HEADER DE NOVO PROTEIN 28-JUL-15 5CWO TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED HELICAL REPEAT PROTEIN DHR76 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED HELICAL REPEAT PROTEIN; COMPND 3 CHAIN: A, B; 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 5CWO 1 JRNL REMARK REVDAT 3 06-JAN-16 5CWO 1 JRNL REVDAT 2 30-DEC-15 5CWO 1 JRNL REVDAT 1 16-DEC-15 5CWO 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. 3.35 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) : 3.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 6484 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.269 REMARK 3 R VALUE (WORKING SET) : 0.268 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 322 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 45.4978 - 4.2204 1.00 3152 166 0.2422 0.2515 REMARK 3 2 4.2204 - 3.3500 1.00 3010 156 0.3307 0.3861 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 111.5 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 120.8 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 : 0.006 3502 REMARK 3 ANGLE : 0.939 4700 REMARK 3 CHIRALITY : 0.039 532 REMARK 3 PLANARITY : 0.005 630 REMARK 3 DIHEDRAL : 10.764 1406 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 5CWO 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_1000212158. 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 : NULL 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 : 6514 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.350 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 : 7.000 REMARK 200 R MERGE (I) : 0.18300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 1.91300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.170 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 (%): 38.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 5.0, 5% (W/V) PEG 6000, 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 31.27000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.11000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.11000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.27000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.15000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 ASN A 2 REMARK 465 GLY A 222 REMARK 465 TRP A 223 REMARK 465 LEU A 224 REMARK 465 GLU A 225 REMARK 465 HIS A 226 REMARK 465 HIS A 227 REMARK 465 HIS A 228 REMARK 465 HIS A 229 REMARK 465 HIS A 230 REMARK 465 HIS A 231 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 GLY B 222 REMARK 465 TRP B 223 REMARK 465 LEU B 224 REMARK 465 GLU B 225 REMARK 465 HIS B 226 REMARK 465 HIS B 227 REMARK 465 HIS B 228 REMARK 465 HIS B 229 REMARK 465 HIS B 230 REMARK 465 HIS B 231 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 62 NH2 ARG B 66 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 213 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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: 5CWN RELATED DB: PDB REMARK 900 RELATED ID: 5CWP RELATED DB: PDB REMARK 900 RELATED ID: 5CWQ RELATED DB: PDB DBREF 5CWO A 1 231 PDB 5CWO 5CWO 1 231 DBREF 5CWO B 1 231 PDB 5CWO 5CWO 1 231 SEQRES 1 A 231 MET ASN PRO GLU LEU GLU GLU TRP ILE ARG ARG