HEADER DE NOVO PROTEIN 28-JUL-15 5CWJ TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED HELICAL REPEAT PROTEIN DHR49 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 5CWJ 1 JRNL REMARK REVDAT 3 06-JAN-16 5CWJ 1 JRNL REVDAT 2 30-DEC-15 5CWJ 1 JRNL REVDAT 1 16-DEC-15 5CWJ 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) : 40.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 15711 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 788 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 40.4617 - 3.0888 0.98 2651 133 0.1854 0.2189 REMARK 3 2 3.0888 - 2.4518 1.00 2667 141 0.2084 0.2223 REMARK 3 3 2.4518 - 2.1419 0.98 2587 139 0.1783 0.2307 REMARK 3 4 2.1419 - 1.9460 0.95 2507 132 0.2163 0.2859 REMARK 3 5 1.9460 - 1.8065 0.90 2356 125 0.2683 0.3281 REMARK 3 6 1.8065 - 1.7000 0.81 2155 118 0.3193 0.4207 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 : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.71 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 : 0.003 1456 REMARK 3 ANGLE : 0.556 1963 REMARK 3 CHIRALITY : 0.027 211 REMARK 3 PLANARITY : 0.002 281 REMARK 3 DIHEDRAL : 13.774 623 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 2:20 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.6941 81.3523 4.6056 REMARK 3 T TENSOR REMARK 3 T11: 0.6385 T22: 0.5883 REMARK 3 T33: 0.4459 T12: -0.2259 REMARK 3 T13: -0.0549 T23: 0.1424 REMARK 3 L TENSOR REMARK 3 L11: 1.2431 L22: 1.4913 REMARK 3 L33: 0.8440 L12: 0.2286 REMARK 3 L13: -0.1053 L23: -0.5214 REMARK 3 S TENSOR REMARK 3 S11: 0.6895 S12: -0.8511 S13: -0.4595 REMARK 3 S21: 1.1290 S22: -0.3735 S23: 0.8657 REMARK 3 S31: 1.0882 S32: -0.4386 S33: 0.0305 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 21:99 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.6606 83.6517 -8.5937 REMARK 3 T TENSOR REMARK 3 T11: 0.3284 T22: 0.1917 REMARK 3 T33: 0.3050 T12: -0.0526 REMARK 3 T13: -0.0472 T23: 0.0337 REMARK 3 L TENSOR REMARK 3 L11: 2.5377 L22: 1.4227 REMARK 3 L33: 3.5132 L12: 0.4409 REMARK 3 L13: 0.7050 L23: -0.0245 REMARK 3 S TENSOR REMARK 3 S11: 0.0751 S12: 0.0339 S13: -0.3332 REMARK 3 S21: 0.2215 S22: 0.0222 S23: -0.1068 REMARK 3 S31: 0.4313 S32: -0.1629 S33: 0.0434 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 100:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9107 83.9417 -23.8934 REMARK 3 T TENSOR REMARK 3 T11: 0.3247 T22: 0.4364 REMARK 3 T33: 0.2917 T12: -0.0972 REMARK 3 T13: -0.0248 T23: 0.0419 REMARK 3 L TENSOR REMARK 3 L11: 2.2727 L22: 1.5625 REMARK 3 L33: 1.6864 L12: -0.7466 REMARK 3 L13: -0.5207 L23: 0.1923 REMARK 3 S TENSOR REMARK 3 S11: -0.2193 S12: 0.9173 S13: 0.1014 REMARK 3 S21: -0.2402 S22: 0.0958 S23: -0.2860 REMARK 3 S31: 0.3079 S32: -0.0633 S33: -0.0414 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:161 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3582 83.3034 -32.4391 REMARK 3 T TENSOR REMARK 3 T11: 0.3998 T22: 0.9232 REMARK 3 T33: 0.2370 T12: -0.1079 REMARK 3 T13: 0.0857 T23: 0.0465 REMARK 3 L TENSOR REMARK 3 L11: 6.9437 L22: 4.6537 REMARK 3 L33: 2.0483 L12: 0.4965 REMARK 3 L13: 1.2720 L23: -1.7843 REMARK 3 S TENSOR REMARK 3 S11: -0.3044 S12: 2.8368 S13: 0.4354 REMARK 3 S21: -1.5482 S22: -0.1186 S23: -0.0536 REMARK 3 S31: 0.2955 S32: 0.3739 S33: -0.6202 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 5CWJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212087. 