PDB Short entry for 2XEN HEADER DE NOVO PROTEIN 17-MAY-10 2XEN TITLE STRUCTURAL DETERMINANTS FOR IMPROVED THERMAL STABILITY OF DESIGNED TITLE 2 ANKYRIN REPEAT PROTEINS WITH A REDESIGNED C-CAPPING MODULE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NI1C MUT4; 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 KEYWDS DE NOVO PROTEIN, PROTEIN ENGINEERING, REPEAT PROTEIN, ANKYRIN, KEYWDS 2 DESIGN, PROTEIN-PROTEIN INTERACTION EXPDTA X-RAY DIFFRACTION AUTHOR M.KRAMER,S.K.WETZEL,A.PLUCKTHUN,P.MITTL,M.GRUTTER REVDAT 4 08-MAY-24 2XEN 1 REMARK REVDAT 3 24-NOV-10 2XEN 1 JRNL REVDAT 2 29-SEP-10 2XEN 1 JRNL REVDAT 1 18-AUG-10 2XEN 0 JRNL AUTH M.KRAMER,S.K.WETZEL,A.PLUCKTHUN,P.MITTL,M.GRUTTER JRNL TITL STRUCTURAL DETERMINANTS FOR IMPROVED THERMAL STABILITY OF JRNL TITL 2 DESIGNED ANKYRIN REPEAT PROTEINS WITH A REDESIGNED C-CAPPING JRNL TITL 3 MODULE. JRNL REF J.MOL.BIOL. V. 404 381 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20851127 JRNL DOI 10.1016/J.JMB.2010.09.023 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 4113 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 407 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 29.5015 - 3.1728 0.99 1260 134 0.1640 0.2048 REMARK 3 2 3.1728 - 2.5188 1.00 1215 133 0.1635 0.2241 REMARK 3 3 2.5188 - 2.2005 0.99 1231 140 0.1809 0.2474 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 : 0.41 REMARK 3 B_SOL : 51.54 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 13.39440 REMARK 3 B22 (A**2) : -6.43510 REMARK 3 B33 (A**2) : -6.95940 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 9.26600 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 : 0.008 700 REMARK 3 ANGLE : 0.944 941 REMARK 3 CHIRALITY : 0.060 108 REMARK 3 PLANARITY : 0.003 126 REMARK 3 DIHEDRAL : 15.763 259 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 2XEN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1290043944. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4117 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 31.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 38.57500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.66500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.57500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.66500 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 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 A2028 LIES ON A SPECIAL POSITION. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MOH A 1105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1106 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XEH RELATED DB: PDB REMARK 900 STRUCTURAL DETERMINANTS FOR IMPROVED THERMAL STABILITY OF DESIGNED REMARK 900 ANKYRIN REPEAT PROTEINS WITH A REDESIGNED C-CAPPING MODULE. REMARK 900 RELATED ID: 2XEE RELATED DB: PDB REMARK 900 STRUCTURAL DETERMINANTS FOR IMPROVED THERMAL STABILITY OF DESIGNED REMARK 900 ANKYRIN REPEAT PROTEINS WITH A REDESIGNED C-CAPPING MODULE. DBREF 2XEN A 13 103 PDB 2XEN 2XEN 13 103 SEQRES 1 A 91 ASP LEU GLY LYS LYS LEU LEU GLU ALA ALA ARG ALA GLY SEQRES 2 A 91 GLN ASP ASP GLU VAL ARG ILE LEU MET ALA ASN GLY ALA SEQRES 3 A 91 ASP VAL ASN ALA LYS ASP LYS ASP GLY TYR THR PRO LEU SEQRES 4 A 91 HIS LEU ALA ALA ARG GLU GLY HIS LEU GLU ILE VAL GLU SEQRES 5 A 91 VAL LEU LEU LYS ALA GLY ALA ASP VAL ASN ALA GLN ASP SEQRES 6 A 91 LYS PHE GLY LYS THR ALA PHE ASP ILE SER ILE ASP ASN SEQRES 7 A 91 GLY ASN GLU ASP LEU ALA GLU ILE LEU GLN LYS ALA ALA HET EDO A1104 4 HET MOH A1105 2 HET SO4 A1106 5 HETNAM EDO 1,2-ETHANEDIOL HETNAM MOH METHANOL HETNAM SO4 SULFATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 MOH C H4 O FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *47(H2 O) HELIX 1 1 ASP A 13 ALA A 24 1 12 HELIX 2 2 GLN A 26 ASN A 36 1 11 HELIX 3 3 THR A 49 GLU A 57 1 9 HELIX 4 4 HIS A 59 ALA A 69 1 11 HELIX 5 5 THR A 82 ASN A 90 1 9 HELIX 6 6 ASN A 92 ALA A 103 1 12 SITE 1 AC1 5 LYS A 16 HIS A 59 LEU A 60 GLU A 61 SITE 2 AC1 5 ASP A 89 SITE 1 AC2 6 TYR A 48 ASP A 77 LYS A 81 ASN A 92 SITE 2 AC2 6 ASP A 94 HOH A2040 SITE 1 AC3 4 ARG A 31 LYS A 45 HOH A2026 HOH A2047 CRYST1 77.150 35.330 32.400 90.00 114.43 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 0.012962 0.000000 0.005888 0.00000 SCALE2 0.000000 0.028305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033899 0.00000