HEADER LIPID BINDING PROTEIN 13-OCT-10 3P7Z TITLE CRYSTAL STRUCTURE OF THE NEUROFIBROMIN SEC14-PH MODULE CONTAINING THE TITLE 2 PATIENT DERIVED MUTATION I1584V 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; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 CODON+RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS SEC14 HOMOLGY DOMAIN, PLECKSTRIN HOMOLOGY DOMAIN, BINDING OF KEYWDS 2 GLYCEROPHOSPHOLIPIDS, GLYCEROPHOSPHOLIPIDS, CYTOPLASMATIC, LIPID KEYWDS 3 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.WELTI,K.SCHEFFZEK REVDAT 3 17-JUL-19 3P7Z 1 REMARK REVDAT 2 16-FEB-11 3P7Z 1 JRNL REVDAT 1 08-DEC-10 3P7Z 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. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 24081 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1228 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 49.1524 - 5.5101 1.00 2742 121 0.2168 0.2683 REMARK 3 2 5.5101 - 4.3744 1.00 2576 146 0.1617 0.2195 REMARK 3 3 4.3744 - 3.8217 1.00 2533 143 0.1651 0.2196 REMARK 3 4 3.8217 - 3.4723 1.00 2521 135 0.1907 0.2252 REMARK 3 5 3.4723 - 3.2235 1.00 2512 137 0.2121 0.2873 REMARK 3 6 3.2235 - 3.0335 1.00 2501 136 0.2537 0.2788 REMARK 3 7 3.0335 - 2.8816 1.00 2503 133 0.2712 0.3282 REMARK 3 8 2.8816 - 2.7562 1.00 2471 137 0.3144 0.3293 REMARK 3 9 2.7562 - 2.6500 1.00 2494 140 0.3544 0.3944 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 : 0.34 REMARK 3 B_SOL : 45.56 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 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) : -2.08070 REMARK 3 B22 (A**2) : -2.08070 REMARK 3 B33 (A**2) : 2.72300 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 : 0.002 4599 REMARK 3 ANGLE : 0.538 6219 REMARK 3 CHIRALITY : 0.039 680 REMARK 3 PLANARITY : 0.002 771 REMARK 3 DIHEDRAL : 15.101 1699 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 1547:1572) REMARK 3 ORIGIN FOR THE GROUP (A): -34.8082 -0.7194 18.7240 REMARK 3 T TENSOR REMARK 3 T11: 0.5331 T22: 0.4927 REMARK 3 T33: 0.7441 T12: -0.1477 REMARK 3 T13: 0.0390 T23: 0.1326 REMARK 3 L TENSOR REMARK 3 L11: 1.7002 L22: 0.6030 REMARK 3 L33: 0.9970 L12: -1.0531 REMARK 3 L13: 0.5776 L23: -0.6410 REMARK 3 S TENSOR REMARK 3 S11: 0.0737 S12: -0.8139 S13: -1.7985 REMARK 3 S21: -0.6885 S22: -0.1666 S23: 1.0964 REMARK 3 S31: 0.9120 S32: -0.1586 S33: 0.0949 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 1573:1715) REMARK 3 ORIGIN FOR THE GROUP (A): -24.3476 14.8168 15.7817 REMARK 3 T TENSOR REMARK 3 T11: 0.2840 T22: 0.3597 REMARK 3 T33: 0.3510 T12: 0.1092 REMARK 3 T13: -0.0255 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 1.7883 L22: 3.1684 REMARK 3 L33: 2.4644 L12: 0.1616 REMARK 3 L13: 0.2826 L23: -0.5622 REMARK 3 S TENSOR REMARK 3 S11: 0.0604 S12: -0.2266 S13: -0.0730 REMARK 3 S21: 0.0231 S22: 0.1344 S23: 0.0743 REMARK 3 S31: 0.1334 S32: -0.0092 S33: 0.0002 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 1716:1816) REMARK 3 ORIGIN FOR THE GROUP (A): -19.3280 25.8899 -6.9192 