HEADER ISOMERASE 29-OCT-03 1R9H TITLE STRUCTURAL GENOMICS OF C.ELEGANS: FKBP-TYPE PEPTIDYLPROLYL ISOMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FK506 BINDING PROTEIN FAMILY; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FKB-6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: F31D4.3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS STRUCTURAL GENOMICS, PEPTIDYLPROLYL ISOMERASE, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS, SECSG, KEYWDS 3 ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.LI,SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS (SECSG) REVDAT 5 14-FEB-24 1R9H 1 REMARK REVDAT 4 24-JAN-18 1R9H 1 AUTHOR REVDAT 3 24-FEB-09 1R9H 1 VERSN REVDAT 2 01-FEB-05 1R9H 1 AUTHOR KEYWDS REMARK REVDAT 1 02-DEC-03 1R9H 0 JRNL AUTH S.LI,J.FINLEY,C.-H.LUAN,S.QIU,R.GRAY,Q.SHANG,D.LUO,C.HONGLI, JRNL AUTH 2 J.ZHAO,W.-Y.HUANG,L.J.DELUCAS,L.NAGY,A.STANTON,M.LUO, JRNL AUTH 3 J.SYMERSKY,N.SCHORMANN,G.LIN,J.TSAO,D.H.JOHNSON,W.M.CARSON JRNL TITL STRUCTURAL GENOMICS OF C.ELEGANS: FKBP-TYPE PEPTIDYLPROLYL JRNL TITL 2 ISOMERASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1552154.380 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 16134 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) : 0.210 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 788 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2425 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 141 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 896 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.92500 REMARK 3 B22 (A**2) : -1.92500 REMARK 3 B33 (A**2) : 3.85000 REMARK 3 B12 (A**2) : -1.08200 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 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) : 1.260 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.950 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.110 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.240 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 43.75 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1R9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020603. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21526 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 38.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M AMMONIUM SULFATE, 0.1M MES, 10% REMARK 280 DIOXANE, SEEDING WAS USED TO GROW THE CRYSTALS, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.26667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 140.53333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 105.40000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 175.66667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.13333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 70.26667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 140.53333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 175.66667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 105.40000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 35.13333 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 SER A 2 REMARK 465 GLY A 3 REMARK 465 GLU A 4 REMARK 465 GLU A 123 REMARK 465 ASP A 124 REMARK 465 ILE A 125 REMARK 465 SER A 126 REMARK 465 PRO A 127 REMARK 465 ASP A 128 REMARK 465 ARG A 129 REMARK 465 ASP A 130 REMARK 465 GLY A 131 REMARK 465 THR A 132 REMARK 465 ILE A 133 REMARK 465 LEU A 134 REMARK 465 ARG A 135 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: F31D4.3 RELATED DB: TARGETDB DBREF 1R9H A 1 135 UNP O45418 O45418_CAEEL 1 135 SEQRES 1 A 135 MET SER GLY GLU LYS ILE ASP ILE THR PRO LYS LYS ASP SEQRES 2 A 135 GLY GLY VAL LEU LYS LEU ILE LYS LYS GLU GLY GLN GLY SEQRES 3 A 135 VAL VAL LYS PRO THR THR GLY THR THR VAL LYS VAL HIS SEQRES 4 A 135 TYR VAL GLY THR LEU GLU ASN GLY THR LYS PHE ASP SER SEQRES 5 A 135 SER ARG ASP ARG GLY ASP GLN PHE SER PHE ASN LEU GLY SEQRES 6 A 135 ARG GLY ASN VAL ILE LYS GLY TRP ASP LEU GLY VAL ALA SEQRES 7 A 135 THR MET THR LYS GLY GLU VAL ALA GLU PHE THR ILE ARG SEQRES 8 A 135 SER ASP TYR GLY TYR GLY ASP ALA GLY SER PRO PRO LYS SEQRES 9 A 135 ILE PRO GLY GLY ALA THR LEU ILE PHE GLU VAL GLU LEU SEQRES 10 A 135 PHE GLU TRP SER ALA GLU ASP ILE SER PRO ASP ARG ASP SEQRES 11 A 135 GLY THR ILE LEU ARG FORMUL 2 HOH *110(H2 O) HELIX 1 1 SER A 53 GLY A 57 1 5 HELIX 2 2 ILE A 70 ALA A 78 1 9 HELIX 3 3 SER A 92 GLY A 95 5 4 SHEET 1 A 6 ILE A 6 ASP A 7 0 SHEET 2 A 6 VAL A 16 LYS A 22 -1 O LYS A 18 N ILE A 6 SHEET 3 A 6 VAL A 85 ILE A 90 -1 O GLU A 87 N LEU A 19 SHEET 4 A 6 LEU A 111 SER A 121 -1 O PHE A 113 N PHE A 88 SHEET 5 A 6 THR A 35 LEU A 44 -1 N THR A 35 O SER A 121 SHEET 6 A 6 LYS A 49 SER A 52 -1 O ASP A 51 N GLY A 42 SHEET 1 B 6 ILE A 6 ASP A 7 0 SHEET 2 B 6 VAL A 16 LYS A 22 -1 O LYS A 18 N ILE A 6 SHEET 3 B 6 VAL A 85 ILE A 90 -1 O GLU A 87 N LEU A 19 SHEET 4 B 6 LEU A 111 SER A 121 -1 O PHE A 113 N PHE A 88 SHEET 5 B 6 THR A 35 LEU A 44 -1 N THR A 35 O SER A 121 SHEET 6 B 6 PHE A 60 ASN A 63 -1 O PHE A 60 N VAL A 38 CISPEP 1 PRO A 102 PRO A 103 0 0.27 CRYST1 52.417 52.417 210.800 90.00 90.00 120.00 P 61 2 2 12 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 0.019078 0.011015 0.000000 0.00000 SCALE2 0.000000 0.022029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004744 0.00000