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 : NULL 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 : 16718 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.05900 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) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 1.39300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.370 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 (%): 36.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M DI-POTASSIUM HYDROGEN PHOSPHATE, REMARK 280 20% (W/V) PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 40.44500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 40.44500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.35500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.44500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.67750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.44500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.03250 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 40.44500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.44500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.35500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 40.44500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 35.03250 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 40.44500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 11.67750 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 306 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 1 REMARK 465 GLY A 162 REMARK 465 TRP A 163 REMARK 465 LEU A 164 REMARK 465 GLU A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 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: 5CWK RELATED DB: PDB REMARK 900 RELATED ID: 5CWL RELATED DB: PDB REMARK 900 RELATED ID: 5CWM RELATED DB: PDB REMARK 900 RELATED ID: 5CWN 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 5CWJ A 1 171 PDB 5CWJ 5CWJ 1 171 SEQRES 1 A 171 MET ASP SER GLU GLU GLU GLN GLU ARG ILE ARG ARG ILE SEQRES 2 A 171 LEU LYS GLU ALA ARG LYS SER GLY THR GLU GLU SER LEU SEQRES 3 A 171 ARG GLN ALA ILE GLU ASP VAL ALA GLN LEU ALA LYS LYS SEQRES 4 A 171 SER GLN ASP SER GLU VAL LEU GLU GLU ALA ILE ARG VAL SEQRES 5 A 171 ILE LEU ARG ILE ALA LYS GLU SER GLY SER GLU GLU ALA SEQRES 6 A 171 LEU ARG GLN ALA ILE ARG ALA VAL ALA GLU ILE ALA LYS SEQRES 7 A 171 GLU ALA GLN ASP SER GLU VAL LEU GLU GLU ALA ILE ARG SEQRES 8 A 171 VAL ILE LEU ARG ILE ALA LYS GLU SER GLY SER GLU GLU SEQRES 9 A 171 ALA LEU ARG GLN ALA ILE ARG ALA VAL ALA GLU ILE ALA SEQRES 10 A 171 LYS GLU ALA GLN ASP PRO ARG VAL LEU GLU GLU ALA ILE SEQRES 11 A 171 ARG VAL ILE ARG GLN ILE ALA GLU GLU SER GLY SER GLU SEQRES 12 A 171 GLU ALA ARG ARG GLN ALA GLU ARG ALA GLU GLU GLU ILE SEQRES 13 A 171 ARG ARG ARG ALA GLN GLY TRP LEU GLU HIS HIS HIS HIS SEQRES 14 A 171 HIS HIS FORMUL 2 HOH *106(H2 O) HELIX 1 AA1 ASP A 2 GLY A 21 1 20 HELIX 2 AA2 THR A 22 LYS A 39 1 18 HELIX 3 AA3 ASP A 42 GLY A 61 1 20 HELIX 4 AA4 SER A 62 GLU A 79 1 18 HELIX 5 AA5 ASP A 82 GLY A 101 1 20 HELIX 6 AA6 SER A 102 ALA A 120 1 19 HELIX 7 AA7 ASP A 122 GLY A 141 1 20 HELIX 8 AA8 SER A 142 GLN A 161 1 20 CRYST1 80.890 80.890 46.710 90.00 90.00 90.00 I 41 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 0.012362 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012362 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021409 0.00000