PDB Short entry for 3O5P HEADER ISOMERASE 28-JUL-10 3O5P TITLE FK1 DOMAIN MUTANT A19T OF FKBP51, CRYSTAL FORM IV COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FKBP5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPIASE FKBP5, FK506-BINDING PROTEIN 5, FKBP-5, ROTAMASE, 51 COMPND 5 KDA FK506-BINDING PROTEIN, 51 KDA FKBP, FKBP-51, 54 KDA PROGESTERONE COMPND 6 RECEPTOR-ASSOCIATED IMMUNOPHILIN, FKBP54, P54, FF1 ANTIGEN, HSP90- COMPND 7 BINDING IMMUNOPHILIN, ANDROGEN-REGULATED PROTEIN 6; COMPND 8 EC: 5.2.1.8; COMPND 9 ENGINEERED: YES; COMPND 10 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: AIG6, FKBP5, FKBP51; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON+ RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPROEX-HTB KEYWDS FK-506 BINDING DOMAIN, HSP90 COCHAPERONE, IMMUNOPHILINE, PEPTIDYL- KEYWDS 2 PROLYL ISOMERASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.BRACHER,C.KOZANY,A.-K.THOST,F.HAUSCH REVDAT 4 03-APR-24 3O5P 1 REMARK REVDAT 3 21-FEB-24 3O5P 1 SEQADV REVDAT 2 28-MAR-12 3O5P 1 JRNL VERSN REVDAT 1 01-JUN-11 3O5P 0 JRNL AUTH A.BRACHER,C.KOZANY,A.K.THOST,F.HAUSCH JRNL TITL STRUCTURAL CHARACTERIZATION OF THE PPIASE DOMAIN OF FKBP51, JRNL TITL 2 A COCHAPERONE OF HUMAN HSP90. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 67 549 2011 JRNL REFN ISSN 0907-4449 JRNL PMID 21636895 JRNL DOI 10.1107/S0907444911013862 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.112 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.116 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3122 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 58981 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.109 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 55618 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 982 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 279 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 13044 REMARK 3 NUMBER OF RESTRAINTS : 17934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.035 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.083 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.102 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.026 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.047 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.085 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3O5P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060697. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-06 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 : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.19 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65715 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 39.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.6 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : 0.04400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 31.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.27300 REMARK 200 R SYM FOR SHELL (I) : 0.27300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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: PDB ENTRY 3O5P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 % PEG3350, 0.2 M NH4OAC, 0.1 M REMARK 280 HEPES, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.14450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.32350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.15100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.32350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.14450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.15100 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 140 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 31 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 39 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 LYS A 65 CD - CE - NZ ANGL. DEV. = 14.9 DEGREES 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 112 -117.57 -135.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3O5D RELATED DB: PDB REMARK 900 RELATED ID: 3O5E RELATED DB: PDB REMARK 900 RELATED ID: 3O5F RELATED DB: PDB REMARK 900 RELATED ID: 3O5G RELATED DB: PDB REMARK 900 RELATED ID: 3O5I RELATED DB: PDB REMARK 900 RELATED ID: 3O5J RELATED DB: PDB REMARK 900 RELATED ID: 3O5K RELATED DB: PDB REMARK 900 RELATED ID: 3O5L RELATED DB: PDB REMARK 900 RELATED ID: 3O5M RELATED DB: PDB REMARK 900 RELATED ID: 3O5O RELATED DB: PDB REMARK 900 RELATED ID: 3O5Q RELATED DB: PDB REMARK 900 RELATED ID: 3O5R RELATED DB: PDB REMARK 900 RELATED ID: 1KT0 RELATED DB: PDB REMARK 900 STRUCTURE OF FULL-LENGTH FKBP51 REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT A19T IS A MUTATION, BUT NOT A NATURALLY REMARK 999 OCCURRING ALLELE. DBREF 3O5P A 16 140 UNP Q13451 FKBP5_HUMAN 16 140 SEQADV 3O5P GLY A 13 UNP Q13451 EXPRESSION TAG SEQADV 3O5P ALA A 14 UNP Q13451 EXPRESSION TAG SEQADV 3O5P PRO A 15 UNP Q13451 EXPRESSION TAG SEQADV 3O5P THR A 19 UNP Q13451 ALA 19 SEE REMARK 999 SEQRES 1 A 128 GLY ALA PRO ALA THR VAL THR GLU GLN GLY GLU ASP ILE SEQRES 2 A 128 THR SER LYS LYS ASP ARG GLY VAL LEU LYS ILE VAL LYS SEQRES 3 A 128 ARG VAL GLY ASN GLY GLU GLU THR PRO MET ILE GLY ASP SEQRES 4 A 128 LYS VAL TYR VAL HIS TYR LYS GLY LYS LEU SER ASN GLY SEQRES 5 A 128 LYS LYS PHE ASP SER SER HIS ASP ARG ASN GLU PRO PHE SEQRES 6 A 128 VAL PHE SER LEU GLY LYS GLY GLN VAL ILE LYS ALA TRP SEQRES 7 A 128 ASP ILE GLY VAL ALA THR MET LYS LYS GLY GLU ILE CYS SEQRES 8 A 128 HIS LEU LEU CYS LYS PRO GLU TYR ALA TYR GLY SER ALA SEQRES 9 A 128 GLY SER LEU PRO LYS ILE PRO SER ASN ALA THR LEU PHE SEQRES 10 A 128 PHE GLU ILE GLU LEU LEU ASP PHE LYS GLY GLU FORMUL 2 HOH *279(H2 O) HELIX 1 1 GLY A 13 GLY A 22 1 10 HELIX 2 2 HIS A 71 ASN A 74 5 4 HELIX 3 3 ILE A 87 ALA A 95 1 9 HELIX 4 4 PRO A 109 ALA A 112 5 4 SHEET 1 A 6 GLU A 23 ASP A 24 0 SHEET 2 A 6 VAL A 33 ARG A 39 -1 O LYS A 35 N GLU A 23 SHEET 3 A 6 ILE A 102 CYS A 107 -1 O HIS A 104 N ILE A 36 SHEET 4 A 6 LEU A 128 LYS A 138 -1 O LEU A 128 N CYS A 107 SHEET 5 A 6 LYS A 52 LEU A 61 -1 N HIS A 56 O GLU A 133 SHEET 6 A 6 LYS A 66 SER A 69 -1 O PHE A 67 N GLY A 59 SHEET 1 B 6 GLU A 23 ASP A 24 0 SHEET 2 B 6 VAL A 33 ARG A 39 -1 O LYS A 35 N GLU A 23 SHEET 3 B 6 ILE A 102 CYS A 107 -1 O HIS A 104 N ILE A 36 SHEET 4 B 6 LEU A 128 LYS A 138 -1 O LEU A 128 N CYS A 107 SHEET 5 B 6 LYS A 52 LEU A 61 -1 N HIS A 56 O GLU A 133 SHEET 6 B 6 PHE A 77 SER A 80 -1 O PHE A 79 N VAL A 53 CISPEP 1 LEU A 119 PRO A 120 0 7.22 CRYST1 42.289 54.302 56.647 90.00 90.00 90.00 P 21 21 21 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 0.023647 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018416 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017653 0.00000