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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
