HEADER ISOMERASE 19-FEB-16 5I98 TITLE STRUCTURE OF APO FKBP12(P104G) FROM C. ALBICANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FK506-BINDING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: FKBP,PEPTIDYL-PROLYL CIS-TRANS ISOMERASE,PPIASE,RAPAMYCIN- COMPND 5 BINDING PROTEIN; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDA ALBICANS (STRAIN SC5314 / ATCC MYA- SOURCE 3 2876); SOURCE 4 ORGANISM_COMMON: YEAST; SOURCE 5 ORGANISM_TAXID: 237561; SOURCE 6 STRAIN: SC5314 / ATCC MYA-2876; SOURCE 7 GENE: RBP1, RBP11, CAO19.11186, CAO19.3702, RBP2, RBP12, CAJ7.0299, SOURCE 8 CAO19.13810, CAO19.6452; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FKBP12, SELF-CATALYSIS, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHUMACHER REVDAT 3 06-MAR-24 5I98 1 REMARK REVDAT 2 06-FEB-19 5I98 1 SOURCE REMARK REVDAT 1 14-SEP-16 5I98 0 JRNL AUTH N.K.TONTHAT,P.R.JUVVADI,H.ZHANG,S.C.LEE,R.VENTERS,L.SPICER, JRNL AUTH 2 W.J.STEINBACH,J.HEITMAN,M.A.SCHUMACHER JRNL TITL STRUCTURES OF PATHOGENIC FUNGAL FKBP12S REVEAL POSSIBLE JRNL TITL 2 SELF-CATALYSIS FUNCTION. JRNL REF MBIO V. 7 00492 2016 JRNL REFN ESSN 2150-7511 JRNL PMID 27118592 JRNL DOI 10.1128/MBIO.00492-16 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1111 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 15510 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1546 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 45.3571 - 4.4448 0.99 1338 146 0.1672 0.1755 REMARK 3 2 4.4448 - 3.5284 0.99 1293 149 0.1524 0.1541 REMARK 3 3 3.5284 - 3.0825 0.99 1285 137 0.1844 0.2037 REMARK 3 4 3.0825 - 2.8007 1.00 1278 142 0.1999 0.2233 REMARK 3 5 2.8007 - 2.6000 0.99 1275 138 0.1993 0.2442 REMARK 3 6 2.6000 - 2.4467 1.00 1280 145 0.2003 0.2141 REMARK 3 7 2.4467 - 2.3242 1.00 1271 142 0.1968 0.2093 REMARK 3 8 2.3242 - 2.2230 1.00 1290 142 0.2012 0.2295 REMARK 3 9 2.2230 - 2.1374 1.00 1290 143 0.1954 0.2005 REMARK 3 10 2.1374 - 2.0637 0.99 1273 134 0.1969 0.2169 REMARK 3 11 2.0637 - 1.9991 0.87 1091 128 0.2114 0.2480 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 1835 REMARK 3 ANGLE : 0.884 2490 REMARK 3 CHIRALITY : 0.048 283 REMARK 3 PLANARITY : 0.003 326 REMARK 3 DIHEDRAL : 13.465 686 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 5I98 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218487. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15510 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M AMMONIUM SULFATE 0.1 M CAPS/NAOH REMARK 280 PH 10.5 0.2 M LITHIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 21.98150 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU B 3 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 267 O HOH A 271 1.85 REMARK 500 O HOH A 265 O HOH A 275 1.94 REMARK 500 OE1 GLN A 7 O HOH A 201 1.96 REMARK 500 OG1 THR B 35 O HOH B 201 2.02 REMARK 500 O HOH A 266 O HOH A 268 2.11 REMARK 500 OE2 GLU A 3 O HOH A 202 2.13 REMARK 500 OE2 GLU A 4 O HOH A 203 2.14 REMARK 500 O HOH B 207 O HOH B 235 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 269 O HOH B 274 2744 2.03 REMARK 500 O HOH A 274 O HOH B 276 2745 2.09 REMARK 500 O HOH A 205 O HOH B 212 2845 2.14 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 