HEADER OXIDOREDUCTASE 10-OCT-19 6L3A TITLE CYTOCHROME P450 107G1 (RAPN) WITH EVEROLIMUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RAPN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES RAPAMYCINICUS (STRAIN ATCC 29253 / SOURCE 3 DSM 41530 / NRRL 5491 / AYB-994); SOURCE 4 ORGANISM_TAXID: 1343740; SOURCE 5 STRAIN: ATCC 29253 / DSM 41530 / NRRL 5491 / AYB-994; SOURCE 6 GENE: D3C57_102975; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A+ KEYWDS CYTOCHROME P450, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR V.C.KM,D.H.KIM,Y.R.LIM,I.H.LEE,J.H.LEE,L.W.KANG REVDAT 2 22-NOV-23 6L3A 1 REMARK REVDAT 1 16-SEP-20 6L3A 0 JRNL AUTH V.KIM,Y.R.LIM,I.LEE,J.H.LEE,S.HAN,T.V.PHAM,H.KIM,R.LEE, JRNL AUTH 2 L.W.KANG,D.KIM JRNL TITL STRUCTURAL INSIGHTS INTO CYP107G1 FROM RAPAMYCIN-PRODUCING JRNL TITL 2 STREPTOMYCES RAPAMYCINICUS. JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 692 08544 2020 JRNL REFN ESSN 1096-0384 JRNL PMID 32822639 JRNL DOI 10.1016/J.ABB.2020.108544 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 18426 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.336 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1055 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1375 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.4490 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.4310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6082 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 154 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.19000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.601 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.574 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 34.474 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.845 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6424 ; 0.006 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6186 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8751 ; 1.630 ; 1.687 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14295 ; 1.144 ; 1.603 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 778 ; 8.276 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 325 ;31.853 ;20.738 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1100 ;21.654 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 59 ;19.438 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 844 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7072 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1330 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6L3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300014103. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-16 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 : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97940 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41761 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 97.3 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 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 : 18.30 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: 4Z5P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE, 0.2 M REMARK 280 MAGNESIUM ACETATE TETRAHYDRATE, 20% POLYETHYLENE GLYCOL 8000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 287.15K 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 63.07100 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 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 THR A 4 REMARK 465 ASP A 5 REMARK 465 GLN A 6 REMARK 465 GLY A 7 REMARK 465 GLU A 8 REMARK 465 THR A 9 REMARK 465 ASP A 86 REMARK 465 SER A 177 REMARK 465 ASN A 178 REMARK 465 GLY A 179 REMARK 465 ALA A 180 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 THR B 3 REMARK 465 THR B 4 REMARK 465 ASP B 5 REMARK 465 GLN B 6 REMARK 465 GLY B 7 REMARK 465 GLU B 8 REMARK 465 THR B 9 REMARK 465 ASN B 178 REMARK 465 GLY B 179 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 MET A 20 CG SD CE REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 GLU A 143 CG CD OE1 OE2 REMARK 470 TYR A 181 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 LYS A 222 CG CD CE NZ REMARK 470 ARG A 392 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 19 CG CD OE1 OE2 REMARK 470 GLU B 21 CG CD OE1 OE2 REMARK 470 GLU B 37 CG CD OE1 OE2 REMARK 470 GLU B 184 CG CD OE1 OE2 REMARK 470 LYS B 222 CG CD CE NZ REMARK 470 LYS B 289 CG CD CE NZ REMARK 470 ARG B 390 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 392 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 393 CG CD1 CD2 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 NH1 ARG A 33 OD1 ASP A 34 1.17 REMARK 500 OD1 ASP A 57 OG SER A 304 1.25 REMARK 500 CG ASP A 57 OG SER A 304 1.28 REMARK 500 ND1 HIS B 351 O1A HEM B 501 1.42 REMARK 500 OE2 GLU A 28 NH1 ARG A 31 1.43 REMARK 500 CD1 TYR A 15 CE1 PHE A 17 1.46 REMARK 500 CB GLU A 37 O SER A 304 1.48 REMARK 500 O LEU A 267 O ASP A 270 1.52 REMARK 500 O MET A 142 O ALA A 146 1.52 REMARK 500 OD2 ASP A 57 OG SER A 304 1.53 REMARK 500 CB GLU B 37 OG SER B 304 1.56 REMARK 500 CB GLU B 37 CB SER B 304 1.63 REMARK 500 O SER B 182 N GLU B 184 1.66 REMARK 500 O ILE A 287 CG1 VAL A 394 1.69 REMARK 500 O ILE B 84 OD1 ASP B 86 1.69 REMARK 500 CE1 TYR A 15 CE1 PHE A 17 1.70 REMARK 500 CE1 TYR A 15 CZ PHE A 17 1.74 REMARK 500 O LEU B 141 O PHE B 145 1.78 REMARK 500 O GLU B 28 CD1 LEU B 32 1.79 REMARK 500 NE2 GLN A 290 O LEU A 393 1.84 REMARK 500 CD GLU A 28 NH1 ARG A 31 1.88 REMARK 500 O TYR A 15 CD1 PHE A 17 1.90 REMARK 500 OH TYR A 15 OH TYR A 29 1.98 REMARK 500 OE1 GLU A 28 NH1 ARG A 31 2.02 REMARK 500 CE2 TYR B 45 N PRO B 82 2.07 REMARK 500 OD1 ASP B 279 NH1 ARG B 360 2.09 REMARK 500 NH2 ARG A 268 O PRO A 375 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 ALA