HEADER HYDROLASE 26-OCT-22 8HAV TITLE AN AUTO-ACTIVATION MECHANISM OF PLANT NON-SPECIFIC PHOSPHOLIPASE C COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-SPECIFIC PHOSPHOLIPASE C4; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.4.3; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: NPC4, AT3G03530, T21P5.5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NPC4, GLYCOSYLINOSITOLPHOSPHORYLCERAMIDE, PHOSPHATIDYLCHOLINE, KEYWDS 2 PHOSPHATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.ZHAO,R.Y.FAN,Z.Y.GUAN,L.GUO,P.YIN REVDAT 1 25-JAN-23 8HAV 0 JRNL AUTH R.FAN,F.ZHAO,Z.GONG,Y.CHEN,B.YANG,C.ZHOU,J.ZHANG,Z.DU, JRNL AUTH 2 X.WANG,P.YIN,L.GUO,Z.LIU JRNL TITL INSIGHTS INTO THE MECHANISM OF PHOSPHOLIPID HYDROLYSIS BY JRNL TITL 2 PLANT NON-SPECIFIC PHOSPHOLIPASE C. JRNL REF NAT COMMUN V. 14 194 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 36635324 JRNL DOI 10.1038/S41467-023-35915-4 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19RC5_4047 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 66897 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 44.0200 - 5.0600 1.00 4925 152 0.1749 0.1936 REMARK 3 2 5.0600 - 4.0200 1.00 4731 146 0.1491 0.1464 REMARK 3 3 4.0200 - 3.5100 1.00 4664 143 0.1713 0.1974 REMARK 3 4 3.5100 - 3.1900 1.00 4674 144 0.1819 0.2236 REMARK 3 5 3.1900 - 2.9600 1.00 4604 143 0.2018 0.2353 REMARK 3 6 2.9600 - 2.7900 1.00 4632 142 0.1999 0.2335 REMARK 3 7 2.7900 - 2.6500 1.00 4621 143 0.1969 0.2456 REMARK 3 8 2.6500 - 2.5300 1.00 4588 140 0.1930 0.2077 REMARK 3 9 2.5300 - 2.4300 1.00 4605 143 0.1906 0.2304 REMARK 3 10 2.4300 - 2.3500 1.00 4578 141 0.1979 0.2551 REMARK 3 11 2.3500 - 2.2800 1.00 4565 141 0.2043 0.2262 REMARK 3 12 2.2800 - 2.2100 1.00 4571 141 0.2048 0.2500 REMARK 3 13 2.2100 - 2.1500 1.00 4603 142 0.2011 0.2891 REMARK 3 14 2.1500 - 2.1000 1.00 4536 139 0.2120 0.2439 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) : 0.202 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.244 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.25 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 : 0.008 6613 REMARK 3 ANGLE : 1.031 9004 REMARK 3 CHIRALITY : 0.079 934 REMARK 3 PLANARITY : 0.009 1188 REMARK 3 DIHEDRAL : 6.582 865 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 : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and resid 12 through 415) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : chain "B" REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8HAV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1300033189. