PDB Short entry for 3KZ7 HEADER ISOMERASE/INHIBITOR 08-DEC-09 3KZ7 TITLE C-TERMINAL DOMAIN OF MURINE FKBP25 RAPAMYCIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: FK506-BINDING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FK506-LIKE BINDING DOMAIN (UNP RESIDUES 106-224); COMPND 5 SYNONYM: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE, PPIASE, ROTAMASE, 25 COMPND 6 KDA FKBP, FKBP-25, RAPAMYCIN-SELECTIVE 25 KDA IMMUNOPHILIN; COMPND 7 EC: 5.2.1.8; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: FKBP25, FKBP3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-2 KEYWDS FKPB PPIASE RAPAMYCIN, ISOMERASE, NUCLEUS, PHOSPHOPROTEIN, ROTAMASE, KEYWDS 2 ISOMERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.A.STURA,A.GALAT REVDAT 3 20-AUG-14 3KZ7 1 JRNL REVDAT 2 18-JUN-14 3KZ7 1 JRNL VERSN REVDAT 1 15-DEC-10 3KZ7 0 JRNL AUTH A.GALAT,R.THAI,E.A.STURA JRNL TITL DIVERSIFIED TARGETS OF FKBP25 AND ITS COMPLEX WITH JRNL TITL 2 RAPAMYCIN. JRNL REF INT.J.BIOL.MACROMOL. V. 69 344 2014 JRNL REFN ISSN 0141-8130 JRNL PMID 24879919 JRNL DOI 10.1016/J.IJBIOMAC.2014.05.060 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.930 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 14836 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 740 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.3106 - 3.3340 0.98 2925 146 0.1653 0.1920 REMARK 3 2 3.3340 - 2.6465 1.00 2832 146 0.1770 0.2298 REMARK 3 3 2.6465 - 2.3120 1.00 2810 138 0.1903 0.2660 REMARK 3 4 2.3120 - 2.1006 1.00 2774 149 0.1763 0.2455 REMARK 3 5 2.1006 - 1.9501 1.00 2755 161 0.1845 0.2191 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 64.66 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.99160 REMARK 3 B22 (A**2) : -0.99160 REMARK 3 B33 (A**2) : 1.98320 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1057 REMARK 3 ANGLE : 1.075 1439 REMARK 3 CHIRALITY : 0.073 162 REMARK 3 PLANARITY : 0.004 180 REMARK 3 DIHEDRAL : 16.972 430 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3KZ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-DEC-09. REMARK 100 THE RCSB ID CODE IS RCSB056631. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND (111) REMARK 200 OPTICS : HORIZONTALLY BENT GE(220) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23011 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 68.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 14.000 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.06800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.00 REMARK 200 R MERGE FOR SHELL (I) : 0.12000 REMARK 200 R SYM FOR SHELL (I) : 0.12000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 12.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1PBK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4M AMMONIUM SULFATE, 120MM NA REMARK 280 CITRATE, PH 5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.54500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.82450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.82450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.27250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.82450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.82450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.81750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.82450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.82450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 13.27250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.82450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.82450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.81750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 26.54500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 106 CD REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 C51 RAP A 225 O HOH A 31 1.90 REMARK 500 CG LYS A 154 ND2 ASN A 158 2.17 REMARK 500 OE1 GLU A 177 O HOH A 65 2.19 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 SER A 153 -8.18 77.03 REMARK 500 ALA A 197 -111.60 -124.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 286 DISTANCE = 7.65 ANGSTROMS 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 225 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PBK RELATED DB: PDB REMARK 900 HUMAN FKBP25 RAPAMYCIN COMPLEX DBREF 3KZ7 A 106 224 UNP Q62446 FKBP3_MOUSE 106 224 SEQRES 1 A 119 GLU GLY PRO PRO LYS TYR THR LYS SER ILE LEU LYS LYS SEQRES 2 A 119 GLY ASP LYS THR ASN PHE PRO LYS LYS GLY ASP VAL VAL SEQRES 3 A 119 HIS CYS TRP TYR THR GLY THR LEU PRO ASP GLY THR VAL SEQRES 4 A 119 PHE ASP THR ASN ILE GLN THR SER SER LYS LYS LYS LYS SEQRES 5 A 119 ASN ALA LYS PRO LEU SER PHE LYS VAL GLY VAL GLY LYS SEQRES 6 A 119 VAL ILE ARG GLY TRP ASP GLU ALA LEU LEU THR MET SER SEQRES 7 A 119 LYS GLY GLU LYS ALA ARG LEU GLU ILE GLU PRO GLU TRP SEQRES 8 A 119 ALA TYR GLY LYS LYS GLY GLN PRO ASP ALA LYS ILE PRO SEQRES 9 A 119 PRO ASN THR LYS LEU ILE PHE GLU VAL GLU LEU VAL ASP SEQRES 10 A 119 ILE ASP HET RAP A 225 65 HETNAM RAP RAPAMYCIN IMMUNOSUPPRESSANT DRUG FORMUL 2 RAP C51 H79 N O13 FORMUL 3 HOH *171(H2 O) HELIX 1 1 ILE A 172 LEU A 180 1 9 HELIX 2 2 PRO A 194 ALA A 197 5 4 HELIX 3 3 GLN A 203 LYS A 207 5 5 SHEET 1 A 5 TYR A 111 LYS A 117 0 SHEET 2 A 5 LYS A 187 ILE A 192 -1 O ARG A 189 N SER A 114 SHEET 3 A 5 LEU A 214 ASP A 224 -1 O PHE A 216 N LEU A 190 SHEET 4 A 5 VAL A 130 THR A 138 -1 N THR A 138 O ILE A 215 SHEET 5 A 5 VAL A 144 THR A 147 -1 O ASP A 146 N GLY A 137 SHEET 1 B 5 TYR A 111 LYS A 117 0 SHEET 2 B 5 LYS A 187 ILE A 192 -1 O ARG A 189 N SER A 114 SHEET 3 B 5 LEU A 214 ASP A 224 -1 O PHE A 216 N LEU A 190 SHEET 4 B 5 VAL A 130 THR A 138 -1 N THR A 138 O ILE A 215 SHEET 5 B 5 LEU A 162 LYS A 165 -1 O PHE A 164 N VAL A 131 CISPEP 1 GLY A 107 PRO A 108 0 0.60 SITE 1 AC1 15 HOH A 31 HOH A 96 TYR A 135 PHE A 145 SITE 2 AC1 15 ASP A 146 LEU A 162 GLY A 169 LYS A 170 SITE 3 AC1 15 VAL A 171 ILE A 172 TRP A 175 TYR A 198 SITE 4 AC1 15 GLN A 203 PHE A 216 HOH A 244 CRYST1 85.649 85.649 53.090 90.00 90.00 90.00 P 41 21 2 8 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 0.011676 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011676 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018836 0.00000