HEADER LIPID BINDING PROTEIN 20-APR-04 1T27 TITLE THE STRUCTURE OF PITP COMPLEXED TO PHOSPHATIDYLCHOLINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN ALPHA ISOFORM; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PTDINS TRANSFER PROTEIN ALPHA, PTDINSTP, PI-TP-ALPHA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 ORGAN: BRAIN; SOURCE 6 GENE: PITPN, PITPNA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.D.YODER,L.M.THOMAS,J.M.TREMBLAY,R.L.OLIVER,L.R.YARBROUGH, AUTHOR 2 G.M.HELMKAMP JR. REVDAT 3 14-FEB-24 1T27 1 REMARK SEQADV REVDAT 2 24-FEB-09 1T27 1 VERSN REVDAT 1 11-MAY-04 1T27 0 SPRSDE 11-MAY-04 1T27 1FVZ JRNL AUTH M.D.YODER,L.M.THOMAS,J.M.TREMBLAY,R.L.OLIVER,L.R.YARBROUGH, JRNL AUTH 2 G.M.HELMKAMP JR. JRNL TITL STRUCTURE OF A MULTIFUNCTIONAL PROTEIN. MAMMALIAN JRNL TITL 2 PHOSPHATIDYLINOSITOL TRANSFER PROTEIN COMPLEXED WITH JRNL TITL 3 PHOSPHATIDYLCHOLINE JRNL REF J.BIOL.CHEM. V. 276 9246 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11104777 JRNL DOI 10.1074/JBC.M010131200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.L.OLIVER,J.M.TREMBLAY,G.M.HELMKAMP JR.,L.R.YARBROUGH, REMARK 1 AUTH 2 N.W.BREAKFIELD,M.D.YODER REMARK 1 TITL X-RAY ANALYSIS OF CRYSTALS OF RAT REMARK 1 TITL 2 PHOSPHATIDYLINOSITOL-TRANSFER PROTEIN WITH BOUND REMARK 1 TITL 3 PHOSPHATIDYLCHOLINE REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 522 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 10089365 REMARK 1 DOI 10.1107/S0907444998009901 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1407892.840 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.4 REMARK 3 NUMBER OF REFLECTIONS : 12145 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 629 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 62.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1396 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 67 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2231 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 144 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.10000 REMARK 3 B22 (A**2) : -2.08000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.99000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.14 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.790 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.750 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.800 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.480 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.860 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 36.32 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PCO.PAR REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : PCO.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1T27 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000022218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791, 0.9794, 0.9500 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38629 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 50.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.08100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, TRIS-HCL, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 36.88650 REMARK 290 SMTRY3 2 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: MONOMERIC 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 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 ASP A 271 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 ASN A 45 81.95 -154.90 REMARK 500 GLN A 66 -74.24 -37.23 REMARK 500 LEU A 76 -21.82 -147.98 REMARK 500 ALA A 91 51.72 -106.99 REMARK 500 TYR A 92 134.01 -39.11 REMARK 500 PRO A 93 0.51 -65.52 REMARK 500 LYS A 105 -119.44 49.74 REMARK 500 ASP A 119 -167.00 -113.46 REMARK 500 CYS A 188 87.07 70.98 REMARK 500 TRP A 204 106.94 -52.44 REMARK 500 LYS A 261 -79.59 -90.66 REMARK 500 ASP A 262 152.66 -36.36 REMARK 500 ALA A 269 156.46 -47.