A 146 O - C - N ANGL. DEV. = 9.7 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 PRO A 16 73.72 -59.84 REMARK 500 ARG A 22 -139.94 -140.15 REMARK 500 LEU A 23 47.19 -101.92 REMARK 500 ASP A 34 34.75 -84.57 REMARK 500 ALA A 35 -85.78 -173.63 REMARK 500 GLU A 37 -73.64 -36.25 REMARK 500 ALA A 71 39.50 -75.06 REMARK 500 LEU A 73 109.09 -43.46 REMARK 500 ASP A 76 47.11 -84.72 REMARK 500 THR A 99 2.70 -69.82 REMARK 500 LEU A 109 50.13 -102.67 REMARK 500 PHE A 145 -53.92 -132.32 REMARK 500 LEU A 147 -44.61 144.52 REMARK 500 LEU A 149 -49.43 -24.98 REMARK 500 VAL A 160 105.38 -44.63 REMARK 500 VAL A 185 -30.05 -133.94 REMARK 500 LYS A 206 -72.54 -64.49 REMARK 500 ASP A 208 86.16 -68.12 REMARK 500 ASN A 210 31.96 -97.35 REMARK 500 ARG A 218 0.56 -66.61 REMARK 500 LYS A 222 -110.85 53.24 REMARK 500 ALA A 235 -71.35 -40.85 REMARK 500 TYR A 243 -80.36 -78.11 REMARK 500 ILE A 250 -70.20 -70.56 REMARK 500 TYR A 255 -37.92 -38.78 REMARK 500 LEU A 264 -73.27 -52.29 REMARK 500 ASP A 270 128.40 -177.64 REMARK 500 LEU A 282 -71.74 -66.35 REMARK 500 GLN A 290 -166.73 -108.53 REMARK 500 ALA A 291 -126.93 -89.71 REMARK 500 VAL A 294 125.37 -34.02 REMARK 500 VAL A 308 104.00 -47.68 REMARK 500 HIS A 330 55.73 34.29 REMARK 500 SER A 369 -77.88 -71.25 REMARK 500 SER A 372 -80.06 -91.79 REMARK 500 ARG A 373 -25.21 -33.94 REMARK 500 ALA A 376 29.97 -74.49 REMARK 500 LEU A 393 -100.44 63.50 REMARK 500 LYS B 11 -102.38 -155.45 REMARK 500 ALA B 12 65.75 61.59 REMARK 500 ALA B 18 -149.67 57.56 REMARK 500 GLU B 21 -97.04 76.15 REMARK 500 ARG B 22 -137.02 -84.48 REMARK 500 ALA B 35 -112.50 -172.01 REMARK 500 ARG B 66 41.52 -91.35 REMARK 500 PHE B 67 87.85 -154.23 REMARK 500 SER B 70 -37.99 -31.29 REMARK 500 LEU B 73 102.03 -58.81 REMARK 500 ALA B 108 -73.06 -82.75 REMARK 500 PHE B 145 155.25 173.95 REMARK 500 REMARK 500 THIS ENTRY HAS 70 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL 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 HEM A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 353 SG REMARK 620 2 HEM A 501 NA 88.3 REMARK 620 3 HEM A 501 NB 82.0 85.6 REMARK 620 4 HEM A 501 NC 84.3 171.1 88.5 REMARK 620 5 HEM A 501 ND 95.1 94.3 177.2 91.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 353 SG REMARK 620 2 HEM B 501 NA 101.7 REMARK 620 3 HEM B 501 NB 80.8 88.8 REMARK 620 4 HEM B 501 NC 71.5 171.9 85.9 REMARK 620 5 HEM B 501 ND 96.1 91.7 176.9 93.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue E53 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide HEC B 501 and HIS B REMARK 800 351 DBREF1 6L3A A 1 404 UNP A0A0A0NSZ7_STRRN DBREF2 6L3A A A0A0A0NSZ7 1 404 DBREF1 6L3A B 1 404 UNP A0A0A0NSZ7_STRRN DBREF2 6L3A B A0A0A0NSZ7 1 404 SEQRES 1 A 404 MET SER THR THR ASP GLN GLY GLU THR GLY LYS ALA CYS SEQRES 2 A 404 PRO TYR PRO PHE ALA GLU MET GLU ARG LEU GLU ILE HIS SEQRES 3 A 404 PRO GLU TYR ASN ARG LEU