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.0 - 8.0 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) : 0.98 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 : 78362 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.88 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.49 REMARK 200 R MERGE FOR SHELL (I) : 0.40600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 51.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, PEG 3350, MAGNESIUM CHLORIDE REMARK 280 POTASSIUM SODIUM TARTRATE TETRAHYDRATE, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 290K 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 29.52750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.69150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 60.72050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 78.69150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.52750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 60.72050 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: 2150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 ILE A 2 REMARK 465 GLU A 3 REMARK 465 THR A 4 REMARK 465 THR A 5 REMARK 465 LYS A 6 REMARK 465 GLY A 7 REMARK 465 GLY A 8 REMARK 465 SER A 9 REMARK 465 GLY A 10 REMARK 465 SER A 11 REMARK 465 PRO A 259 REMARK 465 ALA A 260 REMARK 465 ASN A 261 REMARK 465 ASP A 262 REMARK 465 ASP A 263 REMARK 465 LYS A 416 REMARK 465 LEU A 417 REMARK 465 ARG A 418 REMARK 465 GLY A 419 REMARK 465 THR A 420 REMARK 465 MET A 421 REMARK 465 ALA A 422 REMARK 465 LYS A 423 REMARK 465 GLU A 424 REMARK 465 ASN A 425 REMARK 465 ALA A 426 REMARK 465 GLN A 427 REMARK 465 LEU A 428 REMARK 465 SER A 429 REMARK 465 GLU A 430 REMARK 465 PHE A 431 REMARK 465 GLN A 432 REMARK 465 GLU A 433 REMARK 465 ASP A 434 REMARK 465 LEU A 435 REMARK 465 VAL A 436 REMARK 465 ILE A 437 REMARK 465 MET A 438 REMARK 465 ALA A 439 REMARK 465 ALA A 440 REMARK 465 GLY A 441 REMARK 465 LEU A 442 REMARK 465 LYS A 443 REMARK 465 GLY A 444 REMARK 465 ASP A 445 REMARK 465 TYR A 446 REMARK 465 LYS A 447 REMARK 465 ASN A 448 REMARK 465 GLU A 449 REMARK 465 GLU A 450 REMARK 465 LEU A 451 REMARK 465 ILE A 452 REMARK 465 HIS A 453 REMARK 465 LYS A 454 REMARK 465 LEU A 455 REMARK 465 CYS A 456 REMARK 465 LYS A 457 REMARK 465 GLU A 458 REMARK 465 THR A 459 REMARK 465 CYS A 460 REMARK 465 VAL A 461 REMARK 465 ALA A 462 REMARK 465 ASP A 463 REMARK 465 ALA A 464 REMARK 465 SER A 465 REMARK 465 LYS A 466 REMARK 465 TYR A 467 REMARK 465 VAL A 468 