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PCW A 501 DBREF 1T27 A 2 271 UNP P16446 PIPNA_RAT 1 270 SEQADV 1T27 MET A 1 UNP P16446 INITIATING METHIONINE SEQRES 1 A 271 MET VAL LEU LEU LYS GLU TYR ARG VAL ILE LEU PRO VAL SEQRES 2 A 271 SER VAL ASP GLU TYR GLN VAL GLY GLN LEU TYR SER VAL SEQRES 3 A 271 ALA GLU ALA SER LYS ASN GLU THR GLY GLY GLY GLU GLY SEQRES 4 A 271 VAL GLU VAL LEU VAL ASN GLU PRO TYR GLU LYS ASP ASP SEQRES 5 A 271 GLY GLU LYS GLY GLN TYR THR HIS LYS ILE TYR HIS LEU SEQRES 6 A 271 GLN SER LYS VAL PRO THR PHE VAL ARG MET LEU ALA PRO SEQRES 7 A 271 GLU GLY ALA LEU ASN ILE HIS GLU LYS ALA TRP ASN ALA SEQRES 8 A 271 TYR PRO TYR CYS ARG THR VAL ILE THR ASN GLU TYR MET SEQRES 9 A 271 LYS GLU ASP PHE LEU ILE LYS ILE GLU THR TRP HIS LYS SEQRES 10 A 271 PRO ASP LEU GLY THR GLN GLU ASN VAL HIS LYS LEU GLU SEQRES 11 A 271 PRO GLU ALA TRP LYS HIS VAL GLU ALA ILE TYR ILE ASP SEQRES 12 A 271 ILE ALA ASP ARG SER GLN VAL LEU SER LYS ASP TYR LYS SEQRES 13 A 271 ALA GLU GLU ASP PRO ALA LYS PHE LYS SER ILE LYS THR SEQRES 14 A 271 GLY ARG GLY PRO LEU GLY PRO ASN TRP LYS GLN GLU LEU SEQRES 15 A 271 VAL ASN GLN LYS ASP CYS PRO TYR MET CYS ALA TYR LYS SEQRES 16 A 271 LEU VAL THR VAL LYS PHE LYS TRP TRP GLY LEU GLN ASN SEQRES 17 A 271 LYS VAL GLU ASN PHE ILE HIS LYS GLN GLU LYS ARG LEU SEQRES 18 A 271 PHE THR ASN PHE HIS ARG GLN LEU PHE CYS TRP LEU ASP SEQRES 19 A 271 LYS TRP VAL ASP LEU THR MET ASP ASP ILE ARG ARG MET SEQRES 20 A 271 GLU GLU GLU THR LYS ARG GLN LEU ASP GLU MET ARG GLN SEQRES 21 A 271 LYS ASP PRO VAL LYS GLY MET THR ALA ASP ASP HET PCW A 501 54 HETNAM PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE HETSYN PCW (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9- HETSYN 2 PCW OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN- HETSYN 3 PCW 1-AMINIUM-4-OXIDE FORMUL 2 PCW C44 H85 N O8 P 1+ FORMUL 3 HOH *144(H2 O) HELIX 1 1 SER A 14 GLU A 33 1 20 HELIX 2 2 PRO A 70 MET A 75 1 6 HELIX 3 3 MET A 104 GLU A 106 5 3 HELIX 4 4 GLU A 132 VAL A 137 5 6 HELIX 5 5 ASP A 146 VAL A 150 5 5 HELIX 6 6 LYS A 156 ASP A 160 5 5 HELIX 7 7 ASN A 177 VAL A 183 1 7 HELIX 8 8 LEU A 206 TRP A 232 1 27 HELIX 9 9 TRP A 232 VAL A 237 1 6 HELIX 10 10 THR A 240 LYS A 261 1 22 SHEET 1 A 8 GLY A 39 GLU A 49 0 SHEET 2 A 8 LYS A 55 HIS A 64 -1 O TYR A 58 N GLU A 46 SHEET 3 A 8 ILE A 84 ALA A 91 -1 O GLU A 86 N LYS A 61 SHEET 4 A 8 TYR A 94 THR A 100 -1 O THR A 100 N HIS A 85 SHEET 5 A 8 PHE A 108 LYS A 117 -1 O THR A 114 N CYS A 95 SHEET 6 A 8 MET A 191 PHE A 201 -1 O THR A 198 N LYS A 111 SHEET 7 A 8 LEU A 3 LEU A 11 -1 N LYS A 5 O VAL A 197 SHEET 8 A 8 GLU A 138 ILE A 142 1 O ILE A 140 N GLU A 6 CISPEP 1 TYR A 92 PRO A 93 0 0.56 CISPEP 2 GLY A 172 PRO A 173 0 -0.27 SITE 1 AC1 22 GLN A 22 TYR A 63 LYS A 68 ALA A 77 SITE 2 AC1 22 LEU A 82 GLU A 86 ASN A 90 THR A 97 SITE 3 AC1 22 ILE A 99 ASN A 101 TYR A 103 MET A 104 SITE 4 AC1 22 LYS A 195 TRP A 203 PHE A 213 GLN A 217 SITE 5 AC1 22 GLU A 218 PHE A 222 MET A 267 ASP A 270 SITE 6 AC1 22 HOH A 503 HOH A 628 CRYST1 43.914 73.773 48.185 90.00 114.73 90.00 P 1 21 1 2 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 0.022772 0.000000 0.010488 0.00000 SCALE2 0.000000 0.013555 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022849 0.00000