HEADER LIPID BINDING PROTEIN 31-OCT-10 3PG7 TITLE CRYSTAL STRUCTURE OF THE H. SAPIENS NF1 SEC-PH DOMAIN (DEL1750 MUTANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROFIBROMIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NEUROFIBROMATOSIS-RELATED PROTEIN NF-1, NEUROFIBROMIN COMPND 5 TRUNCATED; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SEC LIPID BINDING DOMAIN, PH DOMAIN, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.WELTI,I.D'ANGELO,K.SCHEFFZEK REVDAT 2 16-FEB-11 3PG7 1 JRNL REVDAT 1 08-DEC-10 3PG7 0 JRNL AUTH S.WELTI,S.KUHN,I.D'ANGELO,B.BRUGGER,D.KAUFMANN,K.SCHEFFZEK JRNL TITL STRUCTURAL AND BIOCHEMICAL CONSEQUENCES OF NF1 ASSOCIATED JRNL TITL 2 NONTRUNCATING MUTATIONS IN THE SEC14-PH MODULE OF JRNL TITL 3 NEUROFIBROMIN. JRNL REF HUM.MUTAT. V. 32 191 2011 JRNL REFN ISSN 1059-7794 JRNL PMID 21089070 JRNL DOI 10.1002/HUMU.21405 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 74716 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 3792 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 36.8621 - 6.5552 0.91 2598 112 0.2409 0.2633 REMARK 3 2 6.5552 - 5.2077 1.00 2814 137 0.2045 0.2370 REMARK 3 3 5.2077 - 4.5508 0.99 2806 131 0.1631 0.1976 REMARK 3 4 4.5508 - 4.1353 0.99 2773 185 0.1518 0.1766 REMARK 3 5 4.1353 - 3.8392 0.99 2782 147 0.1696 0.2236 REMARK 3 6 3.8392 - 3.6131 0.99 2813 144 0.1744 0.2112 REMARK 3 7 3.6131 - 3.4323 0.99 2793 133 0.1832 0.2166 REMARK 3 8 3.4323 - 3.2830 0.98 2758 145 0.1993 0.2440 REMARK 3 9 3.2830 - 3.1567 0.98 2781 136 0.2043 0.2502 REMARK 3 10 3.1567 - 3.0478 0.98 2720 180 0.2091 0.2552 REMARK 3 11 3.0478 - 2.9525 0.96 2689 155 0.2012 0.2552 REMARK 3 12 2.9525 - 2.8682 0.97 2735 128 0.1978 0.2302 REMARK 3 13 2.8682 - 2.7927 0.96 2725 137 0.2112 0.2768 REMARK 3 14 2.7927 - 2.7246 0.95 2669 140 0.2351 0.3161 REMARK 3 15 2.7246 - 2.6627 0.95 2669 136 0.2340 0.3132 REMARK 3 16 2.6627 - 2.6060 0.94 2615 163 0.2271 0.2619 REMARK 3 17 2.6060 - 2.5539 0.93 2593 153 0.2248 0.2624 REMARK 3 18 2.5539 - 2.5057 0.91 2545 129 0.2330 0.2688 REMARK 3 19 2.5057 - 2.4610 0.91 2554 131 0.2303 0.3118 REMARK 3 20 2.4610 - 2.4193 0.91 2533 140 0.2406 0.2457 REMARK 3 21 2.4193 - 2.3802 0.90 2569 134 0.2339 0.3072 REMARK 3 22 2.3802 - 2.3436 0.87 2473 102 0.2257 0.2420 REMARK 3 23 2.3436 - 2.3092 0.86 2373 150 0.2406 0.2881 REMARK 3 24 2.3092 - 2.2766 0.86 2409 152 0.2572 0.2891 REMARK 3 25 2.2766 - 2.2459 0.86 2439 105 0.2518 0.3055 REMARK 3 26 2.2459 - 2.2167 0.86 2409 137 0.2747 0.3484 REMARK 3 27 2.2167 - 2.1890 0.83 2287 150 0.2873 0.3104 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 : 0.35 REMARK 3 B_SOL : 