ARG ASP ALA GLY GLU LEU GLY SEQRES 4 A 404 ARG VAL LEU MET PRO TYR GLY GLY GLU THR TRP LEU ALA SEQRES 5 A 404 THR SER TRP GLU ASP VAL ALA LYS VAL PHE VAL ASP PRO SEQRES 6 A 404 ARG PHE SER ARG SER ALA THR LEU GLY LYS ASP VAL PRO SEQRES 7 A 404 ARG VAL LEU PRO ALA ILE GLN ASP GLN PRO VAL ILE MET SEQRES 8 A 404 LEU MET ASP PRO PRO GLU HIS THR ARG LEU ARG ARG LEU SEQRES 9 A 404 ALA THR LYS ALA LEU THR SER ARG ARG MET GLU ALA LEU SEQRES 10 A 404 ARG PRO ARG THR GLN GLU VAL ALA ASP ASP LEU ILE ASP SEQRES 11 A 404 LYS MET LEU ALA LYS GLY ALA PRO ALA ASP LEU MET GLU SEQRES 12 A 404 ASP PHE ALA LEU PRO LEU PRO ILE ILE MET ILE CYS GLU SEQRES 13 A 404 LEU LEU GLY VAL PRO ILE GLU ASP GLN THR LYS PHE ARG SEQRES 14 A 404 THR TRP SER ASP GLN MET LEU SER ASN GLY ALA TYR SER SEQRES 15 A 404 GLN GLU VAL VAL MET ALA ALA GLY GLN SER LEU TYR LEU SEQRES 16 A 404 TYR LEU SER GLU LEU ILE ALA GLU ARG ARG LYS GLN ASP SEQRES 17 A 404 THR ASN ASP LEU LEU GLY SER LEU VAL ARG ALA ARG ASP SEQRES 18 A 404 LYS ASP ASP ARG LEU SER GLU THR GLU LEU VAL GLY PHE SEQRES 19 A 404 ALA VAL THR LEU LEU ILE ALA GLY TYR GLU THR THR ALA SEQRES 20 A 404 ASN ALA ILE GLY ASN SER VAL TYR THR LEU LEU THR HIS SEQRES 21 A 404 PRO GLU LYS LEU ALA GLU LEU ARG LYS ASP LEU SER LEU SEQRES 22 A 404 ILE PRO LYS ALA VAL ASP GLU LEU LEU ARG ILE ILE PRO SEQRES 23 A 404 ILE ALA LYS GLN ALA SER TRP VAL ARG MET ALA VAL GLU SEQRES 24 A 404 ASP VAL GLU LEU SER GLY THR ILE VAL LYS ALA GLY GLU SEQRES 25 A 404 ALA VAL ALA ILE GLN THR HIS SER ALA ASN THR ASP PRO SEQRES 26 A 404 LYS VAL TYR ASP HIS PRO GLU GLU ILE ASP PHE HIS ARG SEQRES 27 A 404 THR SER ASN PRO HIS MET SER LEU GLY HIS GLY ALA HIS SEQRES 28 A 404 HIS CYS MET GLY ALA GLN LEU VAL ARG VAL GLU MET GLN SEQRES 29 A 404 THR ALA LEU GLY SER LEU ILE SER ARG ILE PRO ALA LEU SEQRES 30 A 404 ARG PHE ALA VAL PRO GLU PRO ARG ILE LYS PHE LEU ARG SEQRES 31 A 404 GLY ARG LEU VAL PRO SER LEU GLU ALA LEU PRO LEU THR SEQRES 32 A 404 TRP SEQRES 1 B 404 MET SER THR THR ASP GLN GLY GLU THR GLY LYS ALA CYS SEQRES 2 B 404 PRO TYR PRO PHE ALA GLU MET GLU ARG LEU GLU ILE HIS SEQRES 3 B 404 PRO GLU TYR ASN ARG LEU ARG ASP ALA GLY GLU LEU GLY SEQRES 4 B 404 ARG VAL LEU MET PRO TYR GLY GLY GLU THR TRP LEU ALA SEQRES 5 B 404 THR SER TRP GLU ASP VAL ALA LYS VAL PHE VAL ASP PRO SEQRES 6 B 404 ARG PHE SER ARG SER ALA THR LEU GLY LYS ASP VAL PRO SEQRES 7 B 404 ARG VAL LEU PRO ALA ILE GLN ASP GLN PRO VAL ILE MET SEQRES 8 B 404 LEU MET ASP PRO PRO GLU HIS THR ARG LEU ARG ARG LEU SEQRES 9 B 404 ALA THR LYS ALA LEU THR SER ARG ARG MET GLU ALA LEU SEQRES 10 B 404 ARG PRO ARG THR GLN GLU VAL ALA ASP ASP LEU ILE ASP SEQRES 11 B 404 LYS MET LEU ALA LYS GLY ALA PRO ALA ASP LEU MET GLU SEQRES 12 B 404 ASP PHE ALA LEU PRO LEU PRO ILE ILE MET ILE CYS GLU SEQRES 13 B 404 LEU LEU GLY VAL PRO ILE GLU ASP GLN THR LYS PHE ARG SEQRES 14 B 404 THR TRP SER ASP GLN