REMARK 465 THR A 469 REMARK 465 ASN A 470 REMARK 465 ALA A 471 REMARK 465 PHE A 472 REMARK 465 GLU A 473 REMARK 465 LYS A 474 REMARK 465 PHE A 475 REMARK 465 LEU A 476 REMARK 465 GLU A 477 REMARK 465 GLU A 478 REMARK 465 SER A 479 REMARK 465 ARG A 480 REMARK 465 LYS A 481 REMARK 465 ALA A 482 REMARK 465 ARG A 483 REMARK 465 ASP A 484 REMARK 465 ARG A 485 REMARK 465 GLY A 486 REMARK 465 CYS A 487 REMARK 465 ASP A 488 REMARK 465 GLU A 489 REMARK 465 ASN A 490 REMARK 465 ASP A 491 REMARK 465 ILE A 492 REMARK 465 VAL A 493 REMARK 465 TYR A 494 REMARK 465 MET B 1 REMARK 465 ILE B 2 REMARK 465 GLU B 3 REMARK 465 THR B 4 REMARK 465 THR B 5 REMARK 465 LYS B 6 REMARK 465 GLY B 7 REMARK 465 GLY B 8 REMARK 465 SER B 9 REMARK 465 GLY B 10 REMARK 465 SER B 11 REMARK 465 PRO B 259 REMARK 465 ALA B 260 REMARK 465 ASN B 261 REMARK 465 ASP B 262 REMARK 465 ASP B 263 REMARK 465 LYS B 416 REMARK 465 LEU B 417 REMARK 465 ARG B 418 REMARK 465 GLY B 419 REMARK 465 THR B 420 REMARK 465 MET B 421 REMARK 465 ALA B 422 REMARK 465 LYS B 423 REMARK 465 GLU B 424 REMARK 465 ASN B 425 REMARK 465 ALA B 426 REMARK 465 GLN B 427 REMARK 465 LEU B 428 REMARK 465 SER B 429 REMARK 465 GLU B 430 REMARK 465 PHE B 431 REMARK 465 GLN B 432 REMARK 465 GLU B 433 REMARK 465 ASP B 434 REMARK 465 LEU B 435 REMARK 465 VAL B 436 REMARK 465 ILE B 437 REMARK 465 MET B 438 REMARK 465 ALA B 439 REMARK 465 ALA B 440 REMARK 465 GLY B 441 REMARK 465 LEU B 442 REMARK 465 LYS B 443 REMARK 465 GLY B 444 REMARK 465 ASP B 445 REMARK 465 TYR B 446 REMARK 465 LYS B 447 REMARK 465 ASN B 448 REMARK 465 GLU B 449 REMARK 465 GLU B 450 REMARK 465 LEU B 451 REMARK 465 ILE B 452 REMARK 465 HIS B 453 REMARK 465 LYS B 454 REMARK 465 LEU B 455 REMARK 465 CYS B 456 REMARK 465 LYS B 457 REMARK 465 GLU B 458 REMARK 465 THR B 459 REMARK 465 CYS B 460 REMARK 465 VAL B 461 REMARK 465 ALA B 462 REMARK 465 ASP B 463 REMARK 465 ALA B 464 REMARK 465 SER B 465 REMARK 465 LYS B 466 REMARK 465 TYR B 467 REMARK 465 VAL B 468 REMARK 465 THR B 469 REMARK 465 ASN B 470 REMARK 465 ALA B 471 REMARK 465 PHE B 472 REMARK 465 GLU B 473 REMARK 465 LYS B 474 REMARK 465 PHE B 475 REMARK 465 LEU B 476 REMARK 465 GLU B 477 REMARK 465 GLU B 478 REMARK 465 SER B 479 REMARK 465 ARG B 480 REMARK 465 LYS B 481 REMARK 465 ALA B 482 REMARK 465 ARG B 483 REMARK 465 ASP B 484 REMARK 465 ARG B 485 REMARK 465 GLY B 486 REMARK 465 CYS B 487 REMARK 465 ASP B 488 REMARK 465 GLU B 489 REMARK 465 ASN B 490 REMARK 465 ASP B 491 REMARK 465 ILE B 492 REMARK 465 VAL B 493 REMARK 465 TYR B 494 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 ILE A 415 CG1 CG2 CD1 REMARK 470 ILE B 415 CG1 CG2 CD1 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 THR B 59 OG1 - CB - CG2 ANGL. DEV. = 14.2 DEGREES REMARK 500 GLU B 348 CG - CD - OE2 ANGL. DEV. = -17.