HEADER DE NOVO PROTEIN 13-JAN-12 4DB6 TITLE DESIGNED ARMADILLO REPEAT PROTEIN (YIIIM3AII) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARMADILLO REPEAT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: XL1 BLUE; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PPANK KEYWDS SOLENOID REPEAT, ARMADILLO REPEAT MOTIF, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.MADHURANTAKAM,G.VARADAMSETTY,M.G.GRUTTER,A.PLUCKTHUN,P.R.E.MITTL REVDAT 4 28-FEB-24 4DB6 1 REMARK REVDAT 3 05-SEP-12 4DB6 1 REMARK TITLE REVDAT 2 18-JUL-12 4DB6 1 JRNL REVDAT 1 16-MAY-12 4DB6 0 JRNL AUTH C.MADHURANTAKAM,G.VARADAMSETTY,M.G.GRUTTER,A.PLUCKTHUN, JRNL AUTH 2 P.R.MITTL JRNL TITL STRUCTURE-BASED OPTIMIZATION OF DESIGNED ARMADILLO-REPEAT JRNL TITL 2 PROTEINS. JRNL REF PROTEIN SCI. V. 21 1015 2012 JRNL REFN ISSN 0961-8368 JRNL PMID 22544642 JRNL DOI 10.1002/PRO.2085 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 25608 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 862 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 22.8968 - 3.2682 0.96 2770 148 0.1869 0.2139 REMARK 3 2 3.2682 - 2.5953 1.00 2772 148 0.1858 0.2483 REMARK 3 3 2.5953 - 2.2675 1.00 2728 144 0.1703 0.2059 REMARK 3 4 2.2675 - 2.0604 0.99 2706 126 0.1625 0.2021 REMARK 3 5 2.0604 - 1.9128 0.99 2665 147 0.1785 0.2471 REMARK 3 6 1.9128 - 1.8000 0.97 2611 149 0.1969 0.2491 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 60.78 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.61700 REMARK 3 B22 (A**2) : 5.92680 REMARK 3 B33 (A**2) : -3.30980 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1587 REMARK 3 ANGLE : 0.951 2181 REMARK 3 CHIRALITY : 0.064 251 REMARK 3 PLANARITY : 0.005 298 REMARK 3 DIHEDRAL : 15.761 601 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 4DB6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000070110. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26356 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 : 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 (%): 39.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES,PH 7.5, 1.4 M SODIUM REMARK 280 CITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 21.48000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.79000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 46.40000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 21.48000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.79000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 46.40000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 21.48000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.79000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 46.40000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 21.48000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.79000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 46.40000 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 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 401 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 425 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 440 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 MET A 0 REMARK 465 ARG A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 GLY A 10 REMARK 465 SER A 11 REMARK 465 HIS A 209 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 GLU A 12 CG CD OE1 OE2 REMARK 470 GLN A 207 CG CD OE1 NE2 REMARK 470 SER A 208 OG REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DB8 RELATED DB: PDB REMARK 900 DESIGNED ARMADILLO REPEAT PROTEIN (YIIM4AII) REMARK 900 RELATED ID: 4DB9 RELATED DB: PDB REMARK 900 DESIGNED ARMADILLO REPEAT PROTEIN (YIIIM3AIII) REMARK 900 RELATED ID: 4DBA RELATED DB: PDB REMARK 900 DESIGNED ARMADILLO REPEAT PROTEIN (YIIM3AII) DBREF 4DB6 A 0 209 PDB 4DB6 4DB6 0 209 SEQRES 1 A 210 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER GLU SEQRES 2 A 210 LEU PRO GLN MET VAL GLN GLN LEU ASN SER PRO ASP GLN SEQRES 3 A 210 GLN GLU LEU GLN SER ALA LEU ARG LYS LEU SER GLN ILE SEQRES 4 A 210 ALA SER GLY GLY ASN GLU GLN ILE GLN ALA VAL ILE ASP SEQRES 5 A 210 ALA GLY ALA LEU PRO ALA LEU VAL GLN LEU LEU SER SER SEQRES 6 A 210 PRO ASN GLU GLN ILE LEU GLN GLU ALA LEU TRP ALA LEU SEQRES 7 A 210 SER ASN ILE ALA SER GLY GLY ASN GLU GLN ILE GLN ALA SEQRES 8 A 210 VAL ILE ASP ALA GLY ALA LEU PRO ALA LEU VAL GLN LEU SEQRES 9 A 210 LEU SER SER PRO ASN GLU GLN ILE LEU GLN GLU ALA LEU SEQRES 10 A 210 TRP ALA LEU SER ASN ILE ALA SER GLY GLY ASN GLU GLN SEQRES 11 A 210 ILE GLN ALA VAL ILE ASP ALA GLY ALA LEU PRO ALA LEU SEQRES 12 A 210 VAL GLN LEU LEU SER SER PRO ASN GLU GLN ILE LEU GLN SEQRES 13 A 210 GLU ALA LEU TRP ALA LEU SER ASN ILE ALA SER GLY GLY SEQRES 14 A 210 ASN GLU GLN LYS GLN ALA VAL LYS GLU ALA GLY ALA LEU SEQRES 15 A 210 GLU LYS LEU GLU GLN LEU GLN SER HIS GLU ASN GLU LYS SEQRES 16 A 210 ILE GLN LYS GLU ALA GLN GLU ALA LEU GLU LYS LEU GLN SEQRES 17 A 210 SER HIS FORMUL 2 HOH *153(H2 O) HELIX 1 1 GLU A 12 LEU A 20 1 9 HELIX 2 2 ASP A 24 SER A 40 1 17 HELIX 3 3 GLY A 42 ALA A 52 1 11 HELIX 4 4 GLY A 53 LEU A 62 1 10 HELIX 5 5 ASN A 66 ALA A 81 1 16 HELIX 6 6 GLY A 84 ALA A 94 1 11 HELIX 7 7 ALA A 96 LEU A 104 1 9 HELIX 8 8 ASN A 108 ALA A 123 1 16 HELIX 9 9 GLY A 126 ALA A 136 1 11 HELIX 10 10 GLY A 137 LEU A 146 1 10 HELIX 11 11 ASN A 150 SER A 166 1 17 HELIX 12 12 GLY A 168 ALA A 178 1 11 HELIX 13 13 GLY A 179 LEU A 187 1 9 HELIX 14 14 GLN A 188 HIS A 190 5 3 HELIX 15 15 ASN A 192 GLN A 207 1 16 CRYST1 42.960 91.580 92.800 90.00 90.00 90.00 I 2 2 2 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 0.023277 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010919 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010776 0.00000