49.84 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.700 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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) : -0.82850 REMARK 3 B22 (A**2) : -0.82850 REMARK 3 B33 (A**2) : -7.02290 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : -0.00000 REMARK 3 B23 (A**2) : -0.00000 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 : 0.004 4218 REMARK 3 ANGLE : 0.897 5735 REMARK 3 CHIRALITY : 0.061 645 REMARK 3 PLANARITY : 0.003 713 REMARK 3 DIHEDRAL : 16.990 1502 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1560:1658) REMARK 3 ORIGIN FOR THE GROUP (A): -27.1640 9.5708 17.3208 REMARK 3 T TENSOR REMARK 3 T11: 0.3531 T22: 0.4257 REMARK 3 T33: 0.3336 T12: 0.1521 REMARK 3 T13: -0.0111 T23: 0.0778 REMARK 3 L TENSOR REMARK 3 L11: 2.7429 L22: 2.9082 REMARK 3 L33: 0.7269 L12: -0.5560 REMARK 3 L13: -1.4757 L23: 0.7839 REMARK 3 S TENSOR REMARK 3 S11: -0.2714 S12: -0.6649 S13: -0.5643 REMARK 3 S21: 0.4106 S22: 0.2740 S23: 0.1365 REMARK 3 S31: 0.2771 S32: 0.2715 S33: -0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 1659:1711) REMARK 3 ORIGIN FOR THE GROUP (A): -21.3641 20.6133 13.3037 REMARK 3 T TENSOR REMARK 3 T11: 0.3363 T22: 0.5821 REMARK 3 T33: 0.3573 T12: 0.1480 REMARK 3 T13: -0.0336 T23: -0.1507 REMARK 3 L TENSOR REMARK 3 L11: 0.3973 L22: 1.6460 REMARK 3 L33: 1.6397 L12: 0.3052 REMARK 3 L13: 0.4262 L23: 0.2424 REMARK 3 S TENSOR REMARK 3 S11: -0.0099 S12: -0.5515 S13: 0.1198 REMARK 3 S21: 0.0527 S22: 0.3664 S23: -0.2568 REMARK 3 S31: -0.0400 S32: 0.3271 S33: -0.0013 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 1712:1815) REMARK 3 ORIGIN FOR THE GROUP (A): -18.9872 24.6681 -6.8242 REMARK 3 T TENSOR REMARK 3 T11: 0.3323 T22: 0.3339 REMARK 3 T33: 0.3492 T12: 0.0336 REMARK 3 T13: 0.0590 T23: -0.1062 REMARK 3 L TENSOR REMARK 3 L11: 1.9937 L22: 1.7929 REMARK 3 L33: 3.9417 L12: 0.0137 REMARK 3 L13: -0.8828 L23: 0.0923 REMARK 3 S TENSOR REMARK 3 S11: 0.1075 S12: -0.0298 S13: 0.2342 REMARK 3 S21: -0.1973 S22: 0.0897 S23: -0.1438 REMARK 3 S31: -0.0779 S32: -0.1133 S33: -0.0004 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 1560:1687) REMARK 3 ORIGIN FOR THE GROUP (A): -28.7954 -3.8765 -34.1803 REMARK 3 T TENSOR REMARK 3 T11: 0.2093 T22: 0.1866 REMARK 3 T33: 0.2699 T12: -0.0353 REMARK 3 T13: -0.0642 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 1.0584 L22: 2.4756 REMARK 3 L33: 2.3871 L12: 0.0486 REMARK 3 L13: 0.1400 L23: -1.3668 REMARK 3 S TENSOR REMARK 3 S11: -0.1110 S12: 0.1198 S13: -0.0058 REMARK 3 S21: -0.1151 S22: 0.2192 S23: 0.2677 REMARK 3 S31: 0.1777 S32: -0.2535 S33: -0.0006 