HEADER DE NOVO PROTEIN 28-JUL-15 5CWH TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED HELICAL REPEAT PROTEIN DHR14 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 5CWH 1 JRNL REMARK REVDAT 3 06-JAN-16 5CWH 1 JRNL REVDAT 2 30-DEC-15 5CWH 1 JRNL REVDAT 1 16-DEC-15 5CWH 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. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 47550 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2377 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 38.1462 - 3.3425 0.96 2749 144 0.1999 0.2025 REMARK 3 2 3.3425 - 2.6532 0.99 2716 142 0.1642 0.1931 REMARK 3 3 2.6532 - 2.3179 1.00 2709 143 0.1363 0.1522 REMARK 3 4 2.3179 - 2.1060 1.00 2690 143 0.1215 0.1438 REMARK 3 5 2.1060 - 1.9550 0.99 2661 139 0.1184 0.1558 REMARK 3 6 1.9550 - 1.8398 0.99 2664 142 0.1268 0.1784 REMARK 3 7 1.8398 - 1.7476 0.99 2637 139 0.1239 0.1567 REMARK 3 8 1.7476 - 1.6716 0.99 2672 142 0.1203 0.1509 REMARK 3 9 1.6716 - 1.6072 0.99 2624 136 0.1264 0.1868 REMARK 3 10 1.6072 - 1.5517 0.99 2639 139 0.1295 0.1738 REMARK 3 11 1.5517 - 1.5032 0.99 2649 138 0.1358 0.1737 REMARK 3 12 1.5032 - 1.4603 0.98 2608 137 0.1659 0.1861 REMARK 3 13 1.4603 - 1.4218 0.99 2624 139 0.1912 0.2159 REMARK 3 14 1.4218 - 1.3871 1.00 2651 140 0.2239 0.2977 REMARK 3 15 1.3871 - 1.3556 0.99 2623 137 0.2455 0.3175 REMARK 3 16 1.3556 - 1.3267 0.99 2625 137 0.2792 0.3020 REMARK 3 17 1.3267 - 1.3000 0.99 2632 140 0.3109 0.3741 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.10 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 : 0.009 1454 REMARK 3 ANGLE : 1.096 1977 REMARK 3 CHIRALITY : 0.067 239 REMARK 3 PLANARITY : 0.004 263 REMARK 3 DIHEDRAL : 12.409 593 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 5CWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-14 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 : 47853 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 20.20 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 17.00 REMARK 200 R MERGE FOR SHELL (I) : 2.50500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.490 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 (%): 50.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM NITRATE, 20% (W/V) PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 45.11500 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 45.11500 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 20.48000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.19500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.48000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.19500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 45.11500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.48000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.19500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 45.11500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.48000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.19500 REMARK 290 SMTRY3 8 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 MET A 1 REMARK 465 THR A 161 REMARK 465 ASP A 162 REMARK 465 GLY A 163 REMARK 465 TRP A 164 REMARK 465 LEU A 165 REMARK 465 GLU 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 465 HIS A 172 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 506 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 507 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH A 508 DISTANCE = 8.04 ANGSTROMS REMARK 525 HOH A 509 DISTANCE = 8.77 ANGSTROMS 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 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: 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: 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 5CWH A 1 172 PDB 5CWH 5CWH 1 172 SEQRES 1 A 172 MET ASP SER GLU GLU VAL ASN GLU ARG VAL LYS GLN LEU SEQRES 2 A 172 ALA GLU LYS ALA LYS GLU ALA THR ASP LYS GLU GLU VAL SEQRES 3 A 172 ILE GLU ILE VAL LYS GLU LEU ALA GLU LEU ALA LYS GLN SEQRES 4 A 172 SER THR ASP SER GLU LEU VAL ASN GLU ILE VAL LYS GLN SEQRES 5 A 172 LEU ALA GLU VAL ALA LYS GLU ALA THR ASP LYS GLU LEU SEQRES 6 A 172 VAL ILE TYR ILE VAL LYS ILE LEU ALA GLU LEU ALA LYS SEQRES 7 A 172 GLN SER THR ASP SER GLU LEU VAL ASN GLU ILE VAL LYS SEQRES 8 A 172 GLN LEU ALA GLU VAL ALA LYS GLU ALA THR ASP LYS GLU SEQRES 9 A 172 LEU VAL ILE TYR ILE VAL LYS ILE LEU ALA GLU LEU ALA SEQRES 10 A 172 LYS GLN SER THR ASP SER GLU LEU VAL ASN GLU ILE VAL SEQRES 11 A 172 LYS GLN LEU GLU GLU VAL ALA LYS GLU ALA THR ASP LYS SEQRES 12 A 172 GLU LEU VAL GLU HIS ILE GLU LYS ILE LEU GLU GLU LEU SEQRES 13 A 172 LYS LYS GLN SER THR ASP GLY TRP LEU GLU HIS HIS HIS SEQRES 14 A 172 HIS HIS HIS HET EDO A 201 10 HET EDO A 202 10 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 2(C2 H6 O2) FORMUL 4 HOH *209(H2 O) HELIX 1 AA1 ASP A 2 ALA A 20 1 19 HELIX 2 AA2 ASP A 22 SER A 40 1 19 HELIX 3 AA3 ASP A 42 ALA A 60 1 19 HELIX 4 AA4 ASP A 62 SER A 80 1 19 HELIX 5 AA5 ASP A 82 ALA A 100 1 19 HELIX 6 AA6 ASP A 102 GLN A 119 1 18 HELIX 7 AA7 ASP A 122 ALA A 140 1 19 HELIX 8 AA8 ASP A 142 SER A 160 1 19 SITE 1 AC1 7 LYS A 78 THR A 101 TYR A 108 LYS A 111 SITE 2 AC1 7 GLU A 115 HOH A 316 HOH A 329 SITE 1 AC2 8 SER A 83 ASN A 87 ASP A 122 GLU A 124 SITE 2 AC2 8 LEU A 125 HOH A 310 HOH A 335 HOH A 349 CRYST1 40.960 104.390 90.230 90.00 90.00 90.00 C 2 2 21 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 0.024414 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009579 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011083 0.00000