HEADER GENE REGULATION 20-MAR-23 8GKV TITLE CRYSTAL STRUCTURE OF ANTI-ADAPTOR IRAP THAT REGULATES RPOS PROTEOLYSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-ADAPTER PROTEIN IRAP; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 1-86; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: IRAP, YAIB, B0382, JW0373; 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: IRAPC23S KEYWDS ALPHA HELIX, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR G.X.SHAW,J.GAN,P.SUBURAMAN,A.BATTESTI,Y.N.ZHOU,S.WICKNER,S.GOTTESMAN, AUTHOR 2 X.JI REVDAT 1 27-MAR-24 8GKV 0 JRNL AUTH A.TRIPATHI,J.HOSKINS,G.X.SHAW,J.GAN,S.TONG,A.BATTESTI, JRNL AUTH 2 L.M.JENKINS,X.JI,S.WICKNER,S.GOTTESMAN JRNL TITL STRUCTURAL AND FUNCTIONAL STUDY OF ANTI-ADAPTOR JRNL TITL 2 IRAP-MEDIATED REGULATION OF RPOS PROTEOLYSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 6390 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.110 REMARK 3 FREE R VALUE TEST SET COUNT : 710 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 22.6999 - 4.0165 0.88 1195 133 0.2135 0.2253 REMARK 3 2 4.0165 - 3.1909 0.89 1184 132 0.2059 0.2298 REMARK 3 3 3.1909 - 2.7883 0.90 1191 132 0.2313 0.2840 REMARK 3 4 2.7883 - 2.5338 0.88 1176 131 0.2363 0.2644 REMARK 3 5 2.5338 - 2.3524 0.75 999 111 0.2651 0.2889 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.30 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: 0.1700 REMARK 3 OPERATOR: K+L,H+L,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 690 REMARK 3 ANGLE : 0.745 916 REMARK 3 CHIRALITY : 0.031 110 REMARK 3 PLANARITY : 0.002 113 REMARK 3 DIHEDRAL : 18.038 274 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 8GKV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000273110. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6391 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.15600 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: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL 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: TRI-NA CITRATE, MPD, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 37.66750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.50650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.66750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.50650 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 218 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 ASN A 43 REMARK 465 ASP A 44 REMARK 465 GLN A 45 REMARK 465 GLN A 46 REMARK 465 ARG A 47 REMARK 465 LEU A 48 REMARK 465 ILE A 49 REMARK 465 ASP A 50 REMARK 465 GLN A 51 REMARK 465 VAL A 52 REMARK 465 GLU A 53 REMARK 465 GLY A 54 REMARK 465 ALA A 55 REMARK 465 LEU A 56 REMARK 465 TYR A 57 REMARK 465 GLU A 58 REMARK 465 VAL A 59 REMARK 465 LYS A 60 REMARK 465 PRO A 61 REMARK 465 ASP A 62 REMARK 465 ALA A 63 REMARK 465 SER A 64 REMARK 465 ILE A 65 REMARK 465 PRO A 66 REMARK 465 ASP A 67 REMARK 465 ASP A 68 REMARK 465 ASP A 69 REMARK 465 THR A 70 REMARK 465 GLU A 71 REMARK 465 LEU A 72 REMARK 465 LEU A 73 REMARK 465 ARG A 74 REMARK 465 ASP A 75 REMARK 465 TYR A 76 REMARK 465 VAL A 77 REMARK 465 LYS A 78 REMARK 465 LYS A 79 REMARK 465 LEU A 80 REMARK 465 