ALA LYS SEQRES 2 A 231 GLU VAL ALA LYS GLU VAL GLU LYS VAL ALA GLN ARG ALA SEQRES 3 A 231 GLU GLU GLU GLY ASN PRO ASP LEU ARG ASP SER ALA LYS SEQRES 4 A 231 GLU LEU ARG ARG ALA VAL GLU GLU ALA ILE GLU GLU ALA SEQRES 5 A 231 LYS LYS GLN GLY ASN PRO GLU LEU VAL GLU TRP VAL ALA SEQRES 6 A 231 ARG ALA ALA LYS VAL ALA ALA GLU VAL ILE LYS VAL ALA SEQRES 7 A 231 ILE GLN ALA GLU LYS GLU GLY ASN ARG ASP LEU PHE ARG SEQRES 8 A 231 ALA ALA LEU GLU LEU VAL ARG ALA VAL ILE GLU ALA ILE SEQRES 9 A 231 GLU GLU ALA VAL LYS GLN GLY ASN PRO GLU LEU VAL GLU SEQRES 10 A 231 TRP VAL ALA ARG ALA ALA LYS VAL ALA ALA GLU VAL ILE SEQRES 11 A 231 LYS VAL ALA ILE GLN ALA GLU LYS GLU GLY ASN ARG ASP SEQRES 12 A 231 LEU PHE ARG ALA ALA LEU GLU LEU VAL ARG ALA VAL ILE SEQRES 13 A 231 GLU ALA ILE GLU GLU ALA VAL LYS GLN GLY ASN PRO GLU SEQRES 14 A 231 LEU VAL GLU ARG VAL ALA ARG LEU ALA LYS LYS ALA ALA SEQRES 15 A 231 GLU LEU ILE LYS ARG ALA ILE ARG ALA GLU LYS GLU GLY SEQRES 16 A 231 ASN ARG ASP GLU ARG ARG GLU ALA LEU GLU ARG VAL ARG SEQRES 17 A 231 GLU VAL ILE GLU ARG ILE GLU GLU LEU VAL ARG GLN GLY SEQRES 18 A 231 GLY TRP LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 231 MET ASN PRO GLU LEU GLU GLU TRP ILE ARG ARG ALA LYS SEQRES 2 B 231 GLU VAL ALA LYS GLU VAL GLU LYS VAL ALA GLN ARG ALA SEQRES 3 B 231 GLU GLU GLU GLY ASN PRO ASP LEU ARG ASP SER ALA LYS SEQRES 4 B 231 GLU LEU ARG ARG ALA VAL GLU GLU ALA ILE GLU GLU ALA SEQRES 5 B 231 LYS LYS GLN GLY ASN PRO GLU LEU VAL GLU TRP VAL ALA SEQRES 6 B 231 ARG ALA ALA LYS VAL ALA ALA GLU VAL ILE LYS VAL ALA SEQRES 7 B 231 ILE GLN ALA GLU LYS GLU GLY ASN ARG ASP LEU PHE ARG SEQRES 8 B 231 ALA ALA LEU GLU LEU VAL ARG ALA VAL ILE GLU ALA ILE SEQRES 9 B 231 GLU GLU ALA VAL LYS GLN GLY ASN PRO GLU LEU VAL GLU SEQRES 10 B 231 TRP VAL ALA ARG ALA ALA LYS VAL ALA ALA GLU VAL ILE SEQRES 11 B 231 LYS VAL ALA ILE GLN ALA GLU LYS GLU GLY ASN ARG ASP SEQRES 12 B 231 LEU PHE ARG ALA ALA LEU GLU LEU VAL ARG ALA VAL ILE SEQRES 13 B 231 GLU ALA ILE GLU GLU ALA VAL LYS GLN GLY ASN PRO GLU SEQRES 14 B 231 LEU VAL GLU ARG VAL ALA ARG LEU ALA LYS LYS ALA ALA SEQRES 15 B 231 GLU LEU ILE LYS ARG ALA ILE ARG ALA GLU LYS GLU GLY SEQRES 16 B 231 ASN ARG ASP GLU ARG ARG GLU ALA LEU GLU ARG VAL ARG SEQRES 17 B 231 GLU VAL ILE GLU ARG ILE GLU GLU LEU VAL ARG GLN GLY SEQRES 18 B 231 GLY TRP LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 AA1 PRO A 3 GLU A 29 1 27 HELIX 2 AA2 ASN A 31 GLY A 56 1 26 HELIX 3 AA3 ASN A 57 GLU A 84 1 28 HELIX 4 AA4 ASN A 86 GLY A 111 1 26 HELIX 5 AA5 ASN A 112 GLY A 140 1 29 HELIX 6 AA6 ASN A 141 GLY A 166 1 26 HELIX 7 AA7 ASN A 167 GLU A 194 1 28 HELIX 8 AA8 ASN A 196 GLY A 221 1 26 HELIX 9 AA9 GLU B 4 GLU B 29 1 26 HELIX 10 AB1 ASN B 31 GLY B 56 1 26 HELIX 11 AB2 ASN B 57 GLU B 84 1 28 HELIX 12 AB3 ASN B 86 GLY B 111 1 26 HELIX 13 AB4 ASN B 112 GLU B 139 1 28 HELIX 14 AB5 ASN B 141 GLY B 166 1 26 HELIX 15 AB6 ASN B 167 GLU B 194 1 28 HELIX 16 AB7 ASN B 196 GLY B 221 1 26 CRYST1 62.540 66.300 102.220 90.00 90.00 90.00 P 21 21 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 0.015990 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009783 0.00000