HEADER DE NOVO PROTEIN 28-JUL-15 5CWN TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED HELICAL REPEAT PROTEIN DHR71 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED HELICAL 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: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21_NESG KEYWDS HELICAL REPEAT PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.BHABHA,D.C.EKIERT REVDAT 4 06-MAR-24 5CWN 1 JRNL REMARK REVDAT 3 06-JAN-16 5CWN 1 JRNL REVDAT 2 30-DEC-15 5CWN 1 JRNL REVDAT 1 16-DEC-15 5CWN 0 JRNL AUTH T.J.BRUNETTE,F.PARMEGGIANI,P.S.HUANG,G.BHABHA,D.C.EKIERT, JRNL AUTH 2 S.E.TSUTAKAWA,G.L.HURA,J.A.TAINER,D.BAKER JRNL TITL EXPLORING THE REPEAT PROTEIN UNIVERSE THROUGH COMPUTATIONAL JRNL TITL 2 PROTEIN DESIGN. JRNL REF NATURE V. 528 580 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26675729 JRNL DOI 10.1038/NATURE16162 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 22891 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1144 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 43.8537 - 3.3991 0.99 2890 150 0.1940 0.2028 REMARK 3 2 3.3991 - 2.6981 1.00 2761 147 0.1916 0.2298 REMARK 3 3 2.6981 - 2.3571 1.00 2694 141 0.1517 0.1796 REMARK 3 4 2.3571 - 2.1416 1.00 2704 142 0.1472 0.1598 REMARK 3 5 2.1416 - 1.9881 1.00 2697 143 0.1808 0.1994 REMARK 3 6 1.9881 - 1.8709 1.00 2684 140 0.2220 0.2615 REMARK 3 7 1.8709 - 1.7772 1.00 2636 139 0.2601 0.2760 REMARK 3 8 1.7772 - 1.7000 1.00 2681 142 0.3068 0.3111 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.770 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.66 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 : 0.008 1778 REMARK 3 ANGLE : 1.010 2373 REMARK 3 CHIRALITY : 0.039 256 REMARK 3 PLANARITY : 0.004 316 REMARK 3 DIHEDRAL : 13.390 748 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 1:99 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.1145 -14.1914 10.6887 REMARK 3 T TENSOR REMARK 3 T11: 0.1838 T22: 0.1910 REMARK 3 T33: 0.2158 T12: -0.0162 REMARK 3 T13: -0.0026 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 2.5231 L22: 1.6979 REMARK 3 L33: 1.6749 L12: -0.2840 REMARK 3 L13: 0.5266 L23: 0.3923 REMARK 3 S TENSOR REMARK 3 S11: -0.0148 S12: 0.1678 S13: -0.1759 REMARK 3 S21: 0.0422 S22: -0.0153 S23: 0.0604 REMARK 3 S31: 0.2444 S32: -0.0364 S33: -0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 100:175 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.8336 -2.9194 27.8604 REMARK 3 T TENSOR REMARK 3 T11: 0.2838 T22: 0.2590 REMARK 3 T33: 0.2385 T12: -0.0060 REMARK 3 T13: 0.0243 T23: -0.0415 REMARK 3 L TENSOR REMARK 3 L11: 1.7817 L22: 1.0288 REMARK 3 L33: 1.6701 L12: 0.0705 REMARK 3 L13: 0.0729 L23: 1.2808 REMARK 3 S TENSOR REMARK 3 S11: 0.0649 S12: -0.2199 S13: 0.0993 REMARK 3 S21: 0.3259 S22: -0.0851 S23: 0.0326 REMARK 3 S31: -0.0704 S32: -0.2003 S33: -0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 176:207 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.3245 -0.7537 42.9277 REMARK 3 T TENSOR REMARK 3 T11: 0.4157 T22: 0.4592 REMARK 3 T33: 0.2630 T12: 0.0423 REMARK 3 T13: 0.0546 T23: -0.1108 REMARK 3 L TENSOR REMARK 3 L11: 1.7355 L22: 0.7619 REMARK 3 L33: 1.1822 L12: 0.1063 REMARK 3 L13: -0.6443 L23: 0.5959 REMARK 3 S TENSOR REMARK 3 S11: -0.1237 S12: -0.6566 S13: 0.0898 REMARK 3 S21: 0.3912 S22: 0.1730 S23: -0.0868 REMARK 3 S31: -0.1146 S32: -0.2498 S33: 0.1668 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 5CWN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212157. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 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) : 1.111 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22958 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 1.64300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.250 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 (%): 41.