REMARK 3 T TENSOR REMARK 3 T11: 0.2557 T22: 0.2279 REMARK 3 T33: 0.1680 T12: 0.0246 REMARK 3 T13: 0.0506 T23: -0.0341 REMARK 3 L TENSOR REMARK 3 L11: 1.6926 L22: 0.7183 REMARK 3 L33: 1.2512 L12: 0.0301 REMARK 3 L13: -0.3821 L23: -0.2757 REMARK 3 S TENSOR REMARK 3 S11: 0.1505 S12: 0.1109 S13: 0.1350 REMARK 3 S21: -0.0119 S22: -0.0139 S23: -0.1167 REMARK 3 S31: 0.0161 S32: -0.1731 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 1547:1697) REMARK 3 ORIGIN FOR THE GROUP (A): -29.3063 -2.8019 -34.4970 REMARK 3 T TENSOR REMARK 3 T11: 0.1778 T22: 0.1916 REMARK 3 T33: 0.2480 T12: -0.0637 REMARK 3 T13: -0.0585 T23: 0.0642 REMARK 3 L TENSOR REMARK 3 L11: 1.5714 L22: 2.4706 REMARK 3 L33: 2.4012 L12: -0.0894 REMARK 3 L13: -0.5287 L23: -0.5110 REMARK 3 S TENSOR REMARK 3 S11: -0.1973 S12: 0.2045 S13: -0.0359 REMARK 3 S21: -0.0552 S22: 0.2560 S23: 0.3536 REMARK 3 S31: 0.1153 S32: -0.3330 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 1698:1762) REMARK 3 ORIGIN FOR THE GROUP (A): -11.3272 -7.7578 -23.2342 REMARK 3 T TENSOR REMARK 3 T11: 0.4500 T22: 0.3917 REMARK 3 T33: 0.3747 T12: -0.0021 REMARK 3 T13: -0.0289 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 0.5510 L22: 0.5799 REMARK 3 L33: 1.4715 L12: -0.9725 REMARK 3 L13: -0.0596 L23: -0.4712 REMARK 3 S TENSOR REMARK 3 S11: -0.2113 S12: 0.0831 S13: 0.2272 REMARK 3 S21: -0.0433 S22: 0.2045 S23: -0.3407 REMARK 3 S31: -0.0674 S32: 0.5078 S33: -0.0003 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 1763:1816) REMARK 3 ORIGIN FOR THE GROUP (A): -13.1450 -8.1337 -6.4808 REMARK 3 T TENSOR REMARK 3 T11: 0.4191 T22: 0.2987 REMARK 3 T33: 0.1516 T12: 0.1607 REMARK 3 T13: -0.0356 T23: -0.0327 REMARK 3 L TENSOR REMARK 3 L11: 0.8310 L22: 1.0684 REMARK 3 L33: 1.2646 L12: 1.1144 REMARK 3 L13: -0.4990 L23: 0.4180 REMARK 3 S TENSOR REMARK 3 S11: 0.2031 S12: -0.0283 S13: -0.0863 REMARK 3 S21: 0.5835 S22: -0.2324 S23: -0.1670 REMARK 3 S31: 0.2257 S32: -0.1194 S33: -0.0001 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 3P7Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000062070. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24081 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 49.144 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 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) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 : 3.830 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, 7.5% PEG 4000, 0.2M NA4P207, REMARK 280 PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 62.30600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 56.53050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 56.53050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.15300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 56.53050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 56.53050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 93.45900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 