HEADER DE NOVO PROTEIN 26-JUL-10 3O4C TITLE CRYSTAL STRUCTURE OF SYMFOIL-4V: DE NOVO DESIGNED BETA-TREFOIL TITLE 2 ARCHITECTURE WITH SYMMETRIC PRIMARY STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED BETA-TREFOIL ARCHITECTURE WITH SYMMETRIC COMPND 3 PRIMARY STRUCTURE; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_COMMON: ARTIFICIAL GENE; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-TREFOIL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LEE,M.BLABER REVDAT 4 21-FEB-24 3O4C 1 REMARK REVDAT 3 22-JUN-11 3O4C 1 SOURCE REVDAT 2 19-JAN-11 3O4C 1 JRNL REVDAT 1 22-DEC-10 3O4C 0 JRNL AUTH J.LEE,M.BLABER JRNL TITL EXPERIMENTAL SUPPORT FOR THE EVOLUTION OF SYMMETRIC PROTEIN JRNL TITL 2 ARCHITECTURE FROM A SIMPLE PEPTIDE MOTIF. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 126 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21173271 JRNL DOI 10.1073/PNAS.1015032108 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.090 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 11700 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1163 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 45.5255 - 3.4964 0.94 1370 150 0.1787 0.1889 REMARK 3 2 3.4964 - 2.7753 0.97 1370 142 0.1866 0.2106 REMARK 3 3 2.7753 - 2.4245 0.97 1333 150 0.2151 0.2606 REMARK 3 4 2.4245 - 2.2029 0.98 1331 147 0.1942 0.2665 REMARK 3 5 2.2029 - 2.0450 0.98 1338 146 0.2024 0.2347 REMARK 3 6 2.0450 - 1.9244 0.97 1312 140 0.1979 0.2472 REMARK 3 7 1.9244 - 1.8280 0.95 1268 149 0.2091 0.2695 REMARK 3 8 1.8280 - 1.7500 0.90 1215 139 0.2122 0.2468 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 61.06 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.50350 REMARK 3 B22 (A**2) : -2.24910 REMARK 3 B33 (A**2) : -6.25440 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1028 REMARK 3 ANGLE : 1.049 1403 REMARK 3 CHIRALITY : 0.073 156 REMARK 3 PLANARITY : 0.004 189 REMARK 3 DIHEDRAL : 14.329 397 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 3O4C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060648. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97940 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11700 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 50.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.34500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 0.2M LI2SO4, 0.1M REMARK 280 TRIS, 15MG/ML PROTEIN CONCENTRATION, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 25.41800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.87300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.77500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.41800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.87300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.77500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.41800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.87300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.77500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.41800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 26.87300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.77500 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 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 PHE A 1 REMARK 465 ASN A 2 REMARK 465 LEU A 3 REMARK 465 PRO A 4 REMARK 465 PRO A 5 REMARK 465 GLY A 6 REMARK 465 ASN A 7 REMARK 465 TYR A 8 REMARK 465 LYS A 9 REMARK 465 LYS A 10 REMARK 465 ASN A 139 REMARK 465 GLY A 140 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 141 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 142 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 143 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 144 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JQZ RELATED DB: PDB REMARK 900 HUMAN ACIDIC FIBROBLAST GROWTH FACTOR. 141 AMINO ACID FORM WITH REMARK 900 AMINO TERMINAL HIS TAG REMARK 900 RELATED ID: 3O3Q RELATED DB: PDB REMARK 900 RELATED ID: 3O49 RELATED DB: PDB REMARK 900 RELATED ID: 3O4A RELATED DB: PDB REMARK 900 RELATED ID: 3O4B RELATED DB: PDB REMARK 900 RELATED ID: 3O4D RELATED DB: PDB REMARK 900 RELATED ID: 3O4E RELATED DB: PDB DBREF 3O4C A -5 140 PDB 3O4C 3O4C -5 140 SEQRES 1 A 142 HIS HIS HIS HIS HIS HIS PHE ASN LEU PRO PRO GLY ASN SEQRES 2 A 142 TYR LYS LYS PRO VAL LEU LEU LYS SER THR GLU THR GLY SEQRES 3 A 142 GLN TYR LEU ARG ILE ASN PRO ASP GLY THR VAL ASP GLY SEQRES 4 A 142 THR ARG ASP ARG SER ASP VAL HIS ILE GLN PHE GLN ILE SEQRES 5 A 142 SER PRO GLU GLY ASN GLY GLU VAL LEU LEU LYS SER THR SEQRES 6 A 142 GLU THR GLY GLN TYR LEU ARG ILE ASN PRO ASP GLY THR SEQRES 7 A 142 VAL ASP GLY THR ARG ASP ARG SER ASP VAL HIS ILE GLN SEQRES 8 A 142 PHE GLN ILE SER PRO GLU GLY ASN GLY GLU VAL LEU LEU SEQRES 9 A 142 LYS SER THR GLU THR GLY GLN TYR LEU ARG ILE ASN PRO SEQRES 10 A 142 ASP GLY THR VAL ASP GLY THR ARG ASP ARG SER ASP VAL SEQRES 11 A 142 HIS ILE GLN PHE GLN ILE SER PRO GLU GLY ASN GLY HET TRS A 200 8 HET SO4 A 141 5 HET SO4 A 142 5 HET CL A 143 1 HET CL A 144 1 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETSYN TRS TRIS BUFFER FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 CL 2(CL 1-) FORMUL 7 HOH *78(H2 O) HELIX 1 1 ASP A 39 ILE A 42 5 4 HELIX 2 2 ASP A 127 ILE A 130 5 4 SHEET 1 A 2 VAL A 12 SER A 16 0 SHEET 2 A 2 PHE A 132 PRO A 136 -1 O SER A 135 N LEU A 13 SHEET 1 B 2 TYR A 22 ILE A 25 0 SHEET 2 B 2 VAL A 31 THR A 34 -1 O THR A 34 N TYR A 22 SHEET 1 C 2 PHE A 44 GLU A 49 0 SHEET 2 C 2 GLU A 53 SER A 58 -1 O LYS A 57 N GLN A 45 SHEET 1 D 2 TYR A 64 ILE A 67 0 SHEET 2 D 2 VAL A 73 THR A 76 -1 O THR A 76 N TYR A 64 SHEET 1 E 2 PHE A 85 PRO A 89 0 SHEET 2 E 2 VAL A 95 SER A 99 -1 O LYS A 98 N GLN A 86 SHEET 1 F 2 TYR A 108 ILE A 111 0 SHEET 2 F 2 VAL A 117 THR A 123 -1 O THR A 123 N TYR A 108 CISPEP 1 GLY A 91 ASN A 92 0 0.13 SITE 1 AC1 10 THR A 30 VAL A 31 THR A 72 VAL A 73 SITE 2 AC1 10 ARG A 78 THR A 116 VAL A 117 HOH A 151 SITE 3 AC1 10 HOH A 153 HOH A 155 SITE 1 AC2 2 ARG A 66 THR A 76 SITE 1 AC3 4 ARG A 110 THR A 123 HOH A 187 HOH A 204 SITE 1 AC4 2 PRO A 113 ASP A 114 SITE 1 AC5 3 ASN A 26 PRO A 27 ASP A 28 CRYST1 50.836 53.746 85.550 90.00 90.00 90.00 I 2 2 2 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 0.019671 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018606 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011689 0.00000