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 1688:1712) REMARK 3 ORIGIN FOR THE GROUP (A): -12.7751 2.4286 -32.5589 REMARK 3 T TENSOR REMARK 3 T11: 0.3203 T22: 0.3199 REMARK 3 T33: 0.3999 T12: -0.1548 REMARK 3 T13: -0.0655 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 0.8747 L22: -0.1982 REMARK 3 L33: 1.4722 L12: -0.8450 REMARK 3 L13: -0.0051 L23: -0.0247 REMARK 3 S TENSOR REMARK 3 S11: 0.0065 S12: 0.1115 S13: 0.5783 REMARK 3 S21: 0.0958 S22: 0.3179 S23: -0.0100 REMARK 3 S31: -0.7715 S32: 0.3549 S33: 0.0320 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 1713:1815) REMARK 3 ORIGIN FOR THE GROUP (A): -12.3204 -10.1085 -13.0989 REMARK 3 T TENSOR REMARK 3 T11: 0.3640 T22: 0.2982 REMARK 3 T33: 0.3117 T12: 0.1172 REMARK 3 T13: -0.0428 T23: -0.0394 REMARK 3 L TENSOR REMARK 3 L11: 2.0830 L22: 1.4827 REMARK 3 L33: 3.0463 L12: -0.5715 REMARK 3 L13: 1.2204 L23: -0.2180 REMARK 3 S TENSOR REMARK 3 S11: -0.2753 S12: -0.2848 S13: 0.0184 REMARK 3 S21: 0.3570 S22: 0.2222 S23: -0.0329 REMARK 3 S31: 0.1772 S32: 0.2143 S33: -0.0003 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 3PG7 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-10. REMARK 100 THE RCSB ID CODE IS RCSB062338. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74716 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 36.857 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.24500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 56.72000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 56.72000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.12250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 56.72000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 56.72000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 93.36750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 56.72000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.72000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.12250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 56.72000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.72000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 93.36750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 62.24500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 A1560 CG CD CE NZ REMARK 470 GLU A1561 CG CD OE1 OE2 REMARK 470 GLU A1562 CG CD OE1 OE2 REMARK 470 LYS A1564 CG CD CE NZ REMARK 470 LYS A1567 CG CD CE NZ REMARK 470 THR A1568 OG1 CG2 REMARK 470 LEU A1569 CG CD1 CD2 REMARK 470 ILE A1597 CG1 CG2 CD1 REMARK 470 LEU A1601 CG CD1 CD2 REMARK 470 LEU A1608 CG CD1 CD2 REMARK 470 LYS A1611 CG CD CE NZ REMARK 470 GLU A1673 CG CD OE1 OE2 