HEADER DE NOVO PROTEIN 28-JUL-15 5CWG TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED HELICAL REPEAT PROTEIN DHR10 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 5CWG 1 JRNL REMARK REVDAT 3 06-JAN-16 5CWG 1 JRNL REVDAT 2 30-DEC-15 5CWG 1 JRNL REVDAT 1 16-DEC-15 5CWG 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. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 54544 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2730 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 41.4830 - 3.2566 0.96 2726 145 0.1777 0.2031 REMARK 3 2 3.2566 - 2.5849 1.00 2693 143 0.1348 0.1655 REMARK 3 3 2.5849 - 2.2582 1.00 2675 135 0.1160 0.1376 REMARK 3 4 2.2582 - 2.0517 1.00 2640 149 0.1072 0.1348 REMARK 3 5 2.0517 - 1.9047 1.00 2641 142 0.1062 0.1358 REMARK 3 6 1.9047 - 1.7924 1.00 2628 143 0.1063 0.1484 REMARK 3 7 1.7924 - 1.7026 1.00 2624 127 0.1015 0.1202 REMARK 3 8 1.7026 - 1.6285 1.00 2622 148 0.0994 0.1495 REMARK 3 9 1.6285 - 1.5658 1.00 2630 129 0.0951 0.1400 REMARK 3 10 1.5658 - 1.5118 1.00 2597 145 0.0940 0.1288 REMARK 3 11 1.5118 - 1.4645 1.00 2619 131 0.1007 0.1470 REMARK 3 12 1.4645 - 1.4226 1.00 2591 138 0.1171 0.1822 REMARK 3 13 1.4226 - 1.3852 1.00 2609 144 0.1309 0.1772 REMARK 3 14 1.3852 - 1.3514 1.00 2606 129 0.1434 0.1841 REMARK 3 15 1.3514 - 1.3207 1.00 2583 149 0.1434 0.2033 REMARK 3 16 1.3207 - 1.2926 1.00 2601 126 0.1560 0.1966 REMARK 3 17 1.2926 - 1.2667 1.00 2590 136 0.1750 0.2396 REMARK 3 18 1.2667 - 1.2428 0.97 2505 138 0.2180 0.2480 REMARK 3 19 1.2428 - 1.2206 0.94 2420 127 0.2448 0.2889 REMARK 3 20 1.2206 - 1.2000 0.85 2214 106 0.2822 0.3020 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.50 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.83 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 1961 REMARK 3 ANGLE : 1.108 2660 REMARK 3 CHIRALITY : 0.064 279 REMARK 3 PLANARITY : 0.005 380 REMARK 3 DIHEDRAL : 13.582 820 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 5CWG 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_1000212084. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-13 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 : 54627 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.52600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.850 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 (%): 33.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM FORMATE, 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: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 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 23.79500 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.21500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 23.79500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.21500 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 477 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 ARG A 197 REMARK 465 ARG A 198 REMARK 465 GLY A 199 REMARK 465 ASP A 200 REMARK 465 GLY A 201 REMARK 465 TRP A 202 REMARK 465 LEU A 203 REMARK 465 GLU A 204 REMARK 465 HIS A 205 REMARK 465 HIS A 206 REMARK 465 HIS A 207 REMARK 465 HIS A 208 REMARK 465 HIS A 209 REMARK 465 HIS A 210 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 196 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 51 49.98 -83.76 REMARK 500 REMARK 500 REMARK: NULL 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 627 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A 628 DISTANCE = 7.26 ANGSTROMS REMARK 525 HOH A 629 DISTANCE = 7.88 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 301 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: 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: 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 5CWG A 1 210 PDB 5CWG 5CWG 1 210 SEQRES 1 A 210 MET SER SER GLU LYS GLU GLU LEU ARG GLU ARG LEU VAL SEQRES 2 A 210 LYS ILE VAL VAL GLU ASN ALA LYS ARG LYS GLY ASP ASP SEQRES 3 A 210 THR GLU GLU ALA ARG GLU ALA ALA ARG GLU ALA PHE GLU SEQRES 4 A 210 LEU VAL ARG GLU ALA ALA GLU ARG ALA GLY ILE ASP SER SEQRES 5 A 210 SER GLU VAL LEU GLU LEU ALA ILE ARG LEU ILE LYS GLU SEQRES 6 A 210 VAL VAL GLU ASN ALA GLN ARG GLU GLY TYR ASP ILE SER SEQRES 7 A 210 GLU ALA ALA ARG ALA ALA ALA GLU ALA PHE LYS ARG VAL SEQRES 8 A 210 ALA GLU ALA ALA LYS ARG ALA GLY ILE THR SER SER GLU SEQRES 9 A 210 VAL LEU GLU LEU ALA ILE ARG LEU ILE LYS GLU VAL VAL SEQRES 10 A 210 GLU ASN ALA GLN ARG GLU GLY TYR ASP ILE SER GLU ALA SEQRES 11 A 210 ALA ARG ALA ALA ALA GLU ALA PHE LYS ARG VAL ALA GLU SEQRES 12 A 210 ALA ALA LYS ARG ALA GLY ILE THR SER SER GLU THR LEU SEQRES 13 A 210 LYS ARG ALA ILE GLU GLU ILE ARG LYS ARG VAL GLU GLU SEQRES 14 A 210 ALA GLN ARG GLU GLY ASN ASP ILE SER GLU ALA ALA ARG SEQRES 15 A 210 GLN ALA ALA GLU GLU PHE ARG LYS LYS ALA GLU GLU LEU SEQRES 16 A 210 LYS ARG ARG GLY ASP GLY TRP LEU GLU HIS HIS HIS HIS SEQRES 17 A 210 HIS HIS HET EDO A 301 10 HET UNL A 302 27 HETNAM EDO 1,2-ETHANEDIOL HETNAM UNL UNKNOWN LIGAND HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 4 HOH *229(H2 O) HELIX 1 AA1 SER A 2 GLY A 24 1 23 HELIX 2 AA2 ASP A 26 ALA A 48 1 23 HELIX 3 AA3 SER A 52 GLY A 74 1 23 HELIX 4 AA4 ASP A 76 GLY A 99 1 24 HELIX 5 AA5 SER A 102 GLY A 124 1 23 HELIX 6 AA6 ASP A 126 GLY A 149 1 24 HELIX 7 AA7 SER A 152 GLY A 174 1 23 HELIX 8 AA8 ASP A 176 LYS A 196 1 21 SITE 1 AC1 4 GLU A 36 ARG A 82 SER A 153 HOH A 458 CRYST1 47.590 50.560 72.430 90.00 90.00 90.00 P 21 2 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 0.021013 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019778 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013806 0.00000