HEADER DE NOVO PROTEIN 20-DEC-13 4O60 TITLE STRUCTURE OF ANKYRIN REPEAT PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANK-N5C-317; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: SYNTHETIC CONSTRUCT KEYWDS ANKYRIN, DESIGNED ANKYRIN REPEATS, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.S.ETHAYATHULLA,L.GUAN REVDAT 3 20-SEP-23 4O60 1 REMARK REVDAT 2 06-MAY-15 4O60 1 AUTHOR REVDAT 1 25-MAR-15 4O60 0 JRNL AUTH E.B.TIKHONOVA,A.S.ETHAYATHULLA,Y.SU,P.HARIHARAN,S.XIE,L.GUAN JRNL TITL A TRANSCRIPTION BLOCKER ISOLATED FROM A DESIGNED REPEAT JRNL TITL 2 PROTEIN COMBINATORIAL LIBRARY BY IN VIVO FUNCTIONAL SCREEN. JRNL REF SCI REP V. 5 8070 2015 JRNL REFN ESSN 2045-2322 JRNL PMID 25627011 JRNL DOI 10.1038/SREP08070 REMARK 2 REMARK 2 RESOLUTION. 2.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 26425 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1319 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 38.3143 - 5.2460 1.00 2843 142 0.1626 0.1739 REMARK 3 2 5.2460 - 4.1655 1.00 2855 116 0.1669 0.2881 REMARK 3 3 4.1655 - 3.6394 1.00 2840 137 0.1651 0.1808 REMARK 3 4 3.6394 - 3.3069 1.00 2796 180 0.1933 0.2491 REMARK 3 5 3.3069 - 3.0700 1.00 2809 127 0.2242 0.3059 REMARK 3 6 3.0700 - 2.8890 1.00 2823 179 0.2303 0.3220 REMARK 3 7 2.8890 - 2.7444 1.00 2805 146 0.2337 0.2558 REMARK 3 8 2.7444 - 2.6250 1.00 2839 154 0.2279 0.3127 REMARK 3 9 2.6250 - 2.5239 0.88 2496 138 0.2540 0.3851 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.720 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 : 0.006 3531 REMARK 3 ANGLE : 1.121 4783 REMARK 3 CHIRALITY : 0.040 565 REMARK 3 PLANARITY : 0.006 629 REMARK 3 DIHEDRAL : 15.373 1287 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 4O60 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 300 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRROR 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27744 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 30.0000 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) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.70000 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: 2XEE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE TRIHYDRATE (PH REMARK 280 4.5), 200 MM (NH3)2SO4, 16-18% PEG 4000, AND 10% GLYCEROL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K, PH 4.2 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 59.73150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.40050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.73150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.40050 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: 2870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 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 HIS A 232 REMARK 465 HIS A 233 REMARK 465 HIS A 234 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 MET B 3 REMARK 465 HIS B 232 REMARK 465 HIS B 233 REMARK 465 HIS B 234 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 HIS B 230 CG ND1 CD2 CE1 NE2 REMARK 470 HIS B 231 CG ND1 CD2 CE1 NE2 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 MET A 3 79.29 -119.96 REMARK 500 MET A 135 -65.63 -140.60 REMARK 500 MET B 135 1.17 82.39 REMARK 500 HIS B 229 68.65 -109.