REMARK 470 LYS A1683 CG CD CE NZ REMARK 470 HIS A1700 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A1701 CG CD OE1 OE2 REMARK 470 LYS A1728 CG CD CE NZ REMARK 470 LYS A1731 CG CD CE NZ REMARK 470 GLU A1768 CG CD OE1 OE2 REMARK 470 GLU A1774 CG CD OE1 OE2 REMARK 470 LYS B1560 CG CD CE NZ REMARK 470 GLU B1561 CG CD OE1 OE2 REMARK 470 GLU B1562 CG CD OE1 OE2 REMARK 470 PHE B1563 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B1564 CG CD CE NZ REMARK 470 LYS B1567 CG CD CE NZ REMARK 470 LYS B1680 CG CD CE NZ REMARK 470 LYS B1683 CG CD CE NZ REMARK 470 LYS B1693 CG CD CE NZ REMARK 470 GLU B1696 CG CD OE1 OE2 REMARK 470 LYS B1717 CG CD CE NZ REMARK 470 LYS B1728 CG CD CE NZ REMARK 470 LYS B1731 CG CD CE NZ REMARK 470 GLU B1774 CG CD OE1 OE2 REMARK 470 ARG B1808 CG CD NE CZ NH1 NH2 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 ALA A1575 104.46 -169.89 REMARK 500 PRO A1814 93.06 -63.95 REMARK 500 GLU B1561 -31.02 -147.25 REMARK 500 ILE B1597 95.70 52.49 REMARK 500 HIS B1626 19.76 59.98 REMARK 500 GLU B1696 -6.32 -54.50 REMARK 500 GLU B1701 1.29 -66.03 REMARK 500 LYS B1704 47.16 -150.22 REMARK 500 ASP B1715 75.56 33.53 REMARK 500 ALA B1726 -159.14 -164.45 REMARK 500 GLU B1747 107.43 -21.26 REMARK 500 VAL B1772 -74.84 -87.29 REMARK 500 GLU B1774 -33.03 61.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PTY A 400 REMARK 610 PTY B 500 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PTY A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PTY B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP B 602 DBREF 3PG7 A 1560 1815 UNP P21359 NF1_HUMAN 1581 1837 DBREF 3PG7 B 1560 1815 UNP P21359 NF1_HUMAN 1581 1837 SEQADV 3PG7 A UNP P21359 LYS 1771 DELETION SEQADV 3PG7 B UNP P21359 LYS 1771 DELETION SEQRES 1 A 256 LYS GLU GLU PHE LYS ALA LEU LYS THR LEU SER ILE PHE SEQRES 2 A 256 TYR GLN ALA GLY THR SER LYS ALA GLY ASN PRO ILE PHE SEQRES 3 A 256 TYR TYR VAL ALA ARG ARG PHE LYS THR GLY GLN ILE ASN SEQRES 4 A 256 GLY ASP LEU LEU ILE TYR HIS VAL LEU LEU THR LEU LYS SEQRES 5 A 256 PRO TYR TYR ALA LYS PRO TYR GLU ILE VAL VAL ASP LEU SEQRES 6 A 256 THR HIS THR GLY PRO SER ASN ARG PHE LYS THR ASP PHE SEQRES 7 A 256 LEU SER LYS TRP PHE VAL VAL PHE PRO GLY PHE ALA TYR SEQRES 8 A 256 ASP ASN VAL SER ALA VAL TYR ILE TYR ASN CYS ASN SER SEQRES 9 A 256 TRP VAL ARG GLU TYR THR LYS TYR HIS GLU ARG LEU LEU SEQRES 10 A 256 THR GLY LEU LYS GLY SER LYS ARG LEU VAL PHE ILE ASP SEQRES 11 A 256 CYS PRO GLY LYS LEU ALA GLU HIS ILE GLU HIS GLU GLN SEQRES 12 A 256 GLN LYS LEU PRO ALA ALA THR LEU ALA LEU GLU GLU ASP SEQRES 13 A 256 LEU LYS VAL PHE HIS ASN ALA LEU LYS LEU ALA