HEADER ISOMERASE 19-SEP-22 8EJX TITLE CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN D (CYPD) WITH IN COMPLEX WITH TITLE 2 THE COVALENTLY BOUND EBSELEN INHIBITOR 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,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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.LOVELL,K.P.BATTAILE,S.YAN REVDAT 4 15-MAY-24 8EJX 1 JRNL REVDAT 3 10-JAN-24 8EJX 1 JRNL REVDAT 2 15-NOV-23 8EJX 1 REMARK REVDAT 1 18-OCT-23 8EJX 0 JRNL AUTH S.SAMANTA,F.AKHTER,A.ROY,D.CHEN,B.TURNER,Y.WANG,N.CLEMENTE, JRNL AUTH 2 C.WANG,R.H.SWERDLOW,K.P.BATTAILE,S.LOVELL,S.F.YAN,S.S.YAN JRNL TITL NEW CYCLOPHILIN D INHIBITOR RESCUES MITOCHONDRIAL AND JRNL TITL 2 COGNITIVE FUNCTION IN ALZHEIMER'S DISEASE. JRNL REF BRAIN V. 147 1710 2024 JRNL REFN ISSN 1460-2156 JRNL PMID 38146639 JRNL DOI 10.1093/BRAIN/AWAD432 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.090 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18036 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 897 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 36.6200 - 3.0000 1.00 3043 151 0.1508 0.1835 REMARK 3 2 3.0000 - 2.3800 1.00 2874 137 0.1719 0.1787 REMARK 3 3 2.3800 - 2.0800 1.00 2854 152 0.1527 0.2090 REMARK 3 4 2.0800 - 1.8900 1.00 2791 157 0.1594 0.2095 REMARK 3 5 1.8900 - 1.7500 1.00 2785 151 0.2032 0.2525 REMARK 3 6 1.7500 - 1.6500 1.00 2792 149 0.2887 0.3020 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.45 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 29 ) REMARK 3 ORIGIN FOR THE GROUP (A): 66.6029 38.2156 92.5114 REMARK 3 T TENSOR REMARK 3 T11: 0.2209 T22: 0.1372 REMARK 3 T33: 0.2073 T12: -0.0168 REMARK 3 T13: -0.0005 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 1.8277 L22: 2.8330 REMARK 3 L33: 1.5891 L12: 0.8530 REMARK 3 L13: -0.5553 L23: -0.0482 REMARK 3 S TENSOR REMARK 3 S11: -0.0820 S12: -0.0406 S13: -0.1006 REMARK 3 S21: -0.2246 S22: 0.0091 S23: 0.1865 REMARK 3 S31: 0.2331 S32: -0.2173 S33: -0.0205 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 30 THROUGH 51 ) REMARK 3 ORIGIN FOR THE GROUP (A): 63.8787 48.4101 96.9110 REMARK 3 T TENSOR REMARK 3 T11: 0.1780 T22: 0.1610 REMARK 3 T33: 0.2134 T12: 0.0095 REMARK 3 T13: 0.0028 T23: -0.0176 REMARK 3 L TENSOR REMARK 3 L11: 3.2850 L22: 2.0284 REMARK 3 L33: 3.6048 L12: -0.9310 REMARK 3 L13: 1.0316 L23: -1.4453 REMARK 3 S TENSOR REMARK 3 S11: -0.0733 S12: -0.2204 S13: 0.1802 REMARK 3 S21: 0.1157 S22: 0.0414 S23: 0.2228 REMARK 3 S31: -0.1067 S32: -0.3224 S33: 0.0505 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 52 THROUGH 61 ) REMARK 3 ORIGIN FOR THE GROUP (A): 73.4599 44.7310 79.2027 REMARK 3 T TENSOR REMARK 3 T11: 0.3535 T22: 0.2497 REMARK 3 T33: 0.2384 T12: -0.0052 REMARK 3 T13: 0.0325 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 2.0361 L22: 5.2482 REMARK 3 L33: 5.0177 L12: -2.4931 REMARK 3 L13: -1.7231 L23: 0.2770 REMARK 3 S TENSOR REMARK 3 S11: 0.0102 S12: 0.5647 S13: 0.2603 REMARK 3 S21: -0.8142 S22: 0.0648 S23: -0.5067 REMARK 3 S31: 0.3078 S32: 0.3496 S33: -0.0332 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 63 