LEU A 81 REMARK 465 LYS A 82 REMARK 465 HIS A 83 REMARK 465 PRO A 84 REMARK 465 ARG A 85 REMARK 465 GLN A 86 REMARK 465 GLY B -1 REMARK 465 GLY B 0 REMARK 465 ALA B 41 REMARK 465 GLN B 42 REMARK 465 ASN B 43 REMARK 465 ASP B 44 REMARK 465 GLN B 45 REMARK 465 GLN B 46 REMARK 465 ARG B 47 REMARK 465 LEU B 48 REMARK 465 ILE B 49 REMARK 465 ASP B 50 REMARK 465 GLN B 51 REMARK 465 VAL B 52 REMARK 465 GLU B 53 REMARK 465 GLY B 54 REMARK 465 ALA B 55 REMARK 465 LEU B 56 REMARK 465 TYR B 57 REMARK 465 GLU B 58 REMARK 465 VAL B 59 REMARK 465 LYS B 60 REMARK 465 PRO B 61 REMARK 465 ASP B 62 REMARK 465 ALA B 63 REMARK 465 SER B 64 REMARK 465 ILE B 65 REMARK 465 PRO B 66 REMARK 465 ASP B 67 REMARK 465 ASP B 68 REMARK 465 ASP B 69 REMARK 465 THR B 70 REMARK 465 GLU B 71 REMARK 465 LEU B 72 REMARK 465 LEU B 73 REMARK 465 ARG B 74 REMARK 465 ASP B 75 REMARK 465 TYR B 76 REMARK 465 VAL B 77 REMARK 465 LYS B 78 REMARK 465 LYS B 79 REMARK 465 LEU B 80 REMARK 465 LEU B 81 REMARK 465 LYS B 82 REMARK 465 HIS B 83 REMARK 465 PRO B 84 REMARK 465 ARG B 85 REMARK 465 GLN B 86 REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 EPE A 101 DBREF 8GKV A 1 86 UNP P0AAN9 IRAP_ECOLI 1 86 DBREF 8GKV B 1 86 UNP P0AAN9 IRAP_ECOLI 1 86 SEQADV 8GKV GLY A -1 UNP P0AAN9 EXPRESSION TAG SEQADV 8GKV GLY A 0 UNP P0AAN9 EXPRESSION TAG SEQADV 8GKV SER A 23 UNP P0AAN9 CYS 23 ENGINEERED MUTATION SEQADV 8GKV GLY B -1 UNP P0AAN9 EXPRESSION TAG SEQADV 8GKV GLY B 0 UNP P0AAN9 EXPRESSION TAG SEQADV 8GKV SER B 23 UNP P0AAN9 CYS 23 ENGINEERED MUTATION SEQRES 1 A 88 GLY GLY MET LYS ASN LEU ILE ALA GLU LEU LEU PHE LYS SEQRES 2 A 88 LEU ALA GLN LYS GLU GLU GLU SER LYS GLU LEU SER ALA SEQRES 3 A 88 GLN VAL GLU ALA LEU GLU ILE ILE VAL THR ALA MET LEU SEQRES 4 A 88 ARG ASN MET ALA GLN ASN ASP GLN GLN ARG LEU ILE ASP SEQRES 5 A 88 GLN VAL GLU GLY ALA LEU TYR GLU VAL LYS PRO ASP ALA SEQRES 6 A 88 SER ILE PRO ASP ASP ASP THR GLU LEU LEU ARG ASP TYR SEQRES 7 A 88 VAL LYS LYS LEU LEU LYS HIS PRO ARG GLN SEQRES 1 B 88 GLY GLY MET LYS ASN LEU ILE ALA GLU LEU LEU PHE LYS SEQRES 2 B 88 LEU ALA GLN LYS GLU GLU GLU SER LYS GLU LEU SER ALA SEQRES 3 B 88 GLN VAL GLU ALA LEU GLU ILE ILE VAL THR ALA MET LEU SEQRES 4 B 88 ARG ASN MET ALA GLN ASN ASP GLN GLN ARG LEU ILE ASP SEQRES 5 B 88 GLN VAL GLU GLY ALA LEU TYR GLU VAL LYS PRO ASP ALA SEQRES 6 B 88 SER ILE PRO ASP ASP ASP THR GLU LEU LEU ARG ASP TYR SEQRES 7 B 88 VAL LYS LYS LEU LEU LYS HIS PRO ARG GLN HET EPE A 101 7 HET EDO A 102 10 HET EDO A 103 10 HET EDO A 104 10 HET CL A 105 1 HET CL A 106 1 HET CL A 107 1 HET CL A 108 1 HET CL A 109 1 HET TRS B 101 20 HET CL B 102 1 HET CL B 103 1 HET CL B 104 1 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL HETSYN TRS TRIS BUFFER FORMUL 3 EPE C8 H18 N2 O4 S FORMUL 4 EDO 3(C2 H6 O2) FORMUL 7 CL 8(CL 1-) FORMUL 12 TRS C4 H12 N O3 1+ FORMUL 16 HOH *30(H2 O) HELIX 1 AA1 GLY A -1 GLN A 42 1 44 HELIX 2 AA2 LYS B 2 MET B 40 1 39 CRYST1 75.335 57.013 48.629 90.00 129.50 90.00 C 1 2 1 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 0.013274 0.000000 0.010943 0.00000 SCALE2 0.000000 0.017540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026651 0.00000