HEADER ISOMERASE 04-FEB-22 7R2J TITLE HUMAN CYCLOPHILIN D IN COMPLEX WITH N-(4-AMINOPHENYL)-7-METHYL-2-OXO- TITLE 2 1H,2H-PYRAZOLO[1,5-A]PYRIMIDINE-6-CARBOXAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPIASE F,CYCLOPHILIN D,CYPD,CYCLOPHILIN F,MITOCHONDRIAL COMPND 5 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 BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS CYCLOPHILIN D PPIASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.O.SILVA,U.GRAEDLER,T.M.BANDEIRAS REVDAT 2 07-FEB-24 7R2J 1 REMARK REVDAT 1 15-FEB-23 7R2J 0 JRNL AUTH D.O.SILVA,U.GRAEDLER,T.M.BANDEIRAS JRNL TITL HUMAN CYCLOPHILIN D IN COMPLEX WITH JRNL TITL 2 N-(4-AMINOPHENYL)-7-METHYL-2-OXO-1H,2H-PYRAZOLO[1, JRNL TITL 3 5-A]PYRIMIDINE-6-CARBOXAMIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 37694 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 1843 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 39.6400 - 2.9500 1.00 3015 157 0.1400 0.1623 REMARK 3 2 2.9500 - 2.3400 1.00 2865 139 0.1385 0.1627 REMARK 3 3 2.3400 - 2.0500 1.00 2840 131 0.1298 0.1470 REMARK 3 4 2.0500 - 1.8600 1.00 2787 150 0.1138 0.1265 REMARK 3 5 1.8600 - 1.7300 1.00 2771 151 0.1338 0.1625 REMARK 3 6 1.7300 - 1.6200 1.00 2796 122 0.1507 0.1771 REMARK 3 7 1.6200 - 1.5400 1.00 2776 129 0.1134 0.1561 REMARK 3 8 1.5400 - 1.4800 1.00 2760 124 0.1180 0.1587 REMARK 3 9 1.4800 - 1.4200 1.00 2764 141 0.1185 0.1624 REMARK 3 10 1.4200 - 1.3700 1.00 2704 162 0.1194 0.1685 REMARK 3 11 1.3700 - 1.3300 1.00 2761 143 0.1432 0.1721 REMARK 3 12 1.3300 - 1.2900 1.00 2726 164 0.2466 0.2531 REMARK 3 13 1.2900 - 1.2600 1.00 2718 130 0.5322 0.5767 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) : 0.183 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.548 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.65 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 : 0.013 1293 REMARK 3 ANGLE : 1.152 1744 REMARK 3 CHIRALITY : 0.079 187 REMARK 3 PLANARITY : 0.009 226 REMARK 3 DIHEDRAL : 14.786 462 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 7R2J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292120826. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-20 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37702 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.260 REMARK 200 RESOLUTION RANGE LOW (A) : 39.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 17.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 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: PHASER REMARK 200 STARTING MODEL: 7R2H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 % PEG 3350, 0.1M K2HPO4, PH 7.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 42.92550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.02950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.02950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.46275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.02950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.02950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 64.38825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.02950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.02950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.46275 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.02950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.02950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 64.38825 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 42.92550 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 TOTAL BURIED SURFACE AREA: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 KCAL/MOL 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 622 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 MET A 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 A 60 -78.64 -141.03 REMARK 500 PHE A 129 12.16 -140.76 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 A 622 DISTANCE = 6.07 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7R2H RELATED DB: PDB REMARK 900 RELATED ID: 7R2I RELATED DB: PDB DBREF 7R2J A 2 165 UNP P30405 PPIF_HUMAN 44 207 SEQADV 7R2J MET A 1 UNP P30405 INITIATING METHIONINE SEQADV 7R2J ILE A 133 UNP P30405 LYS 175 ENGINEERED MUTATION SEQRES 1 A 165 MET GLY ASN PRO LEU VAL TYR LEU ASP VAL ASP ALA ASN SEQRES 2 A 165 GLY LYS PRO LEU GLY ARG VAL VAL LEU GLU LEU LYS ALA SEQRES 3 A 165 ASP VAL VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU SEQRES 4 A 165 CYS THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER THR SEQRES 5 A 165 PHE HIS ARG VAL ILE PRO SER PHE MET CYS GLN ALA GLY SEQRES 6 A 165 ASP PHE THR ASN HIS ASN GLY THR GLY GLY LYS SER ILE SEQRES 7 A 165 TYR GLY SER ARG PHE PRO ASP GLU ASN PHE THR LEU LYS SEQRES 8 A 165 HIS VAL GLY PRO GLY VAL LEU SER MET ALA ASN ALA GLY SEQRES 9 A 165 PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ILE SEQRES 10 A 165 LYS THR ASP TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY SEQRES 11 A 165 HIS VAL ILE GLU GLY MET ASP VAL VAL LYS LYS ILE GLU SEQRES 12 A 165 SER PHE GLY SER LYS SER GLY ARG THR SER LYS LYS ILE SEQRES 13 A 165 VAL ILE THR ASP CYS GLY GLN LEU SER HET V0Z A 201 34 HET DMS A 202 10 HETNAM V0Z N-(4-AMINOPHENYL)-7-METHYL-2-OXO-1H,2H-PYRAZOLO[1,5- HETNAM 2 V0Z A]PYRIMIDINE-6-CARBOXAMIDE HETNAM DMS DIMETHYL SULFOXIDE HETSYN V0Z ~{N}-(4-AMINOPHENYL)-7-METHYL-2-OXIDANYLIDENE-1~{H}- HETSYN 2 V0Z PYRAZOLO[1,5-A]PYRIMIDINE-6-CARBOXAMIDE; N-(4- HETSYN 3 V0Z AMINOPHENYL)-7-METHYL-2-OXIDANYLIDENE-1H-PYRAZOLO[1,5- HETSYN 4 V0Z A]PYRIMIDINE-6-CARBOXAMIDE FORMUL 2 V0Z C14 H13 N5 O2 FORMUL 3 DMS C2 H6 O S FORMUL 4 HOH *322(H2 O) HELIX 1 AA1 VAL A 29 GLY A 42 1 14 HELIX 2 AA2 THR A 119 ASP A 123 5 5 HELIX 3 AA3 GLY A 135 PHE A 145 1 11 SHEET 1 AA1 8 PHE A 53 ILE A 57 0 SHEET 2 AA1 8 MET A 61 ALA A 64 -1 O GLN A 63 N ARG A 55 SHEET 3 AA1 8 PHE A 112 CYS A 115 -1 O PHE A 112 N ALA A 64 SHEET 4 AA1 8 VAL A 97 MET A 100 -1 N SER A 99 O PHE A 113 SHEET 5 AA1 8 VAL A 128 GLU A 134 -1 O PHE A 129 N LEU A 98 SHEET 6 AA1 8 LYS A 15 LEU A 24 -1 N VAL A 21 O ILE A 133 SHEET 7 AA1 8 LEU A 5 ALA A 12 -1 N VAL A 10 O LEU A 17 SHEET 8 AA1 8 ILE A 156 GLN A 163 -1 O ASP A 160 N ASP A 9 CRYST1 56.059 56.059 85.851 90.00 90.00 90.00 P 41 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 0.017838 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017838 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011648 0.00000