PDB Short entry for 1BL4 HEADER ISOMERASE 23-JUL-98 1BL4 TITLE FKBP MUTANT F36V COMPLEXED WITH REMODELED SYNTHETIC LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (FK506 BINDING PROTEIN); COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: FKBP; COMPND 5 EC: 5.2.1.8; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: COMPLEXED WITH REDESIGNED COMPOUND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOMERASE, ROTAMASE EXPDTA X-RAY DIFFRACTION AUTHOR M.H.HATADA,T.CLACKSON,W.YANG,L.W.ROZAMUS,J.AMARA,C.T.ROLLINS, AUTHOR 2 L.F.STEVENSON,S.R.MAGARI,S.A.WOOD,N.L.COURAGE,X.LU,F.CERASOLI AUTHOR 3 JUNIOR,M.GILMAN,D.HOLT REVDAT 7 09-AUG-23 1BL4 1 REMARK REVDAT 6 03-NOV-21 1BL4 1 REMARK SEQADV REVDAT 5 18-APR-18 1BL4 1 REMARK REVDAT 4 24-FEB-09 1BL4 1 VERSN REVDAT 3 01-APR-03 1BL4 1 JRNL REVDAT 2 29-DEC-99 1BL4 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 02-SEP-98 1BL4 0 JRNL AUTH T.CLACKSON,W.YANG,L.W.ROZAMUS,M.HATADA,J.F.AMARA, JRNL AUTH 2 C.T.ROLLINS,L.F.STEVENSON,S.R.MAGARI,S.A.WOOD,N.L.COURAGE, JRNL AUTH 3 X.LU,F.CERASOLI JR.,M.GILMAN,D.A.HOLT JRNL TITL REDESIGNING AN FKBP-LIGAND INTERFACE TO GENERATE CHEMICAL JRNL TITL 2 DIMERIZERS WITH NOVEL SPECIFICITY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 95 10437 1998 JRNL REFN ISSN 0027-8424 JRNL PMID 9724721 JRNL DOI 10.1073/PNAS.95.18.10437 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.0 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 15095 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) : 0.188 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1518 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1624 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE : 0.2500 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 170 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 : 1656 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 100 REMARK 3 SOLVENT ATOMS : 69 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.50 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : NULL 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 3.350 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 1.980 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BL4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008314. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-96 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.0 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 : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16490 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 94.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06300 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.16000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1FKF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION IN HANGING DROPS WITH REMARK 280 40 MG/ML COMPLEX AND 1.2M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 PHOSPHATE, PH 6.0 OVER RESERVOIRS OF 2.4 M AMMONIUM SULFATE, REMARK 280 VAPOR DIFFUSION - HANGING DROP, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,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 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: 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 42 N - CA - C ANGL. DEV. = 17.0 DEGREES REMARK 500 ARG B 42 N - CA - C ANGL. DEV. = 16.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 -21.44 -145.08 REMARK 500 ASN A 43 -13.51 89.55 REMARK 500 ALA A 81 -109.62 -130.88 REMARK 500 PRO A 88 124.76 -38.79 REMARK 500 ILE A 90 -56.83 -123.06 REMARK 500 ARG B 13 -36.14 -140.17 REMARK 500 ASN B 43 -10.00 77.42 REMARK 500 ALA B 81 -106.27 -133.96 REMARK 500 PRO B 88 121.04 -36.73 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 AP1 A 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP1 B 109 DBREF 1BL4 A 1 107 UNP P62942 FKB1A_HUMAN 1 107 DBREF 1BL4 B 1 107 UNP P20071 FKBP_HUMAN 1 107 SEQADV 1BL4 VAL A 36 UNP P62942 PHE 36 ENGINEERED MUTATION SEQADV 1BL4 VAL B 36 UNP P20071 PHE 36 ENGINEERED MUTATION 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 VAL 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 107 GLY VAL GLN VAL GLU THR ILE SER PRO GLY ASP GLY ARG SEQRES 2 B 107 THR PHE PRO LYS ARG GLY GLN THR CYS VAL VAL HIS TYR SEQRES 3 B 107 THR GLY MET LEU GLU ASP GLY LYS LYS VAL ASP SER SER SEQRES 4 B 107 ARG ASP ARG ASN LYS PRO PHE LYS PHE MET LEU GLY LYS SEQRES 5 B 107 GLN GLU VAL ILE ARG GLY TRP GLU GLU GLY VAL ALA GLN SEQRES 6 B 107 MET SER VAL GLY GLN ARG ALA LYS LEU THR ILE SER PRO SEQRES 7 B 107 ASP TYR ALA TYR GLY ALA THR GLY HIS PRO GLY ILE ILE SEQRES 8 B 107 PRO PRO HIS ALA THR LEU VAL PHE ASP VAL GLU LEU LEU SEQRES 9 B 107 LYS LEU GLU HET AP1 A 108 50 HET AP1 B 109 50 HETNAM AP1 {3-[3-(3,4-DIMETHOXY-PHENYL)-1-(1-{1-[2-(3,4,5- HETNAM 2 AP1 TRIMETHOXY-PHENYL)-BUTYRYL]-PIPERIDIN-2YL}-VINYLOXY)- HETNAM 3 AP1 PROPYL]-PHENOXY}-ACETIC ACID FORMUL 3 AP1 2(C38 H47 N O11) FORMUL 5 HOH *69(H2 O) HELIX 1 1 SER A 39 ASP A 41 5 3 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 SER B 39 ASP B 41 5 3 HELIX 5 5 ARG B 57 GLN B 65 1 9 HELIX 6 6 PRO B 78 TYR B 80 5 3 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 SHEET 1 C 5 PHE B 46 MET B 49 0 SHEET 2 C 5 THR B 21 LEU B 30 -1 N VAL B 24 O PHE B 46 SHEET 3 C 5 LEU B 97 GLU B 107 -1 N GLU B 107 O THR B 21 SHEET 4 C 5 ARG B 71 ILE B 76 -1 N ILE B 76 O LEU B 97 SHEET 5 C 5 VAL B 2 SER B 8 -1 N SER B 8 O ARG B 71 SHEET 1 D 2 THR B 27 MET B 29 0 SHEET 2 D 2 LYS B 35 SER B 38 -1 N ASP B 37 O GLY B 28 SITE 1 AC1 22 TYR A 26 VAL A 36 ASP A 37 ARG A 42 SITE 2 AC1 22 PHE A 46 GLN A 53 GLU A 54 VAL A 55 SITE 3 AC1 22 ILE A 56 TRP A 59 ALA A 81 TYR A 82 SITE 4 AC1 22 HIS A 87 PHE A 99 HOH A 140 ASP B 37 SITE 5 AC1 22 ARG B 42 LYS B 44 AP1 B 109 HOH B 126 SITE 6 AC1 22 HOH B 130 HOH B 136 SITE 1 AC2 16 ASP A 37 ARG A 42 LYS A 44 AP1 A 108 SITE 2 AC2 16 HOH A 119 HOH A 120 TYR B 26 VAL B 36 SITE 3 AC2 16 PHE B 46 GLU B 54 VAL B 55 ILE B 56 SITE 4 AC2 16 TRP B 59 TYR B 82 HIS B 87 PHE B 99 CRYST1 32.730 41.850 43.590 62.61 82.75 85.29 P 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 0.030553 -0.002517 -0.003079 0.00000 SCALE2 0.000000 0.023976 -0.012245 0.00000 SCALE3 0.000000 0.000000 0.025967 0.00000