HEADER DE NOVO PROTEIN 26-JUL-10 3O4B TITLE CRYSTAL STRUCTURE OF SYMFOIL-4T: 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 3O4B 1 REMARK REVDAT 3 22-JUN-11 3O4B 1 SOURCE REVDAT 2 19-JAN-11 3O4B 1 JRNL REVDAT 1 22-DEC-10 3O4B 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.140 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 10761 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1080 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 36.7570 - 3.5965 0.99 1310 150 0.1623 0.1990 REMARK 3 2 3.5965 - 2.8550 1.00 1252 144 0.1791 0.1909 REMARK 3 3 2.8550 - 2.4942 0.99 1235 138 0.1959 0.2450 REMARK 3 4 2.4942 - 2.2662 0.99 1218 135 0.1768 0.2433 REMARK 3 5 2.2662 - 2.1037 0.97 1186 132 0.1686 0.2126 REMARK 3 6 2.1037 - 1.9797 0.98 1205 129 0.1709 0.2500 REMARK 3 7 1.9797 - 1.8806 0.95 1152 132 0.1856 0.2140 REMARK 3 8 1.8806 - 1.8000 0.92 1123 120 0.1995 0.2846 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 : 44.53 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 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) : 3.72140 REMARK 3 B22 (A**2) : -2.68680 REMARK 3 B33 (A**2) : -1.03460 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 : 0.007 1023 REMARK 3 ANGLE : 1.098 1397 REMARK 3 CHIRALITY : 0.073 155 REMARK 3 PLANARITY : 0.004 189 REMARK 3 DIHEDRAL : 14.738 393 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 3O4B 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_1000060647. 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 : 10761 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 67.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 9.80 REMARK 200 R MERGE FOR SHELL (I) : 0.37900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.10 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 (%): 32.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 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 25.27500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.76000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.47500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.27500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.76000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.47500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.27500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.76000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.47500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.27500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 26.76000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.47500 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 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 GLY A 138 REMARK 465 ASN A 139 REMARK 465 GLY A 140 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 ASN A 92 -162.77 61.40 REMARK 500 REMARK 500 REMARK: NULL 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 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: 3O4C RELATED DB: PDB REMARK 900 RELATED ID: 3O4D RELATED DB: PDB REMARK 900 RELATED ID: 3O4E RELATED DB: PDB DBREF 3O4B A -5 140 PDB 3O4B 3O4B -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 THR 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 THR 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 THR 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 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 CL 1- FORMUL 6 HOH *85(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 4 VAL A 12 SER A 16 0 SHEET 2 A 4 PHE A 132 PRO A 136 -1 O SER A 135 N LEU A 13 SHEET 3 A 4 GLU A 94 SER A 99 -1 N VAL A 95 O PHE A 132 SHEET 4 A 4 PHE A 85 PRO A 89 -1 N GLN A 86 O LYS A 98 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 TYR A 108 ILE A 111 0 SHEET 2 E 2 VAL A 117 THR A 123 -1 O THR A 123 N TYR A 108 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 148 SITE 3 AC1 10 HOH A 150 HOH A 151 SITE 1 AC2 3 ARG A 66 THR A 76 HOH A 217 SITE 1 AC3 6 ARG A 110 THR A 123 ASP A 124 HOH A 185 SITE 2 AC3 6 HOH A 196 HOH A 199 SITE 1 AC4 2 PRO A 113 ASP A 114 CRYST1 50.550 53.520 84.950 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 0.019782 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018685 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011772 0.00000