HIS LYS SEQRES 14 A 256 ASP THR LYS VAL SER ILE LYS VAL GLY SER THR ALA VAL SEQRES 15 A 256 GLN VAL THR SER ALA GLU ARG THR VAL LEU GLY GLN SER SEQRES 16 A 256 VAL PHE LEU ASN ASP ILE TYR TYR ALA SER GLU ILE GLU SEQRES 17 A 256 GLU ILE CYS LEU VAL ASP GLU ASN GLN PHE THR LEU THR SEQRES 18 A 256 ILE ALA ASN GLN GLY THR PRO LEU THR PHE MET HIS GLN SEQRES 19 A 256 GLU CYS GLU ALA ILE VAL GLN SER ILE ILE HIS ILE ARG SEQRES 20 A 256 THR ARG TRP GLU LEU SER GLN PRO ASP SEQRES 1 B 256 LYS GLU GLU PHE LYS ALA LEU LYS THR LEU SER ILE PHE SEQRES 2 B 256 TYR GLN ALA GLY THR SER LYS ALA GLY ASN PRO ILE PHE SEQRES 3 B 256 TYR TYR VAL ALA ARG ARG PHE LYS THR GLY GLN ILE ASN SEQRES 4 B 256 GLY ASP LEU LEU ILE TYR HIS VAL LEU LEU THR LEU LYS SEQRES 5 B 256 PRO TYR TYR ALA LYS PRO TYR GLU ILE VAL VAL ASP LEU SEQRES 6 B 256 THR HIS THR GLY PRO SER ASN ARG PHE LYS THR ASP PHE SEQRES 7 B 256 LEU SER LYS TRP PHE VAL VAL PHE PRO GLY PHE ALA TYR SEQRES 8 B 256 ASP ASN VAL SER ALA VAL TYR ILE TYR ASN CYS ASN SER SEQRES 9 B 256 TRP VAL ARG GLU TYR THR LYS TYR HIS GLU ARG LEU LEU SEQRES 10 B 256 THR GLY LEU LYS GLY SER LYS ARG LEU VAL PHE ILE ASP SEQRES 11 B 256 CYS PRO GLY LYS LEU ALA GLU HIS ILE GLU HIS GLU GLN SEQRES 12 B 256 GLN LYS LEU PRO ALA ALA THR LEU ALA LEU GLU GLU ASP SEQRES 13 B 256 LEU LYS VAL PHE HIS ASN ALA LEU LYS LEU ALA HIS LYS SEQRES 14 B 256 ASP THR LYS VAL SER ILE LYS VAL GLY SER THR ALA VAL SEQRES 15 B 256 GLN VAL THR SER ALA GLU ARG THR VAL LEU GLY GLN SER SEQRES 16 B 256 VAL PHE LEU ASN ASP ILE TYR TYR ALA SER GLU ILE GLU SEQRES 17 B 256 GLU ILE CYS LEU VAL ASP GLU ASN GLN PHE THR LEU THR SEQRES 18 B 256 ILE ALA ASN GLN GLY THR PRO LEU THR PHE MET HIS GLN SEQRES 19 B 256 GLU CYS GLU ALA ILE VAL GLN SER ILE ILE HIS ILE ARG SEQRES 20 B 256 THR ARG TRP GLU LEU SER GLN PRO ASP HET PTY A 400 46 HET PTY B 500 46 HET POP B 601 9 HET POP B 602 9 HETNAM PTY PHOSPHATIDYLETHANOLAMINE HETNAM POP PYROPHOSPHATE 2- FORMUL 3 PTY 2(C40 H80 N O8 P) FORMUL 5 POP 2(H2 O7 P2 2-) FORMUL 7 HOH *241(H2 O) HELIX 1 1 ALA A 1565 SER A 1570 1 6 HELIX 2 2 ARG A 1590 PHE A 1592 5 3 HELIX 3 3 ASN A 1598 LYS A 1611 1 14 HELIX 4 4 GLY A 1628 ARG A 1632 5 5 HELIX 5 5 LYS A 1634 TRP A 1641 1 8 HELIX 6 6 PRO A 1646 ASN A 1652 1 7 HELIX 7 7 ASN A 1662 HIS A 1672 1 11 HELIX 8 8 HIS A 1672 THR A 1677 1 6 HELIX 9 9 GLY A 1692 HIS A 1697 5 6 HELIX 10 10 GLU A 1699 GLN A 1703 5 5 HELIX 11 11 PRO A 1706 LEU A 1712 1 7 HELIX 12 12 GLU A 1794 SER A 1812 1 19 HELIX 13 13 GLU B 1561 SER B 1570 1 10 HELIX 14 14 ARG B 1590 PHE B 1592 5 3 HELIX 15 15 ASN B 1598 LYS B 1611 1 14 HELIX 16 16 GLY B 1628 ARG B 1632 5 5 HELIX 