HEADER ISOMERASE 25-SEP-23 8UC4 TITLE APO X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN D WITH A SURFACE ENTROPY TITLE 2 REDUCTION MUTATION (K175I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: PPIASE F,CYCLOPHILIN D,CYP-D,CYPD,CYCLOPHILIN F, COMPND 5 MITOCHONDRIAL CYCLOPHILIN,CYP-M,ROTAMASE F; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES; COMPND 8 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: PPIF, CYP3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYCLOPHILIN D, MITOCHONDRIA, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.F.KREITLER,A.M.RANGWALA,M.A.SEELIGER REVDAT 1 07-AUG-24 8UC4 0 JRNL AUTH D.F.KREITLER,M.A.SEELIGER,A.M.RANGWALA JRNL TITL APO X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN D WITH A SURFACE JRNL TITL 2 ENTROPY REDUCTION MUTATION (K175I) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18RC7_3834 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 15394 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1539 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 28.4800 - 4.1600 1.00 1396 155 0.1969 0.2171 REMARK 3 2 4.1600 - 3.3100 1.00 1303 145 0.1792 0.1769 REMARK 3 3 3.3100 - 2.8900 1.00 1271 141 0.1843 0.2025 REMARK 3 4 2.8900 - 2.6300 1.00 1277 141 0.1740 0.2329 REMARK 3 5 2.6300 - 2.4400 1.00 1246 139 0.1831 0.2324 REMARK 3 6 2.4400 - 2.2900 1.00 1248 138 0.1600 0.1952 REMARK 3 7 2.2900 - 2.1800 1.00 1259 141 0.1664 0.2182 REMARK 3 8 2.1800 - 2.0800 1.00 1251 138 0.1706 0.2239 REMARK 3 9 2.0800 - 2.0000 1.00 1233 138 0.1713 0.2368 REMARK 3 10 2.0000 - 1.9300 1.00 1225 136 0.1956 0.2437 REMARK 3 11 1.9300 - 1.8700 0.92 1146 127 0.2077 0.2494 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.175 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.903 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.14 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 : 0.006 1304 REMARK 3 ANGLE : 0.800 1742 REMARK 3 CHIRALITY : 0.056 187 REMARK 3 PLANARITY : 0.005 223 REMARK 3 DIHEDRAL : 13.926 486 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 8UC4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1000276942. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9201 REMARK 200 MONOCHROMATOR : DCM SI(111) REMARK 200 OPTICS : KB REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15443 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 28.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: 3D REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL SOLUTION: 40% W/V PEG3350, 30 MM REMARK 280 NACL, 50 MM POTASSIUM PHOSPHATE MONOBASIC PH 7.0 PROTEIN REMARK 280 SOLUTION: 15 MG/ML PROTEIN, 20 MM TRIS PH 8.0, 50 MM NACL, 1 MM REMARK 280 DTT, AND 5% GLYCEROL DROP: 1 UL PROTEIN SOLUTION, 1 UL WELL REMARK 280 SOLUTION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 54.89050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.47950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.47950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 82.33575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.47950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.47950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.44525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.47950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.47950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 82.33575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.47950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.47950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.44525 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 54.89050 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: X 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 NA NA X 205 LIES ON A SPECIAL POSITION. 