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 79 32.96 -144.72 REMARK 500 LYS A 97 62.60 -153.93 REMARK 500 MET A 126 34.52 -96.13 REMARK 500 PHE A 144 -141.22 -138.67 REMARK 500 ARG A 149 43.37 -142.13 REMARK 500 SER A 157 -165.60 -76.44 REMARK 500 GLN A 206 -69.54 -97.43 REMARK 500 ASP A 319 11.39 -147.02 REMARK 500 SER A 344 142.16 -173.91 REMARK 500 HIS A 354 -134.04 -103.07 REMARK 500 ASN A 357 51.74 -93.30 REMARK 500 HIS B 79 32.69 -144.31 REMARK 500 LYS B 97 64.08 -153.26 REMARK 500 PRO B 105 91.19 -69.44 REMARK 500 MET B 126 36.93 -95.60 REMARK 500 PHE B 144 -138.25 -138.46 REMARK 500 ARG B 149 42.03 -143.69 REMARK 500 SER B 157 -168.30 -77.18 REMARK 500 GLN B 206 -68.25 -98.61 REMARK 500 ASP B 319 11.05 -147.02 REMARK 500 SER B 344 142.52 -176.21 REMARK 500 HIS B 354 -132.93 -101.49 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 GLU A 36 0.08 SIDE CHAIN REMARK 500 GLU B 348 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8HAV A 1 494 UNP Q9SRQ7 NPC4_ARATH 1 494 DBREF 8HAV B 1 494 UNP Q9SRQ7 NPC4_ARATH 1 494 SEQADV 8HAV ALA A 178 UNP Q9SRQ7 LYS 178 ENGINEERED MUTATION SEQADV 8HAV ALA A 179 UNP Q9SRQ7 LYS 179 ENGINEERED MUTATION SEQADV 8HAV ALA B 178 UNP Q9SRQ7 LYS 178 ENGINEERED MUTATION SEQADV 8HAV ALA B 179 UNP Q9SRQ7 LYS 179 ENGINEERED MUTATION SEQRES 1 A 494 MET ILE GLU THR THR LYS GLY GLY SER GLY SER TYR PRO SEQRES 2 A 494 ILE LYS THR ILE VAL VAL LEU VAL GLN GLU ASN ARG SER SEQRES 3 A 494 PHE ASP HIS THR LEU GLY TRP PHE LYS GLU LEU ASN ARG SEQRES 4 A 494 GLU ILE ASP GLY VAL THR LYS SER ASP PRO LYS SER ASN SEQRES 5 A 494 THR VAL SER SER SER ASP THR ASN SER LEU ARG VAL VAL SEQRES 6 A 494 PHE GLY ASP GLN SER GLN TYR VAL ASN PRO ASP PRO GLY SEQRES 7 A 494 HIS SER ILE GLN ASP ILE TYR GLU GLN VAL PHE GLY LYS SEQRES 8 A 494 PRO TRP ASP SER GLY LYS PRO ASP PRO ASN PRO GLY HIS SEQRES 9 A 494 PRO ASN MET SER GLY PHE ALA GLN ASN ALA GLU ARG ASN SEQRES 10 A 494 LYS LYS GLY MET SER SER ALA VAL MET ASN GLY PHE LYS SEQRES 11 A 494 PRO ASN ALA LEU PRO VAL TYR LYS GLU LEU VAL GLN ASN SEQRES 12 A 494 PHE ALA ILE CYS ASP ARG TRP PHE ALA SER VAL PRO ALA SEQRES 13 A 494 SER THR GLN PRO ASN ARG LEU TYR VAL HIS SER ALA THR SEQRES 14 A 494 SER HIS GLY ALA THR SER ASN ASP ALA ALA LEU LEU