HEADER ISOMERASE 10-JAN-13 4IQ2 TITLE P21 CRYSTAL FORM OF FKBP12.6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FKBP1B; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PPIASE FKBP1B, 12.6 KDA FK506-BINDING PROTEIN, 12.6 KDA COMPND 5 FKBP, FKBP-12.6, FK506-BINDING PROTEIN 1B, FKBP-1B, IMMUNOPHILIN COMPND 6 FKBP12.6, ROTAMASE, H-FKBP-12; COMPND 7 EC: 5.2.1.8; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FKBP12.6, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.CHEN,S.M.MUSTAFI,H.M.LI,D.M.LEMASTER,G.HERNANDEZ REVDAT 5 20-SEP-23 4IQ2 1 REMARK SEQADV REVDAT 4 29-APR-15 4IQ2 1 HETSYN REVDAT 3 24-SEP-14 4IQ2 1 JRNL REVDAT 2 12-MAR-14 4IQ2 1 JRNL REVDAT 1 15-JAN-14 4IQ2 0 JRNL AUTH H.CHEN,S.M.MUSTAFI,D.M.LEMASTER,Z.LI,A.HEROUX,H.LI, JRNL AUTH 2 G.HERNANDEZ JRNL TITL CRYSTAL STRUCTURE AND CONFORMATIONAL FLEXIBILITY OF THE JRNL TITL 2 UNLIGATED FK506-BINDING PROTEIN FKBP12.6. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 636 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24598733 JRNL DOI 10.1107/S1399004713032112 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 20126 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 38.2420 - 4.0959 0.99 1394 154 0.1784 0.1934 REMARK 3 2 4.0959 - 3.2516 1.00 1364 150 0.1705 0.1964 REMARK 3 3 3.2516 - 2.8407 0.99 1346 150 0.2051 0.2118 REMARK 3 4 2.8407 - 2.5810 0.99 1347 147 0.2258 0.2707 REMARK 3 5 2.5810 - 2.3961 0.98 1336 148 0.2262 0.2459 REMARK 3 6 2.3961 - 2.2548 0.98 1322 146 0.2234 0.2453 REMARK 3 7 2.2548 - 2.1419 0.98 1318 146 0.2263 0.2608 REMARK 3 8 2.1419 - 2.0487 0.97 1298 143 0.2491 0.2689 REMARK 3 9 2.0487 - 1.9698 0.97 1317 145 0.2630 0.3323 REMARK 3 10 1.9698 - 1.9018 0.97 1310 144 0.3060 0.3542 REMARK 3 11 1.9018 - 1.8424 0.96 1286 142 0.3324 0.3413 REMARK 3 12 1.8424 - 1.7897 0.96 1289 143 0.3569 0.4105 REMARK 3 13 1.7897 - 1.7426 0.90 1212 133 0.4033 0.4059 REMARK 3 14 1.7426 - 1.7000 0.75 987 109 0.4363 0.4578 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 46.08 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.43010 REMARK 3 B22 (A**2) : -2.99270 REMARK 3 B33 (A**2) : -0.43740 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.75310 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 : 0.003 1682 REMARK 3 ANGLE : 0.849 2267 REMARK 3 CHIRALITY : 0.056 248 REMARK 3 PLANARITY : 0.003 302 REMARK 3 DIHEDRAL : 11.839 642 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 4IQ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000077065. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20138 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 38.232 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : 0.13700 REMARK 200 FOR THE DATA SET : 4.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : 0.51000 REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 1C9H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M MALONIC ACID, PH 7.0, 4% REMARK 280 ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 24.67300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 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 3 OE2 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 -35.61 -131.29 REMARK 500 ALA A 81 -101.38 -134.05 REMARK 500 ARG B 13 -42.53 -142.28 REMARK 500 ALA B 81 -101.23 -132.22 