELIX 45 AE9 ASP C 260 HIS C 274 1 15 HELIX 46 AF1 ASP C 277 CYS C 286 1 10 HELIX 47 AF2 PHE D 24 GLN D 32 1 9 HELIX 48 AF3 MET D 33 ARG D 35 5 3 HELIX 49 AF4 ASN D 44 GLY D 55 1 12 HELIX 50 AF5 VAL D 65 GLY D 73 1 9 HELIX 51 AF6 ASP D 80 ALA D 90 1 11 HELIX 52 AF7 HIS D 103 GLY D 114 1 12 HELIX 53 AF8 ASN D 134 PHE D 138 5 5 HELIX 54 AF9 ASN D 148 GLU D 158 1 11 HELIX 55 AG1 ILE D 174 MET D 194 1 21 HELIX 56 AG2 ASP D 195 ASP D 197 5 3 HELIX 57 AG3 GLU D 198 ALA D 207 1 10 HELIX 58 AG4 PRO D 209 GLY D 220 1 12 HELIX 59 AG5 THR D 234 LEU D 244 1 11 HELIX 60 AG6 GLY D 252 LYS D 257 1 6 HELIX 61 AG7 ASP D 260 HIS D 274 1 15 HELIX 62 AG8 ASP D 277 CYS D 286 1 10 SHEET 1 AA1 8 VAL A 225 PHE A 227 0 SHEET 2 AA1 8 MET A 162 THR A 165 1 N ILE A 163 O VAL A 225 SHEET 3 AA1 8 PHE A 142 CYS A 146 1 N CYS A 144 O ARG A 164 SHEET 4 AA1 8 TYR A 117 SER A 121 1 N ILE A 118 O VAL A 143 SHEET 5 AA1 8 VAL A 95 ARG A 100 1 N ALA A 97 O ASP A 119 SHEET 6 AA1 8 ALA A 58 ALA A 61 1 N VAL A 59 O MET A 96 SHEET 7 AA1 8 GLY A 37 VAL A 42 1 N MET A 40 O MET A 60 SHEET 8 AA1 8 GLY A 248 VAL A 251 1 O VAL A 251 N ILE A 39 SHEET 1 AA2 8 VAL B 225 PHE B 227 0 SHEET 2 AA2 8 MET B 162 THR B 165 1 N ILE B 163 O PHE B 227 SHEET 3 AA2 8 PHE B 142 CYS B 146 1 N CYS B 144 O ARG B 164 SHEET 4 AA2 8 TYR B 117 SER B 121 1 N ILE B 118 O VAL B 143 SHEET 5 AA2 8 VAL B 95 ARG B 100 1 N ALA B 97 O ASP B 119 SHEET 6 AA2 8 ALA B 58 ALA B 61 1 N ALA B 61 O MET B 96 SHEET 7 AA2 8 VAL B 38 VAL B 42 1 N MET B 40 O MET B 60 SHEET 8 AA2 8 VAL B 249 VAL B 251 1 O VAL B 251 N ILE B 39 SHEET 1 AA3 9 VAL C 38 VAL C 42 0 SHEET 2 AA3 9 ALA C 58 ALA C 61 1 O MET C 60 N MET C 40 SHEET 3 AA3 9 VAL C 95 ARG C 100 1 O MET C 96 N VAL C 59 SHEET 4 AA3 9 TYR C 117 SER C 121 1 O ASP C 119 N ALA C 97 SHEET 5 AA3 9 PHE C 142 CYS C 146 1 O VAL C 143 N ILE C 118 SHEET 6 AA3 9 MET C 162 THR C 165 1 O ARG C 164 N CYS C 144 SHEET 7 AA3 9 VAL C 225 ALA C 228 1 O VAL C 225 N ILE C 163 SHEET 8 AA3 9 GLY C 248 VAL C 251 1 O PHE C 250 N ALA C 228 SHEET 9 AA3 9 VAL C 38 VAL C 42 1 N ILE C 39 O VAL C 251 SHEET 1 AA4 8 VAL D 225 PHE D 227 0 SHEET 2 AA4 8 MET D 162 THR D 165 1 N ILE D 163 O PHE D 227 SHEET 3 AA4 8 PHE D 142 CYS D 146 1 N CYS D 144 O ARG D 164 SHEET 4 AA4 8 TYR D 117 SER D 121 1 N ILE D 118 O VAL D 143 SHEET 5 AA4 8 VAL D 95 ARG D 100 1 N ALA D 97 O ASP D 119 SHEET 6 AA4 8 ALA D 58 ALA D 61 1 N VAL D 59 O MET D 96 SHEET 7 AA4 8 VAL D 38 VAL D 42 1 N MET D 40 O MET D 60 SHEET 8 AA4 8 VAL D 249 VAL D 251 1 O VAL D 249 N ILE D 39 LINK NZ LYS A 98 C1 KPR A 302 1555 1555 1.45 LINK NZ LYS B 98 C1 KPR B 302 1555 1555 1.46 LINK NZ LYS C 98 C1 KPR C 302 1555 1555 1.46 LINK NZ LYS D 98 C1 KPR D 302 1555 1555 1.46 CRYST1 177.973 177.973 115.121 90.00 90.00 120.00 H 3 36 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 0.005619 0.003244 0.000000 0.00000 SCALE2 0.000000 0.006488 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008687 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.502052 -0.864828 -0.003946 0.06596 1 MTRIX2 2 0.864819 0.502066 -0.004235 -0.10943 1 MTRIX3 2 0.005644 -0.001286 0.999983 0.05130 1 MTRIX1 3 -0.989735 -0.142853 0.004106 0.35655 1 MTRIX2 3 -0.142843 0.989742 0.002572 0.14713 1 MTRIX3 3 -0.004431 0.001959 -0.999988 -76.84097 1 MTRIX1 4 -0.370975 -0.928638 0.003082 0.22638 1 MTRIX2 4 -0.928643 0.370976 -0.000463 -0.00106 1 MTRIX3 4 -0.000714 -0.003034 -0.999995 -76.89907 1