HEADER LIPID BINDING PROTEIN 20-SEP-00 1FVZ OBSLTE 11-MAY-04 1FVZ 1T27 TITLE THE STRUCTURE OF PITP COMPLEXED TO PHOSPHATIDYLCHOLINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL TRANSFER PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PITP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGAN: BRAIN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA KEYWDS PITP, PTDCHO, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.D.YODER,L.M.THOMAS,J.M.TREMBLAY,L.R.YARBROUGH, AUTHOR 2 G.M.HELMKAMP JR. REVDAT 2 11-MAY-04 1FVZ 1 OBSLTE REVDAT 1 04-APR-01 1FVZ 0 JRNL AUTH M.D.YODER,L.M.THOMAS,J.M.TREMBLAY,R.L.OLIVER, JRNL AUTH 2 L.R.YARBROUGH,G.M.HELMKAMP JR. JRNL TITL STRUCTURE OF A MULTIFUNCTIONAL PROTEIN. MAMMALIAN JRNL TITL 2 PHOSPHATIDYLINOSITOL TRANSFER PROTEIN COMPLEXED JRNL TITL 3 WITH PHOSPHATIDYLCHOLINE. JRNL REF J.BIOL.CHEM. V. 276 9246 2001 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.L.OLIVER,J.M.TREMBLAY,G.M.HELMKAMP JR., REMARK 1 AUTH 2 L.R.YARBROUGH,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 ASTM ABCRE6 DK ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 13081 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 639 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2227 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 55 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) : 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.27 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FVZ COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-2000. REMARK 100 THE RCSB ID CODE IS RCSB011947. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-1999 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 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 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS Q4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13081 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 (%) : 90.0 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 44.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, TRIS-HCL, REMARK 280 2-MERCAPTOETHANOL, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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,1/2+Y,-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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 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 MET A 241 CG SD CE REMARK 470 ASP A 242 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 104 SD MET A 104 CE -0.074 REMARK 500 MET A 191 SD MET A 191 CE -0.212 REMARK 500 MET A 247 SD MET A 247 CE 0.083 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 47 N - CA - C ANGL. DEV. = -7.9 DEGREES REMARK 500 HIS A 60 N - CA - C ANGL. DEV. = -9.1 DEGREES REMARK 500 LEU A 65 N - CA - C ANGL. DEV. = 10.6 DEGREES REMARK 500 GLN A 66 N - CA - C ANGL. DEV. = 7.9 DEGREES REMARK 500 TRP A 89 N - CA - C ANGL. DEV. = -8.3 DEGREES REMARK 500 PRO A 93 N - CA - C ANGL. DEV. = 8.5 DEGREES REMARK 500 PRO A 93 C - N - CA ANGL. DEV. = 9.9 DEGREES REMARK 500 ILE A 110 N - CA - C ANGL. DEV. = -8.3 DEGREES REMARK 500 TRP A 236 N - CA - C ANGL. DEV. = 8.0 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 LYS A 105 -115.57 51.50 DBREF 1FVZ A 1 271 UNP P16446 PPI1_RAT 1 271 SEQADV 1FVZ VAL A 139 UNP P16446 ALA 138 CONFLICT 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 VAL 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 PC2 501 54 HETNAM PC2 DI-STEAROYL-3-SN-PHOSPHATIDYLCHOLINE FORMUL 2 PC2 C44 H89 N O8 P 1+ FORMUL 3 HOH *55(H2 O1) HELIX 1 1 SER A 14 THR A 34 1 21 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 GLY A 56 N TYR A 48 SHEET 3 A 8 ILE A 84 ALA A 91 -1 O ILE A 84 N TYR A 63 SHEET 4 A 8 TYR A 94 THR A 100 -1 N TYR A 94 O ALA A 91 SHEET 5 A 8 PHE A 108 LYS A 117 -1 O ILE A 110 N ILE A 99 SHEET 6 A 8 MET A 191 PHE A 201 -1 N CYS A 192 O LYS A 117 SHEET 7 A 8 LEU A 3 LEU A 11 -1 N LEU A 3 O VAL A 199 SHEET 8 A 8 GLU A 138 TYR A 141 1 O GLU A 138 N GLU A 6 CISPEP 1 TYR A 92 PRO A 93 0 0.03 CISPEP 2 GLY A 172 PRO A 173 0 0.20 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