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CHES, PH 9.5, 50% (V/V) PEG 200, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 11.63500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.65000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.45500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.65000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.63500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.45500 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 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 HIS A 208 REMARK 465 HIS A 209 REMARK 465 HIS A 210 REMARK 465 HIS A 211 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NHE A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CWB RELATED DB: PDB REMARK 900 RELATED ID: 5CWC RELATED DB: PDB REMARK 900 RELATED ID: 5CWD RELATED DB: PDB REMARK 900 RELATED ID: 5CWF RELATED DB: PDB REMARK 900 RELATED ID: 5CWG RELATED DB: PDB REMARK 900 RELATED ID: 5CWH RELATED DB: PDB REMARK 900 RELATED ID: 5CWI RELATED DB: PDB REMARK 900 RELATED ID: 5CWJ RELATED DB: PDB REMARK 900 RELATED ID: 5CWK RELATED DB: PDB REMARK 900 RELATED ID: 5CWL RELATED DB: PDB REMARK 900 RELATED ID: 5CWM RELATED DB: PDB REMARK 900 RELATED ID: 5CWO RELATED DB: PDB REMARK 900 RELATED ID: 5CWP RELATED DB: PDB REMARK 900 RELATED ID: 5CWQ RELATED DB: PDB DBREF 5CWN A 1 211 PDB 5CWN 5CWN 1 211 SEQRES 1 A 211 MET ASP PRO GLU GLU ILE LEU GLU ARG ALA LYS GLU SER SEQRES 2 A 211 LEU GLU ARG ALA ARG GLU ALA SER GLU ARG GLY ASP GLU SEQRES 3 A 211 GLU GLU PHE ARG LYS ALA ALA GLU LYS ALA LEU GLU LEU SEQRES 4 A 211 ALA LYS ARG LEU VAL GLU GLN ALA LYS LYS GLU GLY ASP SEQRES 5 A 211 PRO GLU LEU VAL LEU GLU ALA ALA LYS VAL ALA LEU ARG SEQRES 6 A 211 VAL ALA GLU LEU ALA ALA LYS ASN GLY ASP LYS GLU VAL SEQRES 7 A 211 PHE LYS LYS ALA ALA GLU SER ALA LEU GLU VAL ALA LYS SEQRES 8 A 211 ARG LEU VAL GLU VAL ALA SER LYS GLU GLY ASP PRO GLU SEQRES 9 A 211 LEU VAL LEU GLU ALA ALA LYS VAL ALA LEU ARG VAL ALA SEQRES 10 A 211 GLU LEU ALA ALA LYS ASN GLY ASP LYS GLU VAL PHE LYS SEQRES 11 A 211 LYS ALA ALA GLU SER ALA LEU GLU VAL ALA LYS ARG LEU SEQRES 12 A 211 VAL GLU VAL ALA SER LYS GLU GLY ASP PRO GLU LEU VAL SEQRES 13 A 211 GLU GLU ALA ALA LYS VAL ALA GLU GLU VAL ARG LYS LEU SEQRES 14 A 211 ALA LYS LYS GLN GLY ASP GLU GLU VAL TYR GLU LYS ALA SEQRES 15 A 211 ARG GLU THR ALA ARG GLU VAL LYS GLU GLU LEU LYS ARG SEQRES 16 A 211 VAL ARG GLU GLU LYS GLY GLY TRP LEU GLU HIS HIS HIS SEQRES 17 A 211 HIS HIS HIS HET PG4 A 301 31 HET PG4 A 302 31 HET PG4 A 303 31 HET NHE A 304 30 HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID HETSYN NHE N-CYCLOHEXYLTAURINE; CHES FORMUL 2 PG4 3(C8 H18 O5) FORMUL 5 NHE C8 H17 N O3 S FORMUL 6 HOH *49(H2 O) HELIX 1 AA1 ASP A 2 GLY A 24 1 23 HELIX 2 AA2 ASP A 25 GLY A 51 1 27 HELIX 3 AA3 ASP A 52 ASN A 73 1 22 HELIX 4 AA4 ASP A 75 GLU A 100 1 26 HELIX 5 AA5 ASP A 102 ASN A 123 1 22 HELIX 6 AA6 ASP A 125 GLU A 150 1 26 HELIX 7 AA7 ASP A 152 GLY A 174 1 23 HELIX 8 AA8 ASP A 175 HIS A 207 1 33 SITE 1 AC1 10 GLU A 4 LEU A 7 GLU A 8 LYS A 11 SITE 2 AC1 10 GLU A 45 GLU A 58 ARG A 65 GLU A 88 SITE 3 AC1 10 ARG A 92 HOH A 408 SITE 1 AC2 6 GLU A 15 ARG A 18 GLU A 34 LYS A 41 SITE 2 AC2 6 LYS A 81 SER A 85 SITE 1 AC3 8 GLU A 84 GLU A 88 LYS A 91 LYS A 131 SITE 2 AC3 8 SER A 135 GLU A 138 HOH A 407 HOH A 412 SITE 1 AC4 10 ARG A 18 ARG A 65 GLU A 68 LEU A 69 SITE 2 AC4 10 LYS A 72 GLU A 77 LYS A 81 GLU A 84 SITE 3 AC4 10 LYS A 131 HOH A 403 CRYST1 23.270 82.910 103.300 90.00 90.00 90.00 P 21 21 21 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 0.042974 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012061 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009681 0.00000