LEU SEQRES 15 A 494 GLU GLY PHE PRO GLN LYS THR ILE PHE GLU SER LEU ASP SEQRES 16 A 494 GLU ALA GLY PHE SER PHE GLY ILE TYR TYR GLN PHE PRO SEQRES 17 A 494 PRO SER THR LEU PHE TYR ARG ASN LEU ARG LYS LEU LYS SEQRES 18 A 494 TYR LEU THR HIS PHE HIS GLN TYR GLY ILE GLN PHE LYS SEQRES 19 A 494 LYS ASP CYS LYS GLU GLY LYS LEU PRO ASN TYR VAL VAL SEQRES 20 A 494 VAL GLU GLN ARG TRP PHE ASP LEU LEU SER THR PRO ALA SEQRES 21 A 494 ASN ASP ASP HIS PRO SER HIS ASP VAL SER GLU GLY GLN SEQRES 22 A 494 LYS LEU VAL LYS GLU VAL TYR GLU ALA LEU ARG SER SER SEQRES 23 A 494 PRO GLN TRP ASN GLU ILE LEU PHE ILE ILE THR TYR ASP SEQRES 24 A 494 GLU HIS GLY GLY PHE TYR ASP HIS VAL PRO THR PRO VAL SEQRES 25 A 494 ASP GLY VAL PRO ASN PRO ASP GLY ILE LEU GLY PRO PRO SEQRES 26 A 494 PRO TYR ASN PHE GLU PHE ASN ARG LEU GLY VAL ARG VAL SEQRES 27 A 494 PRO THR PHE PHE ILE SER PRO TRP ILE GLU PRO GLY THR SEQRES 28 A 494 VAL ILE HIS GLY PRO ASN GLY PRO TYR PRO ARG SER GLN SEQRES 29 A 494 TYR GLU HIS SER SER ILE PRO ALA THR VAL LYS THR ILE SEQRES 30 A 494 PHE LYS LEU LYS ASP PHE LEU SER LYS ARG ASP SER TRP SEQRES 31 A 494 ALA GLY THR PHE GLU SER VAL ILE THR ARG ASP SER PRO SEQRES 32 A 494 ARG GLN ASP CYS PRO GLU THR LEU SER THR PRO ILE LYS SEQRES 33 A 494 LEU ARG GLY THR MET ALA LYS GLU ASN ALA GLN LEU SER SEQRES 34 A 494 GLU PHE GLN GLU ASP LEU VAL ILE MET ALA ALA GLY LEU SEQRES 35 A 494 LYS GLY ASP TYR LYS ASN GLU GLU LEU ILE HIS LYS LEU SEQRES 36 A 494 CYS LYS GLU THR CYS VAL ALA ASP ALA SER LYS TYR VAL SEQRES 37 A 494 THR ASN ALA PHE GLU LYS PHE LEU GLU GLU SER ARG LYS SEQRES 38 A 494 ALA ARG ASP ARG GLY CYS ASP GLU ASN ASP ILE VAL TYR SEQRES 1 B 494 MET ILE GLU THR THR LYS GLY GLY SER GLY SER TYR PRO SEQRES 2 B 494 ILE LYS THR ILE VAL VAL LEU VAL GLN GLU ASN ARG SER SEQRES 3 B 494 PHE ASP HIS THR LEU GLY TRP PHE LYS GLU LEU ASN ARG SEQRES 4 B 494 GLU ILE ASP GLY VAL THR LYS SER ASP PRO LYS SER ASN SEQRES 5 B 494 THR VAL SER SER SER ASP THR ASN SER LEU ARG VAL VAL SEQRES 6 B 494 PHE GLY ASP GLN SER GLN TYR VAL ASN PRO ASP PRO GLY SEQRES 7 B 494 HIS SER ILE GLN ASP ILE TYR GLU GLN VAL PHE GLY LYS SEQRES 8 B 494 PRO TRP ASP SER GLY LYS PRO ASP PRO ASN PRO GLY HIS SEQRES 9 B 494 PRO ASN MET SER GLY PHE ALA GLN ASN ALA GLU ARG ASN SEQRES 10 B 494 LYS LYS GLY MET SER SER ALA VAL MET ASN GLY PHE LYS SEQRES 11 B 494 PRO ASN ALA LEU PRO VAL TYR LYS GLU LEU VAL GLN ASN SEQRES 12 B 494 PHE ALA ILE CYS ASP ARG TRP PHE ALA SER VAL PRO ALA SEQRES 13 B 494 SER THR GLN PRO ASN ARG LEU TYR VAL HIS SER ALA