HEADER COMPLEX (ISOMERASE/KINASE) 15-MAR-96 1FAP TITLE THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-RAPAMYCIN TITLE 2 COMPLEX INTERACTING WITH HUMAN FRAP COMPND MOL_ID: 1; COMPND 2 MOLECULE: FK506-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FKBP12; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: FRAP; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: FRB; COMPND 11 SYNONYM: FKBP-RAPAMYCIN ASSOCIATED PROTEIN; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: BL21; SOURCE 6 GENE: HUMAN HIPPOCAMPAL CDNA LIBRARY; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) (NOVAGEN); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-3X; SOURCE 11 EXPRESSION_SYSTEM_GENE: HUMAN HIPPOCAMPAL CDNA LIBRARY (CLONTECH, SOURCE 12 PALO ALTO, CA); SOURCE 13 MOL_ID: 2; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 CELL_LINE: BL21; SOURCE 18 GENE: HUMAN HIPPOCAMPAL CDNA LIBRARY; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 21 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) (NOVAGEN); SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PGEX-3X; SOURCE 23 EXPRESSION_SYSTEM_GENE: HUMAN HIPPOCAMPAL CDNA LIBRARY KEYWDS FKBP12, FRAP, RAPAMYCIN, COMPLEX (ISOMERASE-KINASE), COMPLEX KEYWDS 2 (ISOMERASE-KINASE) COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.CHOI,J.CHEN,S.L.SCHREIBER,J.CLARDY REVDAT 3 07-FEB-24 1FAP 1 REMARK REVDAT 2 24-FEB-09 1FAP 1 VERSN REVDAT 1 23-JUL-97 1FAP 0 JRNL AUTH J.CHOI,J.CHEN,S.L.SCHREIBER,J.CLARDY JRNL TITL STRUCTURE OF THE FKBP12-RAPAMYCIN COMPLEX INTERACTING WITH JRNL TITL 2 THE BINDING DOMAIN OF HUMAN FRAP. JRNL REF SCIENCE V. 273 239 1996 JRNL REFN ISSN 0036-8075 JRNL PMID 8662507 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 6206 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 1639 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 23 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.03 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) : 0.23 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.480 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 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 1FAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173208. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-95 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XUONG-HAMLIN MULTIWIRE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : UCSD REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6920 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.07100 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 22.31500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.26500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.26500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.31500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.07000 REMARK 290 SMTRY3 4 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: 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 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 ARG A 13 -27.42 -141.38 REMARK 500 ALA A 81 -118.48 -139.90 REMARK 500 ILE A 90 -51.23 -143.14 REMARK 500 HIS A 94 -4.94 70.98 REMARK 500 LEU B2051 -31.71 -175.06 REMARK 500 GLN B2063 -60.49 -91.47 REMARK 500 VAL B2094 -12.12 72.33 REMARK 500 ILE B2111 36.34 -94.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 87 PRO A 88 -149.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 80 0.08 SIDE CHAIN REMARK 500 ARG B2018 0.08 SIDE CHAIN 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 RAP A 108 DBREF 1FAP A 1 107 UNP P62942 FKB1A_HUMAN 1 107 DBREF 1FAP B 2018 2112 UNP P42345 FRAP_HUMAN 2018 2112 SEQRES 1 A 107 GLY VAL GLN VAL GLU THR ILE SER PRO GLY ASP GLY ARG SEQRES 2 A 107 THR PHE PRO LYS ARG GLY GLN THR CYS VAL VAL HIS TYR SEQRES 3 A 107 THR GLY MET LEU GLU ASP GLY LYS LYS PHE ASP SER SER SEQRES 4 A 107 ARG ASP ARG ASN LYS PRO PHE LYS PHE MET LEU GLY LYS SEQRES 5 A 107 GLN GLU VAL ILE ARG GLY TRP GLU GLU GLY VAL ALA GLN SEQRES 6 A 107 MET SER VAL GLY GLN ARG ALA LYS LEU THR ILE SER PRO SEQRES 7 A 107 ASP TYR ALA TYR GLY ALA THR GLY HIS PRO GLY ILE ILE SEQRES 8 A 107 PRO PRO HIS ALA THR LEU VAL PHE ASP VAL GLU LEU LEU SEQRES 9 A 107 LYS LEU GLU SEQRES 1 B 95 ARG VAL ALA ILE LEU TRP HIS GLU MET TRP HIS GLU GLY SEQRES 2 B 95 LEU GLU GLU ALA SER ARG LEU TYR PHE GLY GLU ARG ASN SEQRES 3 B 95 VAL LYS GLY MET PHE GLU VAL LEU GLU PRO LEU HIS ALA SEQRES 4 B 95 MET MET GLU ARG GLY PRO GLN THR LEU LYS GLU THR SER SEQRES 5 B 95 PHE ASN GLN ALA TYR GLY ARG ASP LEU MET GLU ALA GLN SEQRES 6 B 95 GLU TRP CYS ARG LYS TYR MET LYS SER GLY ASN VAL LYS SEQRES 7 B 95 ASP LEU THR GLN ALA TRP ASP LEU TYR TYR HIS VAL PHE SEQRES 8 B 95 ARG ARG ILE SER HET RAP A 108 68 HETNAM RAP RAPAMYCIN IMMUNOSUPPRESSANT DRUG FORMUL 3 RAP C51 H79 N O13 FORMUL 4 HOH *23(H2 O) HELIX 1 1 SER A 39 ARG A 42 1 4 HELIX 2 2 ARG A 57 GLN A 65 1 9 HELIX 3 3 PRO A 78 TYR A 80 5 3 HELIX 4 4 TRP B 2023 PHE B 2039 1 17 HELIX 5 5 VAL B 2044 ARG B 2060 1 17 HELIX 6 6 LEU B 2065 SER B 2091 1 27 HELIX 7 7 LYS B 2095 ARG B 2110 1 16 SHEET 1 A 5 PHE A 46 MET A 49 0 SHEET 2 A 5 THR A 21 LEU A 30 -1 N VAL A 24 O PHE A 46 SHEET 3 A 5 LEU A 97 GLU A 107 -1 N GLU A 107 O THR A 21 SHEET 4 A 5 ARG A 71 ILE A 76 -1 N ILE A 76 O LEU A 97 SHEET 5 A 5 VAL A 2 SER A 8 -1 N SER A 8 O ARG A 71 SHEET 1 B 2 THR A 27 MET A 29 0 SHEET 2 B 2 LYS A 35 SER A 38 -1 N ASP A 37 O GLY A 28 SITE 1 AC1 19 PHE A 36 ASP A 37 PHE A 46 GLN A 53 SITE 2 AC1 19 GLU A 54 VAL A 55 ILE A 56 TRP A 59 SITE 3 AC1 19 TYR A 82 ILE A 90 PHE A 99 LEU B2031 SITE 4 AC1 19 SER B2035 PHE B2039 THR B2098 TRP B2101 SITE 5 AC1 19 ASP B2102 TYR B2105 PHE B2108 CRYST1 44.630 52.140 102.530 90.00 90.00 90.00 P 21 21 21 4 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 0.022406 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009753 0.00000