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 SER X 0 REMARK 465 ASN X 1 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 PHE X 60 -80.77 -146.04 REMARK 500 THR X 119 58.14 -112.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH X 419 DISTANCE = 6.37 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 15P X 201 REMARK 610 15P X 204 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA X 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PEG X 202 O1 REMARK 620 2 PEG X 202 O4 125.1 REMARK 620 3 PEG X 202 O1 0.0 125.1 REMARK 620 4 PEG X 202 O4 125.1 0.0 125.1 REMARK 620 N 1 2 3 DBREF 8UC4 X 3 165 UNP P30405 PPIF_HUMAN 45 207 SEQADV 8UC4 SER X 0 UNP P30405 EXPRESSION TAG SEQADV 8UC4 ASN X 1 UNP P30405 EXPRESSION TAG SEQADV 8UC4 ALA X 2 UNP P30405 EXPRESSION TAG SEQADV 8UC4 ILE X 133 UNP P30405 LYS 175 ENGINEERED MUTATION SEQRES 1 X 166 SER ASN ALA ASN PRO LEU VAL TYR LEU ASP VAL ASP ALA SEQRES 2 X 166 ASN GLY LYS PRO LEU GLY ARG VAL VAL LEU GLU LEU LYS SEQRES 3 X 166 ALA ASP VAL VAL PRO LYS THR ALA GLU ASN PHE ARG ALA SEQRES 4 X 166 LEU CYS THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER SEQRES 5 X 166 THR PHE HIS ARG VAL ILE PRO SER PHE MET CYS GLN ALA SEQRES 6 X 166 GLY ASP PHE THR ASN HIS ASN GLY THR GLY GLY LYS SER SEQRES 7 X 166 ILE TYR GLY SER ARG PHE PRO ASP GLU ASN PHE THR LEU SEQRES 8 X 166 LYS HIS VAL GLY PRO GLY VAL LEU SER MET ALA ASN ALA SEQRES 9 X 166 GLY PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR SEQRES 10 X 166 ILE LYS THR ASP TRP LEU ASP GLY LYS HIS VAL VAL PHE SEQRES 11 X 166 GLY HIS VAL ILE GLU GLY MET ASP VAL VAL LYS LYS ILE SEQRES 12 X 166 GLU SER PHE GLY SER LYS SER GLY ARG THR SER LYS LYS SEQRES 13 X 166 ILE VAL ILE THR ASP CYS GLY GLN LEU SER HET 15P X 201 11 HET PEG X 202 7 HET PEG X 203 7 HET 15P X 204 15 HET NA X 205 1 HETNAM 15P POLYETHYLENE GLYCOL (N=34) HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM NA SODIUM ION HETSYN 15P PEG 1500 FORMUL 2 15P 2(C69 H140 O35) FORMUL 3 PEG 2(C4 H10 O3) FORMUL 6 NA NA 1+ FORMUL 7 HOH *119(H2 O) HELIX 1 AA1 VAL X 29 GLY X 42 1 14 HELIX 2 AA2 THR X 119 ASP X 123 5 5 HELIX 3 AA3 GLY X 135 PHE X 145 1 11 SHEET 1 AA1 9 THR X 52 PHE X 53 0 SHEET 2 AA1 9 ILE X 156 GLN X 163 -1 O ILE X 156 N PHE X 53 SHEET 3 AA1 9 LEU X 5 ALA X 12 -1 N ASP X 9 O ASP X 160 SHEET 4 AA1 9 LYS X 15 LEU X 24 -1 O LEU X 17 N VAL X 10 SHEET 5 AA1 9 VAL X 128 GLU X 134 -1 O ILE X 133 N VAL X 21 SHEET 6 AA1 9 VAL X 97 MET X 100 -1 N LEU X 98 O GLY X 130 SHEET 7 AA1 9 PHE X 112 CYS X 115 -1 O PHE X 113 N SER X 99 SHEET 8 AA1 9 MET X 61 ALA X 64 -1 N ALA X 64 O PHE X 112 SHEET 9 AA1 9 ARG X 55 ILE X 57 -1 N ARG X 55 O GLN X 63 LINK O1 PEG X 202 NA NA X 205 1555 1555 2.75 LINK O4 PEG X 202 NA NA X 205 1555 1555 2.97 LINK O1 PEG X 202 NA NA X 205 1555 8554 2.75 LINK O4 PEG X 202 NA NA X 205 1555 8554 2.97 CRYST1 56.959 56.959 109.781 90.00 90.00 90.00 P 43 21 2 8 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 0.017556 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009109 0.00000