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 MLA A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IQC RELATED DB: PDB DBREF 4IQ2 A 1 107 UNP P68106 FKB1B_HUMAN 2 108 DBREF 4IQ2 B 1 107 UNP P68106 FKB1B_HUMAN 2 108 SEQADV 4IQ2 VAL A 22 UNP P68106 CYS 23 ENGINEERED MUTATION SEQADV 4IQ2 ILE A 76 UNP P68106 CYS 77 ENGINEERED MUTATION SEQADV 4IQ2 VAL B 22 UNP P68106 CYS 23 ENGINEERED MUTATION SEQADV 4IQ2 ILE B 76 UNP P68106 CYS 77 ENGINEERED MUTATION SEQRES 1 A 107 GLY VAL GLU ILE GLU THR ILE SER PRO GLY ASP GLY ARG SEQRES 2 A 107 THR PHE PRO LYS LYS GLY GLN THR VAL VAL VAL HIS TYR SEQRES 3 A 107 THR GLY MET LEU GLN ASN GLY LYS LYS PHE ASP SER SER SEQRES 4 A 107 ARG ASP ARG ASN LYS PRO PHE LYS PHE ARG ILE GLY LYS SEQRES 5 A 107 GLN GLU VAL ILE LYS GLY PHE GLU GLU GLY ALA ALA GLN SEQRES 6 A 107 MET SER LEU GLY GLN ARG ALA LYS LEU THR ILE THR PRO SEQRES 7 A 107 ASP VAL ALA TYR GLY ALA THR GLY HIS PRO GLY VAL ILE SEQRES 8 A 107 PRO PRO ASN ALA THR LEU ILE PHE ASP VAL GLU LEU LEU SEQRES 9 A 107 ASN LEU GLU SEQRES 1 B 107 GLY VAL GLU ILE GLU THR ILE SER PRO GLY ASP GLY ARG SEQRES 2 B 107 THR PHE PRO LYS LYS GLY GLN THR VAL VAL VAL HIS TYR SEQRES 3 B 107 THR GLY MET LEU GLN ASN GLY LYS LYS PHE ASP SER SER SEQRES 4 B 107 ARG ASP ARG ASN LYS PRO PHE LYS PHE ARG ILE GLY LYS SEQRES 5 B 107 GLN GLU VAL ILE LYS GLY PHE GLU GLU GLY ALA ALA GLN SEQRES 6 B 107 MET SER LEU GLY GLN ARG ALA LYS LEU THR ILE THR PRO SEQRES 7 B 107 ASP VAL ALA TYR GLY ALA THR GLY HIS PRO GLY VAL ILE SEQRES 8 B 107 PRO PRO ASN ALA THR LEU ILE PHE ASP VAL GLU LEU LEU SEQRES 9 B 107 ASN LEU GLU HET MLA A 201 7 HETNAM MLA MALONIC ACID HETSYN MLA DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; HETSYN 2 MLA METHANEDICARBOXYLIC ACID FORMUL 3 MLA C3 H4 O4 FORMUL 4 HOH *241(H2 O) HELIX 1 1 ILE A 56 ALA A 64 1 9 HELIX 2 2 PRO A 78 ALA A 81 5 4 HELIX 3 3 ILE B 56 GLN B 65 1 10 HELIX 4 4 PRO B 78 ALA B 81 5 4 SHEET 1 A 5 VAL A 2 SER A 8 0 SHEET 2 A 5 ARG A 71 ILE A 76 -1 O ARG A 71 N ILE A 7 SHEET 3 A 5 LEU A 97 GLU A 107 -1 O LEU A 97 N ILE A 76 SHEET 4 A 5 THR A 21 LEU A 30 -1 N MET A 29 O ILE A 98 SHEET 5 A 5 LYS A 35 SER A 38 -1 O ASP A 37 N GLY A 28 SHEET 1 B 5 VAL A 2 SER A 8 0 SHEET 2 B 5 ARG A 71 ILE A 76 -1 O ARG A 71 N ILE A 7 SHEET 3 B 5 LEU A 97 GLU A 107 -1 O LEU A 97 N ILE A 76 SHEET 4 B 5 THR A 21 LEU A 30 -1 N MET A 29 O ILE A 98 SHEET 5 B 5 PHE A 46 ARG A 49 -1 O PHE A 46 N VAL A 24 SHEET 1 C 5 VAL B 2 SER B 8 0 SHEET 2 C 5 ARG B 71 ILE B 76 -1 O LYS B 73 N GLU B 5 SHEET 3 C 5 LEU B 97 GLU B 107 -1 O LEU B 97 N ILE B 76 SHEET 4 C 5 THR B 21 LEU B 30 -1 N MET B 29 O ILE B 98 SHEET 5 C 5 LYS B 35 SER B 38 -1 O PHE B 36 N GLY B 28 SHEET 1 D 5 VAL B 2 SER B 8 0 SHEET 2 D 5 ARG B 71 ILE B 76 -1 O LYS B 73 N GLU B 5 SHEET 3 D 5 LEU B 97 GLU B 107 -1 O LEU B 97 N ILE B 76 SHEET 4 D 5 THR B 21 LEU B 30 -1 N MET B 29 O ILE B 98 SHEET 5 D 5 PHE B 46 ARG B 49 -1 O PHE B 48 N VAL B 22 SITE 1 AC1 11 PRO A 78 ASP A 79 GLY A 83 ALA A 84 SITE 2 AC1 11 HOH A 333 HOH A 339 HOH A 413 ALA B 84 SITE 3 AC1 11 THR B 85 HOH B 211 HOH B 254 CRYST1 39.061 49.346 50.980 90.00 101.82 90.00 P 1 21 1 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 0.025601 0.000000 0.005359 0.00000 SCALE2 0.000000 0.020265 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020041 0.00000