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QFV RELATED DB: PDB DBREF 4O60 A 1 234 PDB 4O60 4O60 1 234 DBREF 4O60 B 1 234 PDB 4O60 4O60 1 234 SEQRES 1 A 234 MET SER MET ASP ILE GLY LYS LYS LEU LEU GLU ALA ALA SEQRES 2 A 234 ARG ALA GLY HIS ASP ASP SER VAL GLU VAL LEU LEU LYS SEQRES 3 A 234 LYS GLY ALA ASP ILE ASN ALA LYS ASP ASN VAL GLY VAL SEQRES 4 A 234 THR PRO LEU HIS LEU ALA ALA VAL ASN GLY HIS LEU GLU SEQRES 5 A 234 LEU VAL LYS LEU LEU LEU GLU LYS GLY ALA ASP ILE ASN SEQRES 6 A 234 ALA THR ASP LEU PHE GLY LEU THR PRO LEU HIS PHE ALA SEQRES 7 A 234 ALA THR ASN GLY HIS LEU GLU LEU VAL LYS LEU LEU LEU SEQRES 8 A 234 GLU LYS GLY ALA ASP ILE ASN ALA VAL ASP ASP VAL GLY SEQRES 9 A 234 VAL THR PRO LEU HIS PHE ALA ALA ARG ASN GLY HIS LEU SEQRES 10 A 234 GLU LEU VAL LYS LEU LEU LEU GLU LYS GLY ALA ASP ILE SEQRES 11 A 234 ASN ALA MET ASP MET VAL GLY PRO THR PRO LEU HIS PHE SEQRES 12 A 234 ALA ALA LYS ASN GLY HIS LEU GLU LEU VAL LYS LEU LEU SEQRES 13 A 234 LEU GLU LYS ASP ALA ASP ILE ASN ALA GLU ASP HIS PHE SEQRES 14 A 234 GLY SER THR PRO LEU HIS SER ALA ALA GLU ASN GLY HIS SEQRES 15 A 234 LEU GLU LEU VAL LYS LEU LEU LEU GLU LYS GLY ALA ASP SEQRES 16 A 234 ILE ASN ALA ARG ASP LYS PHE GLY LYS THR PRO PHE ASP SEQRES 17 A 234 LEU ALA ILE ASP ASN GLY ASN GLU ASP ILE ALA GLU VAL SEQRES 18 A 234 LEU GLN LYS ALA ALA ARG SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 234 MET SER MET ASP ILE GLY LYS LYS LEU LEU GLU ALA ALA SEQRES 2 B 234 ARG ALA GLY HIS ASP ASP SER VAL GLU VAL LEU LEU LYS SEQRES 3 B 234 LYS GLY ALA ASP ILE ASN ALA LYS ASP ASN VAL GLY VAL SEQRES 4 B 234 THR PRO LEU HIS LEU ALA ALA VAL ASN GLY HIS LEU GLU SEQRES 5 B 234 LEU VAL LYS LEU LEU LEU GLU LYS GLY ALA ASP ILE ASN SEQRES 6 B 234 ALA THR ASP LEU PHE GLY LEU THR PRO LEU HIS PHE ALA SEQRES 7 B 234 ALA THR ASN GLY HIS LEU GLU LEU VAL LYS LEU LEU LEU SEQRES 8 B 234 GLU LYS GLY ALA ASP ILE ASN ALA VAL ASP ASP VAL GLY SEQRES 9 B 234 VAL THR PRO LEU HIS PHE ALA ALA ARG ASN GLY HIS LEU SEQRES 10 B 234 GLU LEU VAL LYS LEU LEU LEU GLU LYS GLY ALA ASP ILE SEQRES 11 B 234 ASN ALA MET ASP MET VAL GLY PRO THR PRO LEU HIS PHE SEQRES 12 B 234 ALA ALA LYS ASN GLY HIS LEU GLU LEU VAL LYS LEU LEU SEQRES 13 B 234 LEU GLU LYS ASP ALA ASP ILE ASN ALA GLU ASP HIS PHE SEQRES 14 B 234 GLY SER THR PRO LEU HIS SER ALA ALA GLU ASN GLY HIS SEQRES 15 B 234 LEU GLU LEU VAL LYS LEU LEU LEU GLU LYS GLY ALA ASP SEQRES 16 B 234 ILE ASN ALA ARG ASP LYS PHE GLY LYS THR PRO PHE ASP SEQRES 17 B 234 LEU ALA ILE ASP ASN GLY ASN GLU ASP ILE ALA GLU VAL SEQRES 18 B 234 LEU GLN LYS ALA ALA ARG SER HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *55(H2 O) HELIX 1 1 ASP A 4 ALA A 15 1 12 HELIX 2 2 HIS A 17 GLY A 28 1 12 HELIX 3 3 THR A 40 GLY A 49 1 10 HELIX 4 4 HIS A 50 LYS A 60 1 11 HELIX 5 5 THR A 73 GLY A 82 1 10 HELIX 6 6 HIS A 83 LYS A 93 1 11 HELIX 7 7 THR A 106 ASN A 114 1 9 HELIX 8 8 HIS A 116 LYS A 126 1 11 HELIX 9 9 THR A 139 ASN A 147 1 9 HELIX 10 10 HIS A 149 LYS A 159 1 11 HELIX 11 11 THR A 172 GLY A 181 1 10 HELIX 12 12 HIS A 182 LYS A 192 1 11 HELIX 13 13 THR A 205 ASN A 213 1 9 HELIX 14 14 ASN A 215 SER A 228 1 14 HELIX 15 15 ILE B 5 ALA B 15 1 11 HELIX 16 16 HIS B 17 LYS B 27 1 11 HELIX 17 17 THR B 40 GLY B 49 1 10 HELIX 18 18 HIS B 50 LYS B 60 1 11 HELIX 19 19 THR B 73 GLY B 82 1 10 HELIX 20 20 HIS B 83 LYS B 93 1 11 HELIX 21 21 THR B 106 ASN B 114 1 9 HELIX 22 22 HIS B 116 LYS B 126 1 11 HELIX 23 23 THR B 139 ASN B 147 1 9 HELIX 24 24 HIS B 149 LYS B 159 1 11 HELIX 25 25 THR B 172 GLY B 181 1 10 HELIX 26 26 HIS B 182 LYS B 192 1 11 HELIX 27 27 THR B 205 ASN B 213 1 9 HELIX 28 28 ASN B 215 ARG B 227 1 13 CRYST1 119.463 46.801 74.249 90.00 97.87 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 0.008371 0.000000 0.001157 0.00000 SCALE2 0.000000 0.021367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013596 0.00000