HEADER DE NOVO PROTEIN 28-JUL-15 5CWM TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED HELICAL REPEAT PROTEIN DHR64 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 5CWM 1 JRNL REMARK REVDAT 3 06-JAN-16 5CWM 1 JRNL REVDAT 2 30-DEC-15 5CWM 1 JRNL REVDAT 1 16-DEC-15 5CWM 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. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 5645 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 277 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 49.1470 - 3.6537 0.98 2858 149 0.1895 0.2111 REMARK 3 2 3.6537 - 2.9000 0.88 2510 128 0.2952 0.3694 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.30 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 72.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 99.69 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 : 0.002 1818 REMARK 3 ANGLE : 0.419 2432 REMARK 3 CHIRALITY : 0.017 280 REMARK 3 PLANARITY : 0.001 329 REMARK 3 DIHEDRAL : 10.440 758 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 2:227 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.7183 -11.1232 -4.2469 REMARK 3 T TENSOR REMARK 3 T11: 0.6972 T22: 0.5427 REMARK 3 T33: 0.4497 T12: -0.0608 REMARK 3 T13: -0.2034 T23: -0.0635 REMARK 3 L TENSOR REMARK 3 L11: 3.7168 L22: 6.4248 REMARK 3 L33: 4.2005 L12: -1.3452 REMARK 3 L13: -0.8878 L23: 0.4145 REMARK 3 S TENSOR REMARK 3 S11: -0.1441 S12: 0.2339 S13: 0.1904 REMARK 3 S21: 0.0199 S22: -0.3290 S23: 0.3908 REMARK 3 S31: -0.5650 S32: -0.1339 S33: -0.0469 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 5CWM 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_1000212156. 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 : 5.0 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 : 6086 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.15200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.30 REMARK 200 R MERGE FOR SHELL (I) : 2.13800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.340 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 (%): 50.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, PH 5.0, 10% REMARK 280 (V/V) MPD, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.38000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.19000 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 24.28500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 8.09500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.47500 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 MET A 1 REMARK 465 GLU A 228 REMARK 465 GLY A 229 REMARK 465 GLY A 230 REMARK 465 TRP A 231 REMARK 465 LEU A 232 REMARK 465 GLU A 233 REMARK 465 HIS A 234 REMARK 465 HIS A 235 REMARK 465 HIS A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 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: 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 5CWM A 1 239 PDB 5CWM 5CWM 1 239 SEQRES 1 A 239 MET ASP PRO GLU ASP GLU LEU LYS ARG VAL GLU LYS LEU SEQRES 2 A 239 VAL LYS GLU ALA GLU GLU LEU LEU ARG GLN ALA LYS GLU SEQRES 3 A 239 LYS GLY SER GLU GLU ASP LEU GLU LYS ALA LEU ARG THR SEQRES 4 A 239 ALA GLU GLU ALA ALA ARG GLU ALA LYS LYS VAL LEU GLU SEQRES 5 A 239 GLN ALA GLU LYS GLU GLY ASP PRO GLU VAL ALA LEU ARG SEQRES 6 A 239 ALA VAL GLU LEU VAL VAL ARG VAL ALA GLU LEU LEU LEU SEQRES 7 A 239 ARG ILE ALA LYS GLU SER GLY SER GLU GLU ALA LEU GLU SEQRES 8 A 239 ARG ALA LEU ARG VAL ALA GLU GLU ALA ALA ARG LEU ALA SEQRES 9 A 239 LYS ARG VAL LEU GLU LEU ALA GLU LYS GLN GLY ASP PRO SEQRES 10 A 239 GLU VAL ALA LEU ARG ALA VAL GLU LEU VAL VAL ARG VAL SEQRES 11 A 239 ALA GLU LEU LEU LEU ARG ILE ALA LYS GLU SER GLY SER SEQRES 12 A 239 GLU GLU ALA LEU GLU ARG ALA LEU ARG VAL ALA GLU GLU SEQRES 13 A 239 ALA ALA ARG LEU ALA LYS ARG VAL LEU GLU LEU ALA GLU SEQRES 14 A 239 LYS GLN GLY ASP PRO GLU VAL ALA ARG ARG ALA VAL GLU SEQRES 15 A 239 LEU VAL LYS ARG VAL ALA GLU LEU LEU GLU ARG ILE ALA SEQRES 16 A 239 ARG GLU SER GLY SER GLU GLU ALA LYS GLU ARG ALA GLU SEQRES 17 A 239 ARG VAL ARG GLU GLU ALA ARG GLU LEU GLN GLU ARG VAL SEQRES 18 A 239 LYS GLU LEU ARG GLU ARG GLU GLY GLY TRP LEU GLU HIS SEQRES 19 A 239 HIS HIS HIS HIS HIS HELIX 1 AA1 ASP A 2 GLY A 28 1 27 HELIX 2 AA2 SER A 29 GLY A 58 1 30 HELIX 3 AA3 ASP A 59 GLY A 85 1 27 HELIX 4 AA4 SER A 86 GLY A 115 1 30 HELIX 5 AA5 ASP A 116 GLY A 142 1 27 HELIX 6 AA6 SER A 143 GLN A 171 1 29 HELIX 7 AA7 ASP A 173 GLY A 199 1 27 HELIX 8 AA8 SER A 200 ARG A 227 1 28 CRYST1 98.280 98.280 48.570 90.00 90.00 120.00 P 65 6 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 0.010175 0.005875 0.000000 0.00000 SCALE2 0.000000 0.011749 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020589 0.00000