MET LEU SER ASN GLY ALA TYR SER SEQRES 15 B 404 GLN GLU VAL VAL MET ALA ALA GLY GLN SER LEU TYR LEU SEQRES 16 B 404 TYR LEU SER GLU LEU ILE ALA GLU ARG ARG LYS GLN ASP SEQRES 17 B 404 THR ASN ASP LEU LEU GLY SER LEU VAL ARG ALA ARG ASP SEQRES 18 B 404 LYS ASP ASP ARG LEU SER GLU THR GLU LEU VAL GLY PHE SEQRES 19 B 404 ALA VAL THR LEU LEU ILE ALA GLY TYR GLU THR THR ALA SEQRES 20 B 404 ASN ALA ILE GLY ASN SER VAL TYR THR LEU LEU THR HIS SEQRES 21 B 404 PRO GLU LYS LEU ALA GLU LEU ARG LYS ASP LEU SER LEU SEQRES 22 B 404 ILE PRO LYS ALA VAL ASP GLU LEU LEU ARG ILE ILE PRO SEQRES 23 B 404 ILE ALA LYS GLN ALA SER TRP VAL ARG MET ALA VAL GLU SEQRES 24 B 404 ASP VAL GLU LEU SER GLY THR ILE VAL LYS ALA GLY GLU SEQRES 25 B 404 ALA VAL ALA ILE GLN THR HIS SER ALA ASN THR ASP PRO SEQRES 26 B 404 LYS VAL TYR ASP HIS PRO GLU GLU ILE ASP PHE HIS ARG SEQRES 27 B 404 THR SER ASN PRO HIS MET SER LEU GLY HIS GLY ALA HIS SEQRES 28 B 404 HIS CYS MET GLY ALA GLN LEU VAL ARG VAL GLU MET GLN SEQRES 29 B 404 THR ALA LEU GLY SER LEU ILE SER ARG ILE PRO ALA LEU SEQRES 30 B 404 ARG PHE ALA VAL PRO GLU PRO ARG ILE LYS PHE LEU ARG SEQRES 31 B 404 GLY ARG LEU VAL PRO SER LEU GLU ALA LEU PRO LEU THR SEQRES 32 B 404 TRP HET HEM A 501 43 HET HEM B 501 43 HET E53 B 502 68 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM E53 EVEROLIMUS HETSYN HEM HEME HETSYN E53 (1S,9R,12S,15R,16E,18R,19S,21R,23S,24Z,26Z,28Z,30R,32R, HETSYN 2 E53 35S)-12-[(2S)-1-[(1S,3S,4R)-4-(2-HYDROXYETHYLOXY)-3- HETSYN 3 E53 METHOXY-CYCLOHEXYL]PROPAN-2-YL]-19,30-DIMETHOXY-15,17, HETSYN 4 E53 21,23,29,35-HEXAMETHYL-1,18-BIS(OXIDANYL)-11,36-DIOXA- HETSYN 5 E53 4-AZATRICYCLO[30.3.1.0^{4,9}]HEXATRIACONTA-16,24,26, HETSYN 6 E53 28-TETRAENE-2,3,10,14,20-PENTONE FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 E53 C53 H83 N O14 FORMUL 6 HOH *4(H2 O) HELIX 1 AA1 PRO A 27 ASP A 34 1 8 HELIX 2 AA2 SER A 54 ASP A 64 1 11 HELIX 3 AA3 ARG A 69 LEU A 73 5 5 HELIX 4 AA4 GLU A 97 LYS A 107 1 11 HELIX 5 AA5 THR A 110 ALA A 116 1 7 HELIX 6 AA6 LEU A 117 GLY A 136 1 20 HELIX 7 AA7 LEU A 141 PHE A 145 1 5 HELIX 8 AA8 PRO A 148 GLY A 159 1 12 HELIX 9 AA9 PRO A 161 GLU A 163 5 3 HELIX 10 AB1 ASP A 164 ASP A 173 1 10 HELIX 11 AB2 SER A 182 GLN A 207 1 26 HELIX 12 AB3 ASP A 211 ARG A 218 1 8 HELIX 13 AB4 SER A 227 TYR A 243 1 17 HELIX 14 AB5 TYR A 243 LEU A 258 1 16 HELIX 15 AB6 HIS A 260 LYS A 269 1 10 HELIX 16 AB7 LEU A 273 ILE A 285 1 13 HELIX 17 AB8 GLN A 317 THR A 323 1 7 HELIX 18 AB9 HIS A 348 HIS A 352 5 5 HELIX 19 AC1 GLY A 355 ILE A 374 1 20 HELIX 20 AC2 PRO A 382 ILE A 386 5 5 HELIX 21 AC3 PRO B 27 ASP B 34 1 8 HELIX 22 AC4 SER B 54 ASP B 64 1 11 HELIX 23 AC5 ARG B 69 LEU B 73 5 5 HELIX 24 AC6 VAL B 89 MET B 93 5 5 HELIX 25 AC7 PRO B 96 LEU B 109 1 14 HELIX 26 AC8 THR B 110 ALA B 116 1 7 HELIX 27 AC9 LEU B 117 GLY B 136 1 20 HELIX 28 AD1 LEU B 141 PHE B 145 1 5 HELIX 29 