HEADER ISOMERASE 24-JUL-19 6PX0 TITLE CRYSTAL STRUCTURE OF THE TPR DOMAIN OF HUMAN ARYL HYDROCARBON TITLE 2 RECEPTOR-INTERACTING PROTEIN-LIKE 1 (AIPL1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARYL-HYDROCARBON-INTERACTING PROTEIN-LIKE 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: AIPL1, AIPL2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS AIPL1 TPR, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.P.YADAV,N.O.ARTEMYEV REVDAT 4 11-OCT-23 6PX0 1 REMARK REVDAT 3 11-DEC-19 6PX0 1 REMARK REVDAT 2 06-NOV-19 6PX0 1 JRNL REVDAT 1 18-SEP-19 6PX0 0 JRNL AUTH R.P.YADAV,K.BOYD,L.YU,N.O.ARTEMYEV JRNL TITL INTERACTION OF THE TETRATRICOPEPTIDE REPEAT DOMAIN OF ARYL JRNL TITL 2 HYDROCARBON RECEPTOR-INTERACTING PROTEIN-LIKE 1 WITH THE JRNL TITL 3 REGULATORY P GAMMA SUBUNIT OF PHOSPHODIESTERASE 6. JRNL REF J.BIOL.CHEM. V. 294 15795 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31488544 JRNL DOI 10.1074/JBC.RA119.010666 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 24436 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 1176 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 33.2400 - 3.1000 0.97 2921 164 0.1573 0.1826 REMARK 3 2 3.1000 - 2.4600 0.99 2924 144 0.1836 0.2023 REMARK 3 3 2.4600 - 2.1500 0.97 2861 143 0.2075 0.2573 REMARK 3 4 2.1500 - 1.9500 1.00 2937 131 0.1921 0.2299 REMARK 3 5 1.9500 - 1.8100 0.96 2816 151 0.2835 0.3079 REMARK 3 6 1.8100 - 1.7100 1.00 2927 143 0.1909 0.2286 REMARK 3 7 1.7100 - 1.6200 1.00 2925 169 0.2098 0.2612 REMARK 3 8 1.6200 - 1.5500 1.00 2949 131 0.2298 0.2768 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) : 0.152 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.665 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.15 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 : 0.008 1189 REMARK 3 ANGLE : 0.997 1578 REMARK 3 CHIRALITY : 0.056 167 REMARK 3 PLANARITY : 0.007 196 REMARK 3 DIHEDRAL : 5.417 728 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -13.0110 6.6841 -23.0431 REMARK 3 T TENSOR REMARK 3 T11: 0.1247 T22: 0.0986 REMARK 3 T33: 0.1533 T12: 0.0218 REMARK 3 T13: 0.0010 T23: -0.0107 REMARK 3 L TENSOR REMARK 3 L11: 1.1311 L22: 2.2368 REMARK 3 L33: 2.0174 L12: 0.2865 REMARK 3 L13: -0.0003 L23: -1.0755 REMARK 3 S TENSOR REMARK 3 S11: -0.0144 S12: -0.0114 S13: 0.0199 REMARK 3 S21: 0.0932 S22: -0.0371 S23: -0.0593 REMARK 3 S31: -0.0593 S32: 0.0103 S33: 0.0479 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 6PX0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000243208. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24471 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 44.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.68900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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: 4AIF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, 5-15 % PEG 8000 PH-7.5 REMARK 280 -8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 22.08500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 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 162 REMARK 465 GLY A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 GLY A 170 REMARK 465 ASN A 171 REMARK 465 HIS A 172 REMARK 465 GLU A 173 REMARK 465 LYS A 