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): 66.4689 55.4839 88.9698 REMARK 3 T TENSOR REMARK 3 T11: 0.2885 T22: 0.2109 REMARK 3 T33: 0.2876 T12: -0.0036 REMARK 3 T13: -0.0221 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 0.7078 L22: 1.7775 REMARK 3 L33: 3.8750 L12: 0.3265 REMARK 3 L13: -0.5334 L23: 1.2149 REMARK 3 S TENSOR REMARK 3 S11: -0.0740 S12: 0.1246 S13: 0.2718 REMARK 3 S21: -0.2182 S22: 0.1826 S23: 0.2391 REMARK 3 S31: -0.3957 S32: -0.0769 S33: -0.0604 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 83 THROUGH 115 ) REMARK 3 ORIGIN FOR THE GROUP (A): 77.9843 49.0141 92.6297 REMARK 3 T TENSOR REMARK 3 T11: 0.2043 T22: 0.1720 REMARK 3 T33: 0.2007 T12: -0.0031 REMARK 3 T13: 0.0154 T23: 0.0097 REMARK 3 L TENSOR REMARK 3 L11: 1.8423 L22: 2.3434 REMARK 3 L33: 1.4709 L12: 0.3627 REMARK 3 L13: 0.1863 L23: 0.4056 REMARK 3 S TENSOR REMARK 3 S11: 0.0113 S12: 0.0291 S13: 0.0065 REMARK 3 S21: -0.2533 S22: 0.0006 S23: -0.2708 REMARK 3 S31: 0.0062 S32: 0.1843 S33: -0.0190 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 116 THROUGH 127 ) REMARK 3 ORIGIN FOR THE GROUP (A): 84.9996 45.8212 88.6778 REMARK 3 T TENSOR REMARK 3 T11: 0.3701 T22: 0.3896 REMARK 3 T33: 0.3257 T12: 0.0142 REMARK 3 T13: 0.0566 T23: -0.0208 REMARK 3 L TENSOR REMARK 3 L11: 5.2345 L22: 9.8409 REMARK 3 L33: 5.3511 L12: -1.0030 REMARK 3 L13: -0.3444 L23: 2.7752 REMARK 3 S TENSOR REMARK 3 S11: -0.1157 S12: 0.8134 S13: -0.1018 REMARK 3 S21: -0.5964 S22: 0.2379 S23: -0.9017 REMARK 3 S31: 0.5363 S32: 0.7249 S33: -0.0902 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 128 THROUGH 145 ) REMARK 3 ORIGIN FOR THE GROUP (A): 71.6361 35.9932 85.7889 REMARK 3 T TENSOR REMARK 3 T11: 0.3420 T22: 0.2141 REMARK 3 T33: 0.2352 T12: 0.0017 REMARK 3 T13: 0.0368 T23: -0.0288 REMARK 3 L TENSOR REMARK 3 L11: 1.6276 L22: 2.0518 REMARK 3 L33: 4.1689 L12: 0.5769 REMARK 3 L13: 0.5246 L23: -0.3602 REMARK 3 S TENSOR REMARK 3 S11: -0.0189 S12: 0.1719 S13: -0.3431 REMARK 3 S21: -0.5445 S22: -0.0900 S23: -0.2408 REMARK 3 S31: 0.5335 S32: -0.2365 S33: 0.1449 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 146 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 69.2035 44.6047 72.8636 REMARK 3 T TENSOR REMARK 3 T11: 0.6127 T22: 0.5194 REMARK 3 T33: 0.2371 T12: -0.0184 REMARK 3 T13: -0.0115 T23: 0.1076 REMARK 3 L TENSOR REMARK 3 L11: 7.1687 L22: 2.2003 REMARK 3 L33: 2.9378 L12: 1.4983 REMARK 3 L13: -2.1429 L23: -0.5615 REMARK 3 S TENSOR REMARK 3 S11: -0.2019 S12: 0.6764 S13: 0.1661 REMARK 3 S21: -0.6173 S22: 0.1835 S23: -0.1314 REMARK 3 S31: 0.3841 S32: 0.0410 S33: 0.1120 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 165 ) REMARK 3 ORIGIN FOR THE GROUP (A): 60.8938 40.2208 91.4522 REMARK 3 T TENSOR REMARK 3 T11: 0.2347 T22: 0.2036 REMARK 3 T33: 0.2891 T12: -0.0243 REMARK 3 T13: -0.0300 T23: -0.0206 REMARK 3 L TENSOR REMARK 3 L11: 2.5281 L22: 3.5252 REMARK 3 L33: 7.8791 L12: -0.0214 REMARK 3 L13: 0.9412 L23: -3.6060 REMARK 3 S TENSOR REMARK 3 S11: -0.0170 S12: 0.0368 S13: 0.0121 REMARK 3 S21: -0.2432 S22: 0.2286 S23: 0.5812 REMARK 3 S31: 0.2595 S32: -0.5945 S33: -0.1703 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 8EJX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1000267495. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18096 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 47.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.90 REMARK 200 R MERGE FOR SHELL (I) : 1.74500 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: 4O8H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 4000, 100 MM HEPES, 200 REMARK 280 NACL, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 43.80100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.50700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.50700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.90050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.50700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.50700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.70150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.50700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.50700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.90050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.50700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.50700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 65.70150 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 43.80100 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 415 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 A 1 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 LYS A 15 CG CD CE NZ REMARK 470 LYS A 118 CE NZ REMARK 470 TRP A 121 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 121 CZ3 CH2 REMARK 470 LYS A 125 CE NZ REMARK 470 LYS A 140 CD CE NZ REMARK 470 LYS A 148 CG CD CE NZ REMARK 470 ARG A 151 CD NE CZ NH1 NH2 REMARK 470 LYS A 154 CE NZ REMARK 470 LYS A 155 CE NZ 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 59 -0.64 79.12 REMARK 500 PHE A 60 -62.90 -129.83 REMARK 500 PHE A 129 10.81 -141.78 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 415 DISTANCE = 6.28 ANGSTROMS DBREF 8EJX A 1 165 UNP P30405 PPIF_HUMAN 43 207 SEQADV 8EJX ILE A 133 UNP P30405 LYS 175 ENGINEERED MUTATION SEQRES 1 A 165 SER 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 CSO 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 MODRES 8EJX CSO A 62 CYS MODIFIED RESIDUE HET CSO A 62 7 HET 9JT A 201 16 HETNAM CSO S-HYDROXYCYSTEINE HETNAM 9JT N-PHENYL-2-SELANYLBENZAMIDE HETSYN 9JT ~{N}-PHENYL-2-SELANYL-BENZAMIDE; EBSELEN, BOUND FORM FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 9JT C13 H11 N O SE FORMUL 3 HOH *115(H2 O) HELIX 1 AA1 VAL A 29 GLY A 42 1 14 HELIX 2 AA2 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 VAL A 97 O CYS A 115 SHEET 5 AA1 8 VAL A 128 GLU A 134 -1 O GLY A 130 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 LINK C MET A 61 N CSO A 62 1555 1555 1.34 LINK C CSO A 62 N GLN A 63 1555 1555 1.34 LINK SG CYS A 115 SE1 9JT A 201 1555 1555 2.26 CRYST1 57.014 57.014 87.602 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 0.017540 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011415 0.00000