17 17 LYS B 1634 TRP B 1641 1 8 HELIX 18 18 PRO B 1646 ASN B 1652 1 7 HELIX 19 19 ASN B 1662 HIS B 1672 1 11 HELIX 20 20 GLU B 1673 LYS B 1680 5 8 HELIX 21 21 PRO B 1691 HIS B 1697 5 7 HELIX 22 22 GLU B 1699 GLN B 1703 5 5 HELIX 23 23 PRO B 1706 LEU B 1712 1 7 HELIX 24 24 GLU B 1794 SER B 1812 1 19 SHEET 1 A 5 PHE A1572 THR A1577 0 SHEET 2 A 5 PRO A1583 VAL A1588 -1 O TYR A1586 N TYR A1573 SHEET 3 A 5 TYR A1618 ASP A1623 1 O VAL A1621 N PHE A1585 SHEET 4 A 5 VAL A1653 TYR A1659 1 O TYR A1657 N VAL A1622 SHEET 5 A 5 LEU A1685 ILE A1688 1 O ILE A1688 N ILE A1658 SHEET 1 B 7 ASN A1758 TYR A1762 0 SHEET 2 B 7 ALA A1740 SER A1745 -1 N VAL A1741 O TYR A1761 SHEET 3 B 7 THR A1730 VAL A1736 -1 N LYS A1735 O GLN A1742 SHEET 4 B 7 LYS A1717 LEU A1725 -1 N LYS A1717 O VAL A1736 SHEET 5 B 7 LEU A1788 MET A1791 -1 O THR A1789 N LEU A1725 SHEET 6 B 7 GLN A1776 ILE A1781 -1 N PHE A1777 O PHE A1790 SHEET 7 B 7 ILE A1766 ASP A1773 -1 N GLU A1768 O THR A1780 SHEET 1 C 2 ARG A1748 VAL A1750 0 SHEET 2 C 2 GLN A1753 VAL A1755 -1 O VAL A1755 N ARG A1748 SHEET 1 D 5 PHE B1572 THR B1577 0 SHEET 2 D 5 PRO B1583 VAL B1588 -1 O TYR B1586 N TYR B1573 SHEET 3 D 5 TYR B1618 ASP B1623 1 O VAL B1621 N PHE B1585 SHEET 4 D 5 VAL B1653 TYR B1659 1 O TYR B1657 N VAL B1622 SHEET 5 D 5 LEU B1685 ILE B1688 1 O VAL B1686 N VAL B1656 SHEET 1 E 7 ASN B1758 TYR B1762 0 SHEET 2 E 7 ALA B1740 SER B1745 -1 N VAL B1743 O ASP B1759 SHEET 3 E 7 THR B1730 VAL B1736 -1 N LYS B1735 O GLN B1742 SHEET 4 E 7 LYS B1717 LEU B1725 -1 N LYS B1724 O THR B1730 SHEET 5 E 7 LEU B1788 MET B1791 -1 O MET B1791 N LEU B1723 SHEET 6 E 7 GLN B1776 ILE B1781 -1 N PHE B1777 O PHE B1790 SHEET 7 E 7 ILE B1766 LEU B1771 -1 N GLU B1767 O THR B1780 SHEET 1 F 2 ARG B1748 VAL B1750 0 SHEET 2 F 2 GLN B1753 VAL B1755 -1 O VAL B1755 N ARG B1748 SSBOND 1 CYS B 1770 CYS B 1770 1555 7555 2.04 SITE 1 AC1 10 HOH A 105 HOH A 227 PHE A1572 TYR A1587 SITE 2 AC1 10 ILE A1620 TRP A1641 PHE A1642 TYR A1650 SITE 3 AC1 10 VAL A1653 LEU A1679 SITE 1 AC2 12 HOH B 81 ILE B1620 PHE B1633 TRP B1641 SITE 2 AC2 12 PHE B1642 TYR B1650 VAL B1653 VAL B1656 SITE 3 AC2 12 TRP B1664 TYR B1668 GLY B1678 ARG B1684 SITE 1 AC3 6 ARG A1666 LYS A1670 HOH B 67 ARG B1666 SITE 2 AC3 6 LYS B1670 ARG B1748 SITE 1 AC4 9 ARG A1632 LYS A1634 THR A1635 TYR A1671 SITE 2 AC4 9 HIS A1672 HOH B 68 ARG B1632 THR B1635 SITE 3 AC4 9 TYR B1671 CRYST1 113.440 113.440 124.490 90.00 90.00 90.00 P 41 21 2 16 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 0.008815 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008815 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008033 0.00000