56.53050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.53050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.15300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 56.53050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.53050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 93.45900 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 62.30600 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A1817 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 1541 REMARK 465 ALA A 1542 REMARK 465 MET A 1543 REMARK 465 GLY A 1544 REMARK 465 SER A 1545 REMARK 465 SER A 1546 REMARK 465 GLY B 1541 REMARK 465 ALA B 1542 REMARK 465 MET B 1543 REMARK 465 GLY B 1544 REMARK 465 SER B 1545 REMARK 465 SER B 1546 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 LEU A1607 CG CD1 CD2 REMARK 470 LYS A1611 CG CD CE NZ REMARK 470 GLU A1673 CG CD OE1 OE2 REMARK 470 LYS A1680 CG CD CE NZ REMARK 470 LYS A1693 CG CD CE NZ REMARK 470 LEU B1607 CG CD1 CD2 REMARK 470 LYS B1683 CG CD CE NZ 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 A1558 -143.46 91.29 REMARK 500 GLU A1561 -101.93 -109.09 REMARK 500 GLU A1562 -35.51 -39.66 REMARK 500 SER A1570 75.62 38.56 REMARK 500 TYR A1614 -4.25 -59.00 REMARK 500 VAL A1773 -76.30 -85.71 REMARK 500 GLN A1785 -0.72 -144.84 REMARK 500 HIS A1793 141.82 -175.78 REMARK 500 HIS B1558 171.33 -59.31 REMARK 500 LYS B1560 -156.76 -72.08 REMARK 500 TYR B1614 3.03 -66.21 REMARK 500 ALA B1726 -163.25 -172.27 REMARK 500 GLU B1768 -64.20 -90.59 REMARK 500 ASN B1776 33.09 -155.81 REMARK 500 ASN B1784 14.70 59.62 REMARK 500 GLU B1795 50.89 -118.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 PEV A 1 REMARK 615 PEV B 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEV A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1817 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEV B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP B 1817 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP B 1818 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2E2X RELATED DB: PDB REMARK 900 NEUROFIBROMINS SEC14-PH MODULE IN COMPLEX WITH A LIPID LIGAND DBREF 3P7Z A 1545 1816 UNP P21359 NF1_HUMAN 1566 1837 DBREF 3P7Z B 1545 1816 UNP P21359 NF1_HUMAN 1566 1837 SEQADV 3P7Z GLY A 1541 UNP P21359 EXPRESSION TAG SEQADV 3P7Z ALA A 1542 UNP P21359 EXPRESSION TAG SEQADV 3P7Z MET A 1543 UNP P21359 EXPRESSION TAG SEQADV 3P7Z GLY A 1544 UNP P21359 EXPRESSION TAG SEQADV 3P7Z VAL A 1584 UNP P21359 ILE 1605 ENGINEERED MUTATION SEQADV 3P7Z GLY B 1541 UNP P21359 EXPRESSION TAG SEQADV 3P7Z ALA B 1542 UNP P21359 EXPRESSION TAG SEQADV 3P7Z MET B 1543 UNP P21359 EXPRESSION TAG SEQADV 3P7Z GLY B 1544 UNP P21359 EXPRESSION TAG SEQADV 3P7Z VAL B 1584 UNP P21359 ILE 1605 ENGINEERED MUTATION SEQRES 1 A 276 GLY ALA MET GLY SER SER LYS PHE GLU GLU PHE MET THR SEQRES 2 A 276 ARG HIS GLN VAL HIS GLU LYS GLU GLU PHE LYS ALA LEU SEQRES 3 A 276 LYS THR LEU SER ILE PHE TYR GLN ALA GLY THR SER LYS SEQRES 4 A 276 ALA GLY ASN PRO VAL PHE TYR TYR VAL ALA