AD2 LEU B 147 GLY B 159 1 13 HELIX 30 AD3 PRO B 161 GLU B 163 5 3 HELIX 31 AD4 ASP B 164 ASP B 173 1 10 HELIX 32 AD5 GLU B 184 GLN B 207 1 24 HELIX 33 AD6 ASP B 211 ALA B 219 1 9 HELIX 34 AD7 SER B 227 GLY B 242 1 16 HELIX 35 AD8 TYR B 243 LEU B 258 1 16 HELIX 36 AD9 HIS B 260 LYS B 269 1 10 HELIX 37 AE1 ASP B 270 SER B 272 5 3 HELIX 38 AE2 LEU B 273 ILE B 285 1 13 HELIX 39 AE3 GLN B 317 THR B 323 1 7 HELIX 40 AE4 HIS B 348 HIS B 352 5 5 HELIX 41 AE5 GLY B 355 ILE B 374 1 20 HELIX 42 AE6 PRO B 382 ILE B 386 5 5 SHEET 1 AA1 6 CYS A 13 PRO A 14 0 SHEET 2 AA1 6 GLY A 39 LEU A 42 1 O LEU A 42 N CYS A 13 SHEET 3 AA1 6 GLU A 48 ALA A 52 -1 O THR A 49 N VAL A 41 SHEET 4 AA1 6 ALA A 313 ILE A 316 1 O ALA A 313 N TRP A 50 SHEET 5 AA1 6 ARG A 295 ALA A 297 -1 N ARG A 295 O VAL A 314 SHEET 6 AA1 6 PHE A 67 SER A 68 -1 N SER A 68 O MET A 296 SHEET 1 AA2 3 ALA A 139 ASP A 140 0 SHEET 2 AA2 3 PRO A 401 THR A 403 -1 O LEU A 402 N ALA A 139 SHEET 3 AA2 3 ARG A 378 PHE A 379 -1 N ARG A 378 O THR A 403 SHEET 1 AA3 2 VAL A 301 LEU A 303 0 SHEET 2 AA3 2 THR A 306 VAL A 308 -1 O THR A 306 N LEU A 303 SHEET 1 AA4 5 CYS B 13 PRO B 14 0 SHEET 2 AA4 5 ARG B 40 LEU B 42 1 O LEU B 42 N CYS B 13 SHEET 3 AA4 5 GLU B 48 ALA B 52 -1 O THR B 49 N VAL B 41 SHEET 4 AA4 5 ALA B 313 ILE B 316 1 O ALA B 315 N TRP B 50 SHEET 5 AA4 5 ARG B 295 MET B 296 -1 N ARG B 295 O VAL B 314 SHEET 1 AA5 3 ALA B 139 ASP B 140 0 SHEET 2 AA5 3 PRO B 401 THR B 403 -1 O LEU B 402 N ALA B 139 SHEET 3 AA5 3 ARG B 378 PHE B 379 -1 N ARG B 378 O THR B 403 SHEET 1 AA6 2 VAL B 301 GLU B 302 0 SHEET 2 AA6 2 ILE B 307 VAL B 308 -1 O VAL B 308 N VAL B 301 LINK SG CYS A 353 FE HEM A 501 1555 1555 2.66 LINK SG CYS B 353 FE HEM B 501 1555 1555 2.58 CISPEP 1 PRO A 95 PRO A 96 0 -3.31 CISPEP 2 ALA A 137 PRO A 138 0 -10.58 CISPEP 3 TYR B 15 PRO B 16 0 -9.32 CISPEP 4 PRO B 95 PRO B 96 0 16.21 CISPEP 5 ALA B 137 PRO B 138 0 3.57 SITE 1 AC1 19 PHE A 62 ARG A 69 ILE A 90 MET A 91 SITE 2 AC1 19 HIS A 98 ARG A 102 LEU A 238 ALA A 241 SITE 3 AC1 19 GLY A 242 THR A 245 THR A 246 ARG A 295 SITE 4 AC1 19 SER A 345 HIS A 351 CYS A 353 MET A 354 SITE 5 AC1 19 GLY A 355 LEU A 358 VAL A 359 SITE 1 AC2 13 ALA B 83 GLN B 85 GLN B 87 MET B 91 SITE 2 AC2 13 LEU B 176 VAL B 186 MET B 187 ALA B 241 SITE 3 AC2 13 THR B 245 ILE B 287 TRP B 293 HEM B 501 SITE 4 AC2 13 HOH B 603 SITE 1 AC3 23 PHE B 62 ARG B 69 ILE B 90 MET B 93 SITE 2 AC3 23 HIS B 98 ARG B 102 LEU B 238 ALA B 241 SITE 3 AC3 23 GLY B 242 THR B 245 ARG B 295 SER B 345 SITE 4 AC3 23 LEU B 346 GLY B 347 GLY B 349 ALA B 350 SITE 5 AC3 23 HIS B 352 CYS B 353 MET B 354 GLY B 355 SITE 6 AC3 23 LEU B 358 VAL B 359 E53 B 502 CRYST1 63.028 126.142 70.099 90.00 116.46 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 0.015866 0.000000 0.007897 0.00000 SCALE2 0.000000 0.007928 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015935 0.00000