HEADER DE NOVO PROTEIN 11-OCT-10 3P6I TITLE CRYSTAL STRUCTURE OF SYMFOIL-4T PERMUTATION #2: DE NOVO DESIGNED BETA- TITLE 2 TREFOIL 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 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CIRCULARLY PERMUTED SYNTHETIC SEQUENCE DERIVED FROM SOURCE 4 HUMAN ACIDIC FIBROBLAST GROWTH FACTOR WITH A SYMMETRIC SOURCE 5 DECONSTRUCTION METHOD. THE PROTEIN PRODUCED BY THIS SEQUENCE ADOPTS SOURCE 6 A BETA-TREFOIL ARCHITECTURE WITH SYMMETRIC PRIMARY STRUCTURE. KEYWDS BETA-TREFOIL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.BLABER,J.LEE REVDAT 2 21-FEB-24 3P6I 1 REMARK REVDAT 1 12-OCT-11 3P6I 0 JRNL AUTH M.BLABER,J.LEE JRNL TITL PERMUTATIONS STUDY OF DE NOVO DESIGNED SYMMETRIC JRNL TITL 2 BETA-TREFOIL ARCHITECTURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 4.480 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 25102 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1257 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 36.8118 - 2.7440 0.99 3024 158 0.1563 0.1633 REMARK 3 2 2.7440 - 2.1781 1.00 2912 155 0.1369 0.1621 REMARK 3 3 2.1781 - 1.9027 0.99 2890 149 0.1351 0.1670 REMARK 3 4 1.9027 - 1.7288 0.98 2831 152 0.1274 0.1799 REMARK 3 5 1.7288 - 1.6049 0.97 2777 146 0.1350 0.2148 REMARK 3 6 1.6049 - 1.5102 0.95 2729 146 0.1383 0.2254 REMARK 3 7 1.5102 - 1.4346 0.92 2607 140 0.1527 0.2460 REMARK 3 8 1.4346 - 1.3722 0.83 2386 121 0.1761 0.2269 REMARK 3 9 1.3722 - 1.3200 0.59 1689 90 0.2029 0.2436 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL 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) : -1.29650 REMARK 3 B22 (A**2) : 1.29140 REMARK 3 B33 (A**2) : NULL 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 : 0.005 1063 REMARK 3 ANGLE : 0.966 1456 REMARK 3 CHIRALITY : 0.059 164 REMARK 3 PLANARITY : 0.004 197 REMARK 3 DIHEDRAL : 13.213 418 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 3P6I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000062017. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07500 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 : 25102 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 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 (%) : 91.8 REMARK 200 DATA REDUNDANCY : 35.80 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 106.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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 (%): 31.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M AMMONIUM SULFATE, 0.2M LI2SO4, REMARK 280 0.1M TRIS, 17MG/ML PROTEIN CONCENTRATION, PH 7.0, VAPOR REMARK 280 DIFFUSION, 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 25.45050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.62900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.26950 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.45050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.62900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.26950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.45050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.62900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.26950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.45050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 26.62900 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.26950 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 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 228 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: 3O4B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SYMFOIL-4T: DE NOVO DESIGNED BETA-TREFOIL REMARK 900 ARCHITECTURE WITH SYMMETRIC PRIMARY STRUCTURE REMARK 900 RELATED ID: 3P6J RELATED DB: PDB DBREF 3P6I A -5 227 PDB 3P6I 3P6I -5 227 SEQRES 1 A 142 HIS HIS HIS HIS HIS HIS PHE ASN LEU PRO PRO GLY ASN SEQRES 2 A 142 TYR LYS LYS GLY GLY THR VAL ASP GLY THR ARG ASP ARG SEQRES 3 A 142 SER ASP THR HIS ILE GLN PHE GLN ILE SER PRO GLU GLY SEQRES 4 A 142 ASN GLY GLU VAL LEU LEU LYS SER THR GLU THR GLY GLN SEQRES 5 A 142 TYR LEU ARG ILE ASN PRO ASP GLY THR VAL ASP GLY THR SEQRES 6 A 142 ARG ASP ARG SER ASP THR HIS ILE GLN PHE GLN ILE SER SEQRES 7 A 142 PRO GLU GLY ASN GLY GLU VAL LEU LEU LYS SER THR GLU SEQRES 8 A 142 THR GLY GLN TYR LEU ARG ILE ASN PRO ASP GLY THR VAL SEQRES 9 A 142 ASP GLY THR ARG ASP ARG SER ASP THR HIS ILE GLN PHE SEQRES 10 A 142 GLN ILE SER PRO GLU GLY ASN GLY GLU VAL LEU LEU LYS SEQRES 11 A 142 SER THR GLU THR GLY GLN TYR LEU ARG ILE ASN PRO HET TRS A 200 8 HET SO4 A 228 10 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM SO4 SULFATE ION HETSYN TRS TRIS BUFFER FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *151(H2 O) HELIX 1 1 ASP A 39 ILE A 42 5 4 SHEET 1 A 4 VAL A 31 THR A 34 0 SHEET 2 A 4 GLN A 221 ILE A 225 -1 O TYR A 222 N THR A 34 SHEET 3 A 4 VAL A 212 SER A 216 -1 N SER A 216 O GLN A 221 SHEET 4 A 4 PHE A 132 PRO A 136 -1 N SER A 135 O LEU A 213 SHEET 1 B 2 PHE A 44 GLU A 49 0 SHEET 2 B 2 GLU A 53 SER A 58 -1 O LYS A 57 N GLN A 45 SHEET 1 C 2 TYR A 64 ILE A 67 0 SHEET 2 C 2 VAL A 73 THR A 76 -1 O THR A 76 N TYR A 64 SHEET 1 D 2 PHE A 85 GLY A 91 0 SHEET 2 D 2 GLU A 94 SER A 99 -1 O GLU A 94 N GLU A 90 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 320 SITE 3 AC1 10 HOH A 352 HOH A 353 SITE 1 AC2 6 ARG A 110 THR A 123 ASP A 124 HOH A 146 SITE 2 AC2 6 HOH A 251 HOH A 266 CRYST1 50.901 53.258 84.539 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 0.019646 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018777 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011829 0.00000