ARG ARG PHE SEQRES 5 A 276 LYS THR GLY GLN ILE ASN GLY ASP LEU LEU ILE TYR HIS SEQRES 6 A 276 VAL LEU LEU THR LEU LYS PRO TYR TYR ALA LYS PRO TYR SEQRES 7 A 276 GLU ILE VAL VAL ASP LEU THR HIS THR GLY PRO SER ASN SEQRES 8 A 276 ARG PHE LYS THR ASP PHE LEU SER LYS TRP PHE VAL VAL SEQRES 9 A 276 PHE PRO GLY PHE ALA TYR ASP ASN VAL SER ALA VAL TYR SEQRES 10 A 276 ILE TYR ASN CYS ASN SER TRP VAL ARG GLU TYR THR LYS SEQRES 11 A 276 TYR HIS GLU ARG LEU LEU THR GLY LEU LYS GLY SER LYS SEQRES 12 A 276 ARG LEU VAL PHE ILE ASP CYS PRO GLY LYS LEU ALA GLU SEQRES 13 A 276 HIS ILE GLU HIS GLU GLN GLN LYS LEU PRO ALA ALA THR SEQRES 14 A 276 LEU ALA LEU GLU GLU ASP LEU LYS VAL PHE HIS ASN ALA SEQRES 15 A 276 LEU LYS LEU ALA HIS LYS ASP THR LYS VAL SER ILE LYS SEQRES 16 A 276 VAL GLY SER THR ALA VAL GLN VAL THR SER ALA GLU ARG SEQRES 17 A 276 THR LYS VAL LEU GLY GLN SER VAL PHE LEU ASN ASP ILE SEQRES 18 A 276 TYR TYR ALA SER GLU ILE GLU GLU ILE CYS LEU VAL ASP SEQRES 19 A 276 GLU ASN GLN PHE THR LEU THR ILE ALA ASN GLN GLY THR SEQRES 20 A 276 PRO LEU THR PHE MET HIS GLN GLU CYS GLU ALA ILE VAL SEQRES 21 A 276 GLN SER ILE ILE HIS ILE ARG THR ARG TRP GLU LEU SER SEQRES 22 A 276 GLN PRO ASP SEQRES 1 B 276 GLY ALA MET GLY SER SER LYS PHE GLU GLU PHE MET THR SEQRES 2 B 276 ARG HIS GLN VAL HIS GLU LYS GLU GLU PHE LYS ALA LEU SEQRES 3 B 276 LYS THR LEU SER ILE PHE TYR GLN ALA GLY THR SER LYS SEQRES 4 B 276 ALA GLY ASN PRO VAL PHE TYR TYR VAL ALA ARG ARG PHE SEQRES 5 B 276 LYS THR GLY GLN ILE ASN GLY ASP LEU LEU ILE TYR HIS SEQRES 6 B 276 VAL LEU LEU THR LEU LYS PRO TYR TYR ALA LYS PRO TYR SEQRES 7 B 276 GLU ILE VAL VAL ASP LEU THR HIS THR GLY PRO SER ASN SEQRES 8 B 276 ARG PHE LYS THR ASP PHE LEU SER LYS TRP PHE VAL VAL SEQRES 9 B 276 PHE PRO GLY PHE ALA TYR ASP ASN VAL SER ALA VAL TYR SEQRES 10 B 276 ILE TYR ASN CYS ASN SER TRP VAL ARG GLU TYR THR LYS SEQRES 11 B 276 TYR HIS GLU ARG LEU LEU THR GLY LEU LYS GLY SER LYS SEQRES 12 B 276 ARG LEU VAL PHE ILE ASP CYS PRO GLY LYS LEU ALA GLU SEQRES 13 B 276 HIS ILE GLU HIS GLU GLN GLN LYS LEU PRO ALA ALA THR SEQRES 14 B 276 LEU ALA LEU GLU GLU ASP LEU LYS VAL PHE HIS ASN ALA SEQRES 15 B 276 LEU LYS LEU ALA HIS LYS ASP THR LYS VAL SER ILE LYS SEQRES 16 B 276 VAL GLY SER THR ALA VAL GLN VAL THR SER ALA GLU ARG SEQRES 17 B 276 THR LYS VAL LEU GLY GLN SER VAL PHE LEU ASN ASP ILE SEQRES 18 B 276 TYR TYR ALA SER GLU ILE GLU GLU ILE CYS LEU VAL ASP SEQRES 19 B 276 GLU ASN GLN PHE THR LEU THR ILE ALA ASN GLN GLY THR SEQRES 20 B 276 PRO LEU THR PHE MET HIS GLN GLU CYS GLU ALA ILE VAL SEQRES 21 B 276 GLN SER ILE ILE HIS ILE ARG THR ARG TRP GLU LEU SER SEQRES 22 B 276 GLN PRO ASP HET PEV A 1 49 HET NA A1817 1 HET PEV B 1 49 HET POP B1817 9 HET POP B1818 9 HETNAM PEV (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1- HETNAM 2 PEV [(PALMITOYLOXY)METHYL]ETHYL STEARATE HETNAM NA SODIUM ION HETNAM POP PYROPHOSPHATE 2- HETSYN PEV PHOSPHATIDYLETHANOLAMINE; 1-PALMITOYL-2-OLEOYL-SN- HETSYN 2 PEV GLYCERO-3-PHOSPHOETHANOLAMINE