HEADER ISOMERASE 11-JAN-13 4IQC TITLE P3121 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 4 20-SEP-23 4IQC 1 SEQADV REVDAT 3 24-SEP-14 4IQC 1 JRNL REVDAT 2 12-MAR-14 4IQC 1 JRNL REVDAT 1 15-JAN-14 4IQC 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 20089 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1009 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 45.7532 - 3.6395 1.00 2917 156 0.1715 0.1713 REMARK 3 2 3.6395 - 2.8889 1.00 2767 147 0.1900 0.2508 REMARK 3 3 2.8889 - 2.5237 1.00 2721 149 0.2244 0.2432 REMARK 3 4 2.5237 - 2.2930 1.00 2679 138 0.2194 0.2481 REMARK 3 5 2.2930 - 2.1287 0.99 2694 144 0.2095 0.2520 REMARK 3 6 2.1287 - 2.0031 0.99 2655 139 0.2220 0.2824 REMARK 3 7 2.0031 - 1.9030 0.98 2647 136 0.2567 0.2884 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 47.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.460 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) : 2.52370 REMARK 3 B22 (A**2) : 2.52370 REMARK 3 B33 (A**2) : -5.04740 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 : 0.008 1676 REMARK 3 ANGLE : 1.075 2260 REMARK 3 CHIRALITY : 0.075 248 REMARK 3 PLANARITY : 0.005 300 REMARK 3 DIHEDRAL : 13.487 638 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 4IQC 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_1000077075. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20094 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 22.5000 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) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.89400 REMARK 200 R SYM FOR SHELL (I) : 0.89400 REMARK 200 FOR SHELL : 0.900 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 (%): 53.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 62% AMMONIUM SULFATE, 0.1 M HEPES, PH REMARK 280 7.5, 4% ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 50.98300 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 101.96600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 101.96600 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 50.98300 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 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 O HOH A 245 O HOH A 251 2.05 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 ALA A 81 -110.35 -125.81 REMARK 500 ARG B 13 -18.47 -141.90 REMARK 500 ALA B 81 -107.09 -128.49 REMARK 500 VAL B 90 -56.23 -128.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IQ2 RELATED DB: PDB DBREF 4IQC A 1 107 UNP P68106 FKB1B_HUMAN 2 108 DBREF 4IQC B 1 107 UNP P68106 FKB1B_HUMAN 2 108 SEQADV 4IQC VAL A 22 UNP P68106 CYS 23 ENGINEERED MUTATION SEQADV 4IQC ILE A 76 UNP P68106 CYS 77 ENGINEERED MUTATION SEQADV 4IQC VAL B 22 UNP P68106 CYS 23 ENGINEERED MUTATION SEQADV 4IQC 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 FORMUL 3 HOH *111(H2 O) HELIX 1 1 ILE A 56 GLN A 65 1 10 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 PHE A 99 N LEU A 74 SHEET 4 A 5 THR A 21 LEU A 30 -1 N THR A 21 O GLU A 107 SHEET 5 A 5 LYS A 35 SER A 38 -1 O PHE A 36 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 PHE A 99 N LEU A 74 SHEET 4 B 5 THR A 21 LEU A 30 -1 N THR A 21 O GLU A 107 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 ARG B 71 N ILE B 7 SHEET 3 C 5 LEU B 97 GLU B 107 -1 O PHE B 99 N LEU B 74 SHEET 4 C 5 THR B 21 LEU B 30 -1 N THR B 21 O GLU B 107 SHEET 5 C 5 LYS B 35 SER B 38 -1 O ASP B 37 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 ARG B 71 N ILE B 7 SHEET 3 D 5 LEU B 97 GLU B 107 -1 O PHE B 99 N LEU B 74 SHEET 4 D 5 THR B 21 LEU B 30 -1 N THR B 21 O GLU B 107 SHEET 5 D 5 PHE B 46 ARG B 49 -1 O PHE B 46 N VAL B 24 CRYST1 52.816 52.816 152.949 90.00 90.00 120.00 P 31 2 1 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 0.018934 0.010931 0.000000 0.00000 SCALE2 0.000000 0.021863 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006538 0.00000