174 REMARK 465 MET A 175 REMARK 465 LYS A 176 REMARK 465 ALA A 177 REMARK 465 VAL A 178 REMARK 465 PRO A 179 REMARK 465 LYS A 315 REMARK 465 GLN A 316 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 770 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A 771 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 772 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 773 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 774 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 775 DISTANCE = 8.05 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 DBREF 6PX0 A 171 316 UNP Q9NZN9 AIPL1_HUMAN 171 316 SEQADV 6PX0 MET A 162 UNP Q9NZN9 EXPRESSION TAG SEQADV 6PX0 GLY A 163 UNP Q9NZN9 EXPRESSION TAG SEQADV 6PX0 HIS A 164 UNP Q9NZN9 EXPRESSION TAG SEQADV 6PX0 HIS A 165 UNP Q9NZN9 EXPRESSION TAG SEQADV 6PX0 HIS A 166 UNP Q9NZN9 EXPRESSION TAG SEQADV 6PX0 HIS A 167 UNP Q9NZN9 EXPRESSION TAG SEQADV 6PX0 HIS A 168 UNP Q9NZN9 EXPRESSION TAG SEQADV 6PX0 HIS A 169 UNP Q9NZN9 EXPRESSION TAG SEQADV 6PX0 GLY A 170 UNP Q9NZN9 EXPRESSION TAG SEQRES 1 A 155 MET GLY HIS HIS HIS HIS HIS HIS GLY ASN HIS GLU LYS SEQRES 2 A 155 MET LYS ALA VAL PRO VAL LEU HIS GLY GLU GLY ASN ARG SEQRES 3 A 155 LEU PHE LYS LEU GLY ARG TYR GLU GLU ALA SER SER LYS SEQRES 4 A 155 TYR GLN GLU ALA ILE ILE CYS LEU ARG ASN LEU GLN THR SEQRES 5 A 155 LYS GLU LYS PRO TRP GLU VAL GLN TRP LEU LYS LEU GLU SEQRES 6 A 155 LYS MET ILE ASN THR LEU ILE LEU ASN TYR CYS GLN CYS SEQRES 7 A 155 LEU LEU LYS LYS GLU GLU TYR TYR GLU VAL LEU GLU HIS SEQRES 8 A 155 THR SER ASP ILE LEU ARG HIS HIS PRO GLY ILE VAL LYS SEQRES 9 A 155 ALA TYR TYR VAL ARG ALA ARG ALA HIS ALA GLU VAL TRP SEQRES 10 A 155 ASN GLU ALA GLU ALA LYS ALA ASP LEU GLN LYS VAL LEU SEQRES 11 A 155 GLU LEU GLU PRO SER MET GLN LYS ALA VAL ARG ARG GLU SEQRES 12 A 155 LEU ARG LEU LEU GLU ASN ARG MET ALA GLU LYS GLN HET PEG A 501 7 HET PEG A 502 7 HET PG4 A 503 13 HET BME A 504 4 HET BME A 505 4 HET EDO A 506 4 HET EDO A 507 4 HET EDO A 508 4 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM BME BETA-MERCAPTOETHANOL HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 PEG 2(C4 H10 O3) FORMUL 4 PG4 C8 H18 O5 FORMUL 5 BME 2(C2 H6 O S) FORMUL 7 EDO 3(C2 H6 O2) FORMUL 10 HOH *175(H2 O) HELIX 1 AA1 VAL A 180 LEU A 191 1 12 HELIX 2 AA2 ARG A 193 THR A 213 1 21 HELIX 3 AA3 GLU A 219 LYS A 243 1 25 HELIX 4 AA4 GLU A 245 HIS A 260 1 16 HELIX 5 AA5 ILE A 263 VAL A 277 1 15 HELIX 6 AA6 ASN A 279 GLU A 294 1 16 HELIX 7 AA7 MET A 297 ALA A 313 1 17 SITE 1 AC1 7 GLN A 238 LEU A 241 TYR A 268 VAL A 269 SITE 2 AC1 7 ARG A 272 HOH A 604 HOH A 679 SITE 1 AC2 6 LEU A 241 LYS A 242 TYR A 246 ARG A 272 SITE 2 AC2 6 GLU A 276 HOH A 635 SITE 1 AC3 5 HIS A 182 GLY A 183 ASN A 186 HOH A 602 SITE 2 AC3 5 HOH A 685 SITE 1 AC4 4 ASN A 186 PHE A 189 TYR A 201 HOH A 602 SITE 1 AC5 3 TYR A 236 HIS A 252 HOH A 653 SITE 1 AC6 3 ARG A 209 GLU A 226 EDO A 507 SITE 1 AC7 4 TRP A 218 HIS A 259 EDO A 506 HOH A 607 SITE 1 AC8 3 GLU A 251 HIS A 252 HOH A 605 CRYST1 37.750 44.170 52.530 90.00 100.96 90.00 P 1 21 1 2 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 0.026490 0.000000 0.005128 0.00000 SCALE2 0.000000 0.022640 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019390 0.00000