THR SEQRES 14 B 494 SER HIS GLY ALA THR SER ASN ASP ALA ALA LEU LEU LEU SEQRES 15 B 494 GLU GLY PHE PRO GLN LYS THR ILE PHE GLU SER LEU ASP SEQRES 16 B 494 GLU ALA GLY PHE SER PHE GLY ILE TYR TYR GLN PHE PRO SEQRES 17 B 494 PRO SER THR LEU PHE TYR ARG ASN LEU ARG LYS LEU LYS SEQRES 18 B 494 TYR LEU THR HIS PHE HIS GLN TYR GLY ILE GLN PHE LYS SEQRES 19 B 494 LYS ASP CYS LYS GLU GLY LYS LEU PRO ASN TYR VAL VAL SEQRES 20 B 494 VAL GLU GLN ARG TRP PHE ASP LEU LEU SER THR PRO ALA SEQRES 21 B 494 ASN ASP ASP HIS PRO SER HIS ASP VAL SER GLU GLY GLN SEQRES 22 B 494 LYS LEU VAL LYS GLU VAL TYR GLU ALA LEU ARG SER SER SEQRES 23 B 494 PRO GLN TRP ASN GLU ILE LEU PHE ILE ILE THR TYR ASP SEQRES 24 B 494 GLU HIS GLY GLY PHE TYR ASP HIS VAL PRO THR PRO VAL SEQRES 25 B 494 ASP GLY VAL PRO ASN PRO ASP GLY ILE LEU GLY PRO PRO SEQRES 26 B 494 PRO TYR ASN PHE GLU PHE ASN ARG LEU GLY VAL ARG VAL SEQRES 27 B 494 PRO THR PHE PHE ILE SER PRO TRP ILE GLU PRO GLY THR SEQRES 28 B 494 VAL ILE HIS GLY PRO ASN GLY PRO TYR PRO ARG SER GLN SEQRES 29 B 494 TYR GLU HIS SER SER ILE PRO ALA THR VAL LYS THR ILE SEQRES 30 B 494 PHE LYS LEU LYS ASP PHE LEU SER LYS ARG ASP SER TRP SEQRES 31 B 494 ALA GLY THR PHE GLU SER VAL ILE THR ARG ASP SER PRO SEQRES 32 B 494 ARG GLN ASP CYS PRO GLU THR LEU SER THR PRO ILE LYS SEQRES 33 B 494 LEU ARG GLY THR MET ALA LYS GLU ASN ALA GLN LEU SER SEQRES 34 B 494 GLU PHE GLN GLU ASP LEU VAL ILE MET ALA ALA GLY LEU SEQRES 35 B 494 LYS GLY ASP TYR LYS ASN GLU GLU LEU ILE HIS LYS LEU SEQRES 36 B 494 CYS LYS GLU THR CYS VAL ALA ASP ALA SER LYS TYR VAL SEQRES 37 B 494 THR ASN ALA PHE GLU LYS PHE LEU GLU GLU SER ARG LYS SEQRES 38 B 494 ALA ARG ASP ARG GLY CYS ASP GLU ASN ASP ILE VAL TYR HET GOL A 501 6 HET PEG A 502 7 HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL C3 H8 O3 FORMUL 4 PEG C4 H10 O3 FORMUL 5 HOH *579(H2 O) HELIX 1 AA1 SER A 26 GLY A 32 1 7 HELIX 2 AA2 TRP A 33 LEU A 37 5 5 HELIX 3 AA3 SER A 80 GLY A 90 1 11 HELIX 4 AA4 GLY A 109 LYS A 118 1 10 HELIX 5 AA5 MET A 121 MET A 126 1 6 HELIX 6 AA6 LYS A 130 ALA A 133 5 4 HELIX 7 AA7 LEU A 134 PHE A 144 1 11 HELIX 8 AA8 SER A 157 ALA A 168 1 12 HELIX 9 AA9 ASP A 177 GLY A 184 1 8 HELIX 10 AB1 THR A 189 ALA A 197 1 9 HELIX 11 AB2 PRO A 209 ARG A 218 5 10 HELIX 12 AB3 LYS A 219 THR A 224 1 6 HELIX 13 AB4 TYR A 229 GLU A 239 1 11 HELIX 14 AB5 VAL A 269 SER A 285 1 17 HELIX 15 AB6 GLN A 288 ASN A 290 5 3 HELIX 16 AB7 SER A 368 PHE A 378 1 11 HELIX 17 AB8 PHE A 394 ILE A 398 5 5 HELIX 18 AB9 SER B 26 GLY B 32 1 7 HELIX 