FORMUL 3 PEV 2(C39 H78 N O8 P) FORMUL 4 NA NA 1+ FORMUL 6 POP 2(H2 O7 P2 2-) FORMUL 8 HOH *166(H2 O) HELIX 1 1 LYS A 1547 HIS A 1558 1 12 HELIX 2 2 GLU A 1561 LEU A 1566 5 6 HELIX 3 3 ARG A 1590 PHE A 1592 5 3 HELIX 4 4 ASN A 1598 LYS A 1611 1 14 HELIX 5 5 GLY A 1628 ARG A 1632 5 5 HELIX 6 6 LYS A 1634 TRP A 1641 1 8 HELIX 7 7 PRO A 1646 ASN A 1652 1 7 HELIX 8 8 ASN A 1662 HIS A 1672 1 11 HELIX 9 9 CYS A 1690 HIS A 1697 5 8 HELIX 10 10 PRO A 1706 LEU A 1712 1 7 HELIX 11 11 GLU A 1795 LEU A 1812 1 18 HELIX 12 12 LYS B 1547 ARG B 1554 1 8 HELIX 13 13 GLU B 1562 LEU B 1569 1 8 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 LEU B 1676 LYS B 1680 5 5 HELIX 21 21 CYS B 1690 HIS B 1697 5 8 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 1795 SER B 1813 1 19 SHEET 1 A 5 PHE A1572 THR A1577 0 SHEET 2 A 5 PRO A1583 VAL A1588 -1 O VAL A1584 N ALA A1575 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 ILE A1620 SHEET 5 A 5 LEU A1685 PHE A1687 1 O VAL A1686 N VAL A1656 SHEET 1 B 7 ASN A1759 TYR A1763 0 SHEET 2 B 7 ALA A1740 SER A1745 -1 N VAL A1741 O TYR A1762 SHEET 3 B 7 THR A1730 VAL A1736 -1 N LYS A1735 O GLN A1742 SHEET 4 B 7 LYS A1717 LYS A1724 -1 N LYS A1717 O VAL A1736 SHEET 5 B 7 LEU A1789 MET A1792 -1 O MET A1792 N LEU A1723 SHEET 6 B 7 GLN A1777 ILE A1782 -1 N LEU A1780 O LEU A1789 SHEET 7 B 7 ILE A1767 ASP A1774 -1 N CYS A1771 O THR A1779 SHEET 1 C 2 THR A1749 VAL A1751 0 SHEET 2 C 2 GLN A1754 VAL A1756 -1 O GLN A1754 N VAL A1751 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 ILE B1620 SHEET 5 D 5 LEU B1685 PHE B1687 1 O VAL B1686 N VAL B1656 SHEET 1 E 7 ASN B1759 TYR B1763 0 SHEET 2 E 7 ALA B1740 SER B1745 -1 N VAL B1741 O TYR B1762 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 PHE B1719 O ILE B1734 SHEET 5 E 7 LEU B1789 MET B1792 -1 O MET B1792 N LEU B1723 SHEET 6 E 7 GLN B1777 ILE B1782 -1 N LEU B1780 O LEU B1789 SHEET 7 E 7 ILE B1767 ASP B1774 -1 N GLU B1768 O THR B1781 SHEET 1 F 2 THR B1749 VAL B1751 0 SHEET 2 F 2 GLN B1754 VAL B1756 -1 O VAL B1756 N THR B1749 SSBOND 1 CYS B 1771 CYS B 1771 1555 7555 2.03 SITE 1 AC1 14 HOH A 41 TYR A1587 VAL A1606 LEU A1610 SITE 2 AC1 14 TYR A1618 ASN A1631 PHE A1633 LEU A1638 SITE 3 AC1 14 PHE A1642 TYR A1650 VAL A1653 VAL A1656 SITE 4 AC1 14 LEU A1679 ARG A1684 SITE 1 AC2 3 ALA A1580 GLY A1581 ASN A1582 SITE 1 AC3 12 HOH B 71 HOH B 118 ILE B1620 PHE B1633 SITE 2 AC3 12 TRP B1641 PHE B1642 TYR B1650 VAL B1653 SITE 3 AC3 12 VAL B1656 THR B1669 GLY B1678 LEU B1679 SITE 1 AC4 8 ARG A1666 LYS A1670 HOH B 58 HOH B 63 SITE 2 AC4 8 HOH B 76 ARG B1666 LYS B1670 LYS B1728 SITE 1 AC5 12 HOH A 13 ARG A1632 LYS A1634 THR A1635 SITE 2 AC5 12 TYR A1671 HIS A1672 HOH B 15 HOH B 65 SITE 3 AC5 12 HOH B 66 ARG B1632 LYS B1634 THR B1635 CRYST1 113.061 113.061 124.612 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 0.008845 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008845 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008025 0.00000