HEADER CELL CYCLE 06-MAY-99 4FAP TITLE ATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH HUMAN TITLE 2 FKBP12 AND FRB DOMAIN OF 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: FKBP12-RAPAMYCIN ASSOCIATED PROTEIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: FRB; COMPND 11 SYNONYM: FRAP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: BL21 (DE3) (NOVAGEN); SOURCE 6 GENE: HUMAN HIPPOCAMPAL CDNA LIBRARY SOURCE 8 (CLONTECH, PALO ALTO, SOURCE 7 CA); SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) (NOVAGEN); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PGEX-3X; SOURCE 13 MOL_ID: 2; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606 KEYWDS FKBP12, FRAP, RAPAMYCIN, COMPLEX, GENE THERAPY, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR J.LIANG,J.CLARDY REVDAT 5 13-SEP-23 4FAP 1 REMARK REVDAT 4 04-OCT-17 4FAP 1 REMARK REVDAT 3 24-FEB-09 4FAP 1 VERSN REVDAT 2 01-APR-03 4FAP 1 JRNL REVDAT 1 13-SEP-00 4FAP 0 JRNL AUTH J.LIANG,J.CHOI,J.CLARDY JRNL TITL REFINED STRUCTURE OF THE FKBP12-RAPAMYCIN-FRB TERNARY JRNL TITL 2 COMPLEX AT 2.2 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 736 1999 JRNL REFN ISSN 0907-4449 JRNL PMID 10089303 JRNL DOI 10.1107/S0907444998014747 REMARK 2 REMARK 2 RESOLUTION. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 4851 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) : 0.184 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 480 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 324 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1628 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 69 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 19.13000 REMARK 3 B22 (A**2) : -5.90000 REMARK 3 B33 (A**2) : -13.20000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.35 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) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.50 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.930 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) : 8.150 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 11.660; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 11.410; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 16.450; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.27 REMARK 3 BSOL : 11.96 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 : 1703.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : 1703.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 4FAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000001020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : FEB-97 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SDMS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : UCSD-SYSTEM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5598 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 8.60000 REMARK 200 FOR THE DATA SET : 10.4000 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2FAP 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): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG8000, 10% MPD, 0.1 M TRIS-HCL REMARK 280 PH 8.5, PH 8.0 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 22.70000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.28000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.28000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.70000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.05000 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 ASP A 37 151.45 176.21 REMARK 500 SER A 38 126.50 -170.22 REMARK 500 ILE A 56 156.08 -48.80 REMARK 500 ALA A 81 -116.15 -115.74 REMARK 500 PRO A 88 118.96 -24.85 REMARK 500 ILE A 90 -62.62 -125.68 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 ARD A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FAP RELATED DB: PDB REMARK 900 RELATED ID: 3FAP RELATED DB: PDB DBREF 4FAP A 1 107 UNP P62942 FKB1A_HUMAN 1 107 DBREF 4FAP B 108 201 UNP P42345 FRAP_HUMAN 2019 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 94 VAL ALA ILE LEU TRP HIS GLU MET TRP HIS GLU GLY LEU SEQRES 2 B 94 GLU GLU ALA SER ARG LEU TYR PHE GLY GLU ARG ASN VAL SEQRES 3 B 94 LYS GLY MET PHE GLU VAL LEU GLU PRO LEU HIS ALA MET SEQRES 4 B 94 MET GLU ARG GLY PRO GLN THR LEU LYS GLU THR SER PHE SEQRES 5 B 94 ASN GLN ALA TYR GLY ARG ASP LEU MET GLU ALA GLN GLU SEQRES 6 B 94 TRP CYS ARG LYS TYR MET LYS SER GLY ASN VAL LYS ASP SEQRES 7 B 94 LEU THR GLN ALA TRP ASP LEU TYR TYR HIS VAL PHE ARG SEQRES 8 B 94 ARG ILE SER HET ARD A 402 69 HETNAM ARD C15-(R)-METHYLTHIENYL RAPAMYCIN HETSYN ARD RAPAMYCIN IMMUNOSUPPRESSANT DRUG FORMUL 3 ARD C55 H81 N O12 S 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 112 PHE B 128 1 17 HELIX 5 5 VAL B 133 ARG B 149 1 17 HELIX 6 6 LEU B 154 SER B 180 1 27 HELIX 7 7 VAL B 183 ARG B 199 1 17 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 TYR A 26 PHE A 36 ASP A 37 ARG A 42 SITE 2 AC1 19 PHE A 46 GLN A 53 GLU A 54 VAL A 55 SITE 3 AC1 19 ILE A 56 TRP A 59 TYR A 82 ILE A 91 SITE 4 AC1 19 PHE A 99 LEU B 120 SER B 124 PHE B 128 SITE 5 AC1 19 THR B 187 TYR B 194 PHE B 197 CRYST1 45.400 52.100 102.560 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 0.022026 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019194 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009750 0.00000