19 AC1 TRP B 33 LEU B 37 5 5 HELIX 20 AC2 SER B 80 GLY B 90 1 11 HELIX 21 AC3 GLY B 109 LYS B 118 1 10 HELIX 22 AC4 MET B 121 MET B 126 1 6 HELIX 23 AC5 LYS B 130 ALA B 133 5 4 HELIX 24 AC6 LEU B 134 PHE B 144 1 11 HELIX 25 AC7 SER B 157 ALA B 168 1 12 HELIX 26 AC8 ASP B 177 GLY B 184 1 8 HELIX 27 AC9 THR B 189 ALA B 197 1 9 HELIX 28 AD1 PRO B 209 ARG B 218 5 10 HELIX 29 AD2 LYS B 219 THR B 224 1 6 HELIX 30 AD3 TYR B 229 GLU B 239 1 11 HELIX 31 AD4 VAL B 269 SER B 285 1 17 HELIX 32 AD5 GLN B 288 ASN B 290 5 3 HELIX 33 AD6 SER B 368 PHE B 378 1 11 HELIX 34 AD7 SER B 385 ALA B 391 1 7 HELIX 35 AD8 PHE B 394 ILE B 398 5 5 SHEET 1 AA1 8 PHE A 226 GLN A 228 0 SHEET 2 AA1 8 GLY A 202 TYR A 205 1 N ILE A 203 O HIS A 227 SHEET 3 AA1 8 TYR A 245 GLU A 249 1 O VAL A 247 N TYR A 204 SHEET 4 AA1 8 THR A 16 GLN A 22 1 N ILE A 17 O VAL A 246 SHEET 5 AA1 8 ILE A 292 TYR A 298 1 O THR A 297 N GLN A 22 SHEET 6 AA1 8 THR A 340 ILE A 343 -1 O ILE A 343 N PHE A 294 SHEET 7 AA1 8 ALA A 145 CYS A 147 -1 N ALA A 145 O PHE A 342 SHEET 8 AA1 8 THR A 351 ILE A 353 1 O ILE A 353 N ILE A 146 SHEET 1 AA2 2 SER A 51 VAL A 54 0 SHEET 2 AA2 2 LEU A 62 VAL A 65 -1 O VAL A 64 N ASN A 52 SHEET 1 AA3 2 VAL A 73 PRO A 75 0 SHEET 2 AA3 2 SER A 266 ASP A 268 -1 O HIS A 267 N ASN A 74 SHEET 1 AA4 2 TRP A 150 PHE A 151 0 SHEET 2 AA4 2 TYR A 365 GLU A 366 1 O TYR A 365 N PHE A 151 SHEET 1 AA5 8 PHE B 226 GLN B 228 0 SHEET 2 AA5 8 PHE B 201 TYR B 205 1 N ILE B 203 O HIS B 227 SHEET 3 AA5 8 TYR B 245 GLU B 249 1 O VAL B 247 N TYR B 204 SHEET 4 AA5 8 THR B 16 GLN B 22 1 N ILE B 17 O VAL B 246 SHEET 5 AA5 8 ILE B 292 TYR B 298 1 O THR B 297 N GLN B 22 SHEET 6 AA5 8 THR B 340 ILE B 343 -1 O PHE B 341 N ILE B 296 SHEET 7 AA5 8 ALA B 145 CYS B 147 -1 N ALA B 145 O PHE B 342 SHEET 8 AA5 8 THR B 351 ILE B 353 1 O ILE B 353 N ILE B 146 SHEET 1 AA6 2 SER B 51 VAL B 54 0 SHEET 2 AA6 2 LEU B 62 VAL B 65 -1 O VAL B 64 N ASN B 52 SHEET 1 AA7 2 VAL B 73 ASN B 74 0 SHEET 2 AA7 2 HIS B 267 ASP B 268 -1 O HIS B 267 N ASN B 74 SHEET 1 AA8 2 TRP B 150 PHE B 151 0 SHEET 2 AA8 2 TYR B 365 GLU B 366 1 O TYR B 365 N PHE B 151 CISPEP 1 PRO A 325 PRO A 326 0 0.38 CISPEP 2 PRO B 325 PRO B 326 0 1.10 CISPEP 3 GLY B 358 PRO B 359 0 7.14 CRYST1 59.055 121.441 157.383 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 0.016933 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006354 0.00000 MTRIX1 1 0.982405 0.028385 0.184594 -6.71089 1 MTRIX2 1 0.033890 -0.999068 -0.026735 -60.21636 1 MTRIX3 1 0.183663 0.032520 -0.982451 83.27148 1