HEADER ISOMERASE 10-JAN-13 4IPX TITLE ANALYZING THE VISIBLE CONFORMATIONAL SUBSTATES OF THE FK506 BINDING TITLE 2 PROTEIN FKBP12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FKBP1A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPIASE FKBP1A, 12 KDA FK506-BINDING PROTEIN, 12 KDA FKBP, COMPND 5 FKBP-12, CALSTABIN-1, FK506-BINDING PROTEIN 1A, FKBP-1A, IMMUNOPHILIN COMPND 6 FKBP12, ROTAMASE; 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: FKBP1A, FKBP1, FKBP12; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.CHEN,S.M.MUSTAFI,H.M.LI,D.M.LEMASTER,G.HERNANDEZ REVDAT 3 20-SEP-23 4IPX 1 REMARK SEQADV REVDAT 2 31-JUL-13 4IPX 1 JRNL REVDAT 1 05-JUN-13 4IPX 0 JRNL AUTH S.M.MUSTAFI,H.CHEN,H.LI,D.M.LEMASTER,G.HERNANDEZ JRNL TITL ANALYSING THE VISIBLE CONFORMATIONAL SUBSTATES OF THE JRNL TITL 2 FK506-BINDING PROTEIN FKBP12. JRNL REF BIOCHEM.J. V. 453 371 2013 JRNL REFN ISSN 0264-6021 JRNL PMID 23688288 JRNL DOI 10.1042/BJ20130276 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) : 19.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.550 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 10991 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 543 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 19.6079 - 2.6968 0.98 2703 140 0.1994 0.1916 REMARK 3 2 2.6968 - 2.1414 0.98 2650 124 0.1819 0.1968 REMARK 3 3 2.1414 - 1.8710 0.96 2583 137 0.1865 0.2275 REMARK 3 4 1.8710 - 1.7000 0.95 2512 142 0.3629 0.4038 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.47 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 56.49 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.800 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) : -4.36100 REMARK 3 B22 (A**2) : 6.11640 REMARK 3 B33 (A**2) : -1.75540 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.56480 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 : 0.006 862 REMARK 3 ANGLE : 1.111 1165 REMARK 3 CHIRALITY : 0.069 126 REMARK 3 PLANARITY : 0.005 150 REMARK 3 DIHEDRAL : 14.809 325 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 4IPX 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_1000077060. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 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 : 10996 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 3.230 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : 0.09700 REMARK 200 FOR THE DATA SET : 29.4000 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 (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.29600 REMARK 200 R SYM FOR SHELL (I) : 0.29600 REMARK 200 FOR SHELL : 6.300 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 2PPN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M SODIUM MALONATE, PH 7.0, 0.1 M REMARK 280 HEPES, PH 7.4, 5% MPD, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.27500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.97400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.27500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.97400 REMARK 290 SMTRY3 4 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 405 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 409 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 410 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 411 LIES ON A SPECIAL POSITION. 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 -36.19 -132.35 REMARK 500 ALA A 81 -108.00 -131.75 REMARK 500 ILE A 90 -56.94 -132.25 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 MPD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 202 DBREF 4IPX A 1 107 UNP P62942 FKB1A_HUMAN 2 108 SEQADV 4IPX VAL A 22 UNP P62942 CYS 23 ENGINEERED MUTATION SEQADV 4IPX VAL A 87 UNP P62942 HIS 88 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 VAL VAL VAL HIS TYR SEQRES 3 A 107 THR GLY MET LEU GLU ASP GLY LYS LYS PHE 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 VAL 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 HET MPD A 201 8 HET MPD A 202 8 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 MPD 2(C6 H14 O2) FORMUL 4 HOH *127(H2 O) HELIX 1 1 ILE A 56 ALA A 64 1 9 HELIX 2 2 PRO A 78 ALA A 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 LYS A 73 N GLU A 5 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 MET A 29 -1 N THR A 21 O GLU A 107 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 LYS A 73 N GLU A 5 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 MET A 29 -1 N THR A 21 O GLU A 107 SHEET 5 B 5 PHE A 46 MET A 49 -1 O PHE A 48 N VAL A 22 SITE 1 AC1 6 LYS A 52 GLN A 53 GLU A 54 PRO A 88 SITE 2 AC1 6 GLY A 89 PRO A 92 SITE 1 AC2 2 PRO A 93 HOH A 391 CRYST1 70.550 35.948 40.923 90.00 95.89 90.00 C 1 2 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 0.014174 0.000000 0.001462 0.00000 SCALE2 0.000000 0.027818 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024566 0.00000