42 132.44 -171.48 REMARK 500 ALA A 96 -109.87 -130.17 REMARK 500 ILE A 105 -54.36 -126.52 REMARK 500 THR B 17 -31.63 -133.65 REMARK 500 ALA B 96 -113.56 -121.13 REMARK 500 ILE B 105 -50.76 -126.76 REMARK 500 REMARK 500 REMARK: NULL DBREF 5I98 A 3 122 UNP P28870 FKBP_CANAL 3 122 DBREF 5I98 B 3 122 UNP P28870 FKBP_CANAL 3 122 SEQADV 5I98 GLY A 104 UNP P28870 PRO 104 ENGINEERED MUTATION SEQADV 5I98 GLY B 104 UNP P28870 PRO 104 ENGINEERED MUTATION SEQRES 1 A 120 GLU GLU LEU PRO GLN ILE GLU ILE VAL GLN GLU GLY ASP SEQRES 2 A 120 ASN THR THR PHE ALA LYS PRO GLY ASP THR VAL THR ILE SEQRES 3 A 120 HIS TYR ASP GLY LYS LEU THR ASN GLY LYS GLU PHE ASP SEQRES 4 A 120 SER SER ARG LYS ARG GLY LYS PRO PHE THR CYS THR VAL SEQRES 5 A 120 GLY VAL GLY GLN VAL ILE LYS GLY TRP ASP ILE SER LEU SEQRES 6 A 120 THR ASN ASN TYR GLY LYS GLY GLY ALA ASN LEU PRO LYS SEQRES 7 A 120 ILE SER LYS GLY THR LYS ALA ILE LEU THR ILE PRO PRO SEQRES 8 A 120 ASN LEU ALA TYR GLY PRO ARG GLY ILE PRO GLY ILE ILE SEQRES 9 A 120 GLY PRO ASN GLU THR LEU VAL PHE GLU VAL GLU LEU LEU SEQRES 10 A 120 GLY VAL ASN SEQRES 1 B 120 GLU GLU LEU PRO GLN ILE GLU ILE VAL GLN GLU GLY ASP SEQRES 2 B 120 ASN THR THR PHE ALA LYS PRO GLY ASP THR VAL THR ILE SEQRES 3 B 120 HIS TYR ASP GLY LYS LEU THR ASN GLY LYS GLU PHE ASP SEQRES 4 B 120 SER SER ARG LYS ARG GLY LYS PRO PHE THR CYS THR VAL SEQRES 5 B 120 GLY VAL GLY GLN VAL ILE LYS GLY TRP ASP ILE SER LEU SEQRES 6 B 120 THR ASN ASN TYR GLY LYS GLY GLY ALA ASN LEU PRO LYS SEQRES 7 B 120 ILE SER LYS GLY THR LYS ALA ILE LEU THR ILE PRO PRO SEQRES 8 B 120 ASN LEU ALA TYR GLY PRO ARG GLY ILE PRO GLY ILE ILE SEQRES 9 B 120 GLY PRO ASN GLU THR LEU VAL PHE GLU VAL GLU LEU LEU SEQRES 10 B 120 GLY VAL ASN FORMUL 3 HOH *161(H2 O) HELIX 1 AA1 ILE A 60 THR A 68 1 9 HELIX 2 AA2 PRO A 92 ALA A 96 5 5 HELIX 3 AA3 ILE B 60 THR B 68 1 9 HELIX 4 AA4 PRO B 92 ALA B 96 5 5 SHEET 1 AA1 5 GLN A 7 GLN A 12 0 SHEET 2 AA1 5 LYS A 86 ILE A 91 -1 O THR A 90 N GLN A 7 SHEET 3 AA1 5 LEU A 112 VAL A 121 -1 O PHE A 114 N LEU A 89 SHEET 4 AA1 5 THR A 25 LEU A 34 -1 N LYS A 33 O VAL A 113 SHEET 5 AA1 5 GLU A 39 SER A 42 -1 O ASP A 41 N GLY A 32 SHEET 1 AA2 5 GLN A 7 GLN A 12 0 SHEET 2 AA2 5 LYS A 86 ILE A 91 -1 O THR A 90 N GLN A 7 SHEET 3 AA2 5 LEU A 112 VAL A 121 -1 O PHE A 114 N LEU A 89 SHEET 4 AA2 5 THR A 25 LEU A 34 -1 N LYS A 33 O VAL A 113 SHEET 5 AA2 5 PHE A 50 THR A 53 -1 O PHE A 50 N ILE A 28 SHEET 1 AA3 5 GLN B 7 GLN B 12 0 SHEET 2 AA3 5 LYS B 86 ILE B 91 -1 O THR B 90 N GLN B 7 SHEET 3 AA3 5 LEU B 112 VAL B 121 -1 O PHE B 114 N LEU B 89 SHEET 4 AA3 5 THR B 25 LEU B 34 -1 N LYS B 33 O VAL B 113 SHEET 5 AA3 5 GLU B 39 SER B 42 -1 O ASP B 41 N GLY B 32 SHEET 1 AA4 5 GLN B 7 GLN B 12 0 SHEET 2 AA4 5 LYS B 86 ILE B 91 -1 O THR B 90 N GLN B 7 SHEET 3 AA4 5 LEU B 112 VAL B 121 -1 O PHE B 114 N LEU B 89 SHEET 4 AA4 5 THR B 25 LEU B 34 -1 N LYS B 33 O VAL B 113 SHEET 5 AA4 5 PHE B 50 THR B 53 -1 O PHE B 50 N ILE B 28 CRYST1 51.225 43.963 56.989 90.00 115.00 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 0.019522 0.000000 0.009103 0.00000 SCALE2 0.000000 0.022746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019361 0.00000