HEADER PROTEIN BINDING 28-AUG-14 4R7V TITLE CRYSTAL STRUCTURE OF N-LOBE OF HUMAN ARRDC3(1-165) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARRESTIN DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-165; COMPND 5 SYNONYM: TBP-2-LIKE INDUCIBLE MEMBRANE PROTEIN, TLIMP; COMPND 6 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: ARRDC3, KIAA1376; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARRESTIN FOLD, GPCR DOWN REGULATION, BETA 2 ADRENERGIC RECEPTOR, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.QI,J.HURLEY REVDAT 3 28-FEB-24 4R7V 1 SEQADV REVDAT 2 10-DEC-14 4R7V 1 JRNL REVDAT 1 01-OCT-14 4R7V 0 JRNL AUTH S.QI,M.O'HAYRE,J.S.GUTKIND,J.H.HURLEY JRNL TITL INSIGHTS INTO BETA 2-ADRENERGIC RECEPTOR BINDING FROM JRNL TITL 2 STRUCTURES OF THE N-TERMINAL LOBE OF ARRDC3. JRNL REF PROTEIN SCI. V. 23 1708 2014 JRNL REFN ISSN 0961-8368 JRNL PMID 25220262 JRNL DOI 10.1002/PRO.2549 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.3_1479) 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 17176 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 878 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 28.8330 - 3.1488 0.97 2798 165 0.1762 0.1949 REMARK 3 2 3.1488 - 2.4998 0.98 2774 154 0.2056 0.2705 REMARK 3 3 2.4998 - 2.1839 0.97 2736 140 0.2013 0.2134 REMARK 3 4 2.1839 - 1.9843 0.97 2711 130 0.1886 0.2239 REMARK 3 5 1.9843 - 1.8421 0.96 2690 146 0.2067 0.2495 REMARK 3 6 1.8421 - 1.7300 0.94 2589 143 0.2181 0.2382 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 1280 REMARK 3 ANGLE : 0.925 1738 REMARK 3 CHIRALITY : 0.050 189 REMARK 3 PLANARITY : 0.003 219 REMARK 3 DIHEDRAL : 10.740 466 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND ( RESID 4:170 OR RESID 201:261 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.5046 22.8323 16.3766 REMARK 3 T TENSOR REMARK 3 T11: 0.1701 T22: 0.1738 REMARK 3 T33: 0.1688 T12: -0.0178 REMARK 3 T13: -0.0032 T23: 0.0118 REMARK 3 L TENSOR REMARK 3 L11: 0.4944 L22: 0.5498 REMARK 3 L33: 0.6120 L12: -0.1239 REMARK 3 L13: -0.2393 L23: -0.2706 REMARK 3 S TENSOR REMARK 3 S11: -0.0016 S12: -0.0855 S13: 0.0418 REMARK 3 S21: 0.1029 S22: 0.0556 S23: 0.0813 REMARK 3 S31: 0.0524 S32: -0.0976 S33: 0.0025 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 4R7V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-14 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 : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11587 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) 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 : 17177 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.1M TRIS-HCL, 0.2M REMARK 280 (NH4)2SO4, 50MM GUANIDINE-HCL, PH 7.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 33.77350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.07900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.77350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.07900 REMARK 290 SMTRY3 4 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 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 1 REMARK 465 VAL A 2 REMARK 465 LEU A 3 REMARK 465 LEU A 16 REMARK 465 ASN A 17 REMARK 465 ASP A 18 REMARK 465 ARG A 63 REMARK 465 ASN A 64 REMARK 465 ALA A 65 REMARK 465 GLY A 66 REMARK 465 SER A 67 REMARK 465 ASN A 68 REMARK 465 THR A 69 REMARK 465 ALA A 70 REMARK 465 TYR A 71 REMARK 465 ASP A 95 REMARK 465 ASP A 96 REMARK 465 ASN A 97 REMARK 465 SER A 98 REMARK 465 GLU A 99 REMARK 465 GLU A 100 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 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 SER A 19 OG REMARK 470 ASP A 94 CG OD1 OD2 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 ILE A 162 -87.27 -124.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4R7X RELATED DB: PDB DBREF 4R7V A 1 165 UNP Q96B67 ARRD3_HUMAN 1 165 SEQADV 4R7V LEU A 166 UNP Q96B67 EXPRESSION TAG SEQADV 4R7V GLU A 167 UNP Q96B67 EXPRESSION TAG SEQADV 4R7V HIS A 168 UNP Q96B67 EXPRESSION TAG SEQADV 4R7V HIS A 169 UNP Q96B67 EXPRESSION TAG SEQADV 4R7V HIS A 170 UNP Q96B67 EXPRESSION TAG SEQADV 4R7V HIS A 171 UNP Q96B67 EXPRESSION TAG SEQADV 4R7V HIS A 172 UNP Q96B67 EXPRESSION TAG SEQADV 4R7V HIS A 173 UNP Q96B67 EXPRESSION TAG SEQRES 1 A 173 MET VAL LEU GLY LYS VAL LYS SER LEU THR ILE SER PHE SEQRES 2 A 173 ASP CYS LEU ASN ASP SER ASN VAL PRO VAL TYR SER SER SEQRES 3 A 173 GLY ASP THR VAL SER GLY ARG VAL ASN LEU GLU VAL THR SEQRES 4 A 173 GLY GLU ILE ARG VAL LYS SER LEU LYS ILE HIS ALA ARG SEQRES 5 A 173 GLY HIS ALA LYS VAL ARG TRP THR GLU SER ARG ASN ALA SEQRES 6 A 173 GLY SER ASN THR ALA TYR THR GLN ASN TYR THR GLU GLU SEQRES 7 A 173 VAL GLU TYR PHE ASN HIS LYS ASP ILE LEU ILE GLY HIS SEQRES 8 A 173 GLU ARG ASP ASP ASP ASN SER GLU GLU GLY PHE HIS THR SEQRES 9 A 173 ILE HIS SER GLY ARG HIS GLU TYR ALA PHE SER PHE GLU SEQRES 10 A 173 LEU PRO GLN THR PRO LEU ALA THR SER PHE GLU GLY ARG SEQRES 11 A 173 HIS GLY SER VAL ARG TYR TRP VAL LYS ALA GLU LEU HIS SEQRES 12 A 173 ARG PRO TRP LEU LEU PRO VAL LYS LEU LYS LYS GLU PHE SEQRES 13 A 173 THR VAL PHE GLU HIS ILE ASP ILE ASN LEU GLU HIS HIS SEQRES 14 A 173 HIS HIS HIS HIS FORMUL 2 HOH *61(H2 O) SHEET 1 A 3 LYS A 5 PHE A 13 0 SHEET 2 A 3 THR A 29 THR A 39 -1 O ASN A 35 N THR A 10 SHEET 3 A 3 GLY A 108 GLU A 117 -1 O HIS A 110 N LEU A 36 SHEET 1 B 2 VAL A 23 TYR A 24 0 SHEET 2 B 2 THR A 157 VAL A 158 1 O THR A 157 N TYR A 24 SHEET 1 C 2 ILE A 42 VAL A 44 0 SHEET 2 C 2 HIS A 103 ILE A 105 -1 O HIS A 103 N VAL A 44 SHEET 1 D 4 GLN A 73 GLY A 90 0 SHEET 2 D 4 SER A 46 GLU A 61 -1 N TRP A 59 O TYR A 75 SHEET 3 D 4 GLY A 132 HIS A 143 -1 O LYS A 139 N HIS A 50 SHEET 4 D 4 PHE A 127 GLU A 128 -1 N PHE A 127 O VAL A 134 SHEET 1 E 4 GLN A 73 GLY A 90 0 SHEET 2 E 4 SER A 46 GLU A 61 -1 N TRP A 59 O TYR A 75 SHEET 3 E 4 GLY A 132 HIS A 143 -1 O LYS A 139 N HIS A 50 SHEET 4 E 4 VAL A 150 GLU A 155 -1 O LEU A 152 N ALA A 140 CRYST1 67.547 36.158 74.331 90.00 109.47 90.00 C 1 2 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 0.014805 0.000000 0.005234 0.00000 SCALE2 0.000000 0.027656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014269 0.00000