HEADER DE NOVO PROTEIN 25-AUG-10 3OL0 TITLE CRYSTAL STRUCTURE OF MONOFOIL-4P HOMO-TRIMER: DE NOVO DESIGNED MONOMER TITLE 2 TREFOIL-FOLD SUB-DOMAIN WHICH FORMS HOMO-TRIMER ASSEMBLY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED MONOMER TREFOIL-FOLD SUB-DOMAIN WHICH COMPND 3 FORMS HOMO-TRIMER ASSEMBLY; COMPND 4 CHAIN: A, B, C; 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, TREFOIL-FOLD, SYNTHETIC PROTEIN, FUNCTION-COMPETENT KEYWDS 2 ONLY, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LEE,M.BLABER REVDAT 4 21-FEB-24 3OL0 1 REMARK REVDAT 3 22-JUN-11 3OL0 1 SOURCE REVDAT 2 19-JAN-11 3OL0 1 JRNL REVDAT 1 22-DEC-10 3OL0 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. 1.48 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 4.480 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 27734 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1385 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 41.5335 - 3.1939 0.96 2886 158 0.1825 0.1985 REMARK 3 2 3.1939 - 2.5352 1.00 2857 144 0.1913 0.2115 REMARK 3 3 2.5352 - 2.2147 0.99 2810 149 0.1767 0.1908 REMARK 3 4 2.2147 - 2.0122 0.99 2795 145 0.1750 0.2146 REMARK 3 5 2.0122 - 1.8680 0.98 2754 137 0.1782 0.1962 REMARK 3 6 1.8680 - 1.7579 0.96 2668 151 0.1656 0.1837 REMARK 3 7 1.7579 - 1.6698 0.93 2582 138 0.1723 0.2132 REMARK 3 8 1.6698 - 1.5971 0.89 2479 127 0.1793 0.2351 REMARK 3 9 1.5971 - 1.5357 0.87 2389 121 0.1784 0.2224 REMARK 3 10 1.5357 - 1.4830 0.77 2129 115 0.1825 0.2380 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 : 0.38 REMARK 3 B_SOL : 37.18 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 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) : 3.31290 REMARK 3 B22 (A**2) : -3.30530 REMARK 3 B33 (A**2) : -0.00760 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 1130 REMARK 3 ANGLE : 1.069 1558 REMARK 3 CHIRALITY : 0.072 169 REMARK 3 PLANARITY : 0.005 208 REMARK 3 DIHEDRAL : 14.010 450 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 3OL0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000061248. 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 : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 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 : 29337 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 19.40 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 82.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 16.60 REMARK 200 R MERGE FOR SHELL (I) : 0.35800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.380 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 (%): 53.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 0.1M NA CITRATE, REMARK 280 15MG/ML PROTEIN CONCENTRATION, PH 5.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K 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 24.76000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.93400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.73900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.93400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.76000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.73900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 ASN A 51 REMARK 465 GLY A 52 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 ASN B 51 REMARK 465 GLY B 52 REMARK 465 HIS C -5 REMARK 465 HIS C -4 REMARK 465 HIS C -3 REMARK 465 HIS C -2 REMARK 465 HIS C -1 REMARK 465 ASN C 51 REMARK 465 GLY C 52 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JQZ RELATED DB: PDB REMARK 900 HUMAN ACIDIC FIBROBLAST GROWTH FACTOR-1 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: 3O4C RELATED DB: PDB REMARK 900 RELATED ID: 3O4D RELATED DB: PDB REMARK 900 RELATED ID: 3OGF RELATED DB: PDB REMARK 900 RELATED ID: 3OL0 RELATED DB: PDB DBREF 3OL0 A -5 52 PDB 3OL0 3OL0 -5 52 DBREF 3OL0 B -5 52 PDB 3OL0 3OL0 -5 52 DBREF 3OL0 C -5 52 PDB 3OL0 3OL0 -5 52 SEQRES 1 A 48 HIS HIS HIS HIS HIS HIS PRO VAL LEU LEU LYS SER THR SEQRES 2 A 48 GLU THR GLY GLN TYR LEU ARG ILE ASN PRO ASP GLY THR SEQRES 3 A 48 VAL ASP GLY THR ARG ASP ARG SER ASP PRO HIS ILE GLN SEQRES 4 A 48 PHE GLN ILE SER PRO GLU GLY ASN GLY SEQRES 1 B 48 HIS HIS HIS HIS HIS HIS PRO VAL LEU LEU LYS SER THR SEQRES 2 B 48 GLU THR GLY GLN TYR LEU ARG ILE ASN PRO ASP GLY THR SEQRES 3 B 48 VAL ASP GLY THR ARG ASP ARG SER ASP PRO HIS ILE GLN SEQRES 4 B 48 PHE GLN ILE SER PRO GLU GLY ASN GLY SEQRES 1 C 48 HIS HIS HIS HIS HIS HIS PRO VAL LEU LEU LYS SER THR SEQRES 2 C 48 GLU THR GLY GLN TYR LEU ARG ILE ASN PRO ASP GLY THR SEQRES 3 C 48 VAL ASP GLY THR ARG ASP ARG SER ASP PRO HIS ILE GLN SEQRES 4 C 48 PHE GLN ILE SER PRO GLU GLY ASN GLY HET SO4 A 3 5 HET SO4 A 5 5 HET SO4 B 2 5 HET SO4 C 1 5 HET SO4 C 4 5 HETNAM SO4 SULFATE ION FORMUL 4 SO4 5(O4 S 2-) FORMUL 9 HOH *203(H2 O) HELIX 1 1 ASP A 39 ILE A 42 5 4 HELIX 2 2 ASP B 39 ILE B 42 5 4 HELIX 3 3 ASP C 39 ILE C 42 5 4 SHEET 1 A 2 VAL A 12 SER A 16 0 SHEET 2 A 2 PHE C 44 PRO C 48 -1 O SER C 47 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 PRO A 48 0 SHEET 2 C 2 VAL B 12 SER B 16 -1 O LYS B 15 N GLN A 45 SHEET 1 D 2 TYR B 22 ILE B 25 0 SHEET 2 D 2 VAL B 31 THR B 34 -1 O THR B 34 N TYR B 22 SHEET 1 E 2 PHE B 44 PRO B 48 0 SHEET 2 E 2 VAL C 12 SER C 16 -1 O LEU C 13 N SER B 47 SHEET 1 F 2 TYR C 22 ILE C 25 0 SHEET 2 F 2 VAL C 31 THR C 34 -1 O THR C 34 N TYR C 22 SITE 1 AC1 5 LYS A 15 TYR A 22 ARG A 37 HOH A 62 SITE 2 AC1 5 SER C 47 SITE 1 AC2 5 ARG A 24 THR A 34 HOH A 59 HOH A 100 SITE 2 AC2 5 HOH A 169 SITE 1 AC3 5 ARG B 24 THR B 34 HOH B 65 HOH B 136 SITE 2 AC3 5 HOH B 162 SITE 1 AC4 5 ARG C 24 THR C 34 HOH C 61 HOH C 73 SITE 2 AC4 5 HOH C 158 SITE 1 AC5 6 ARG B 35 HOH B 65 LYS C 15 ARG C 35 SITE 2 AC5 6 HOH C 176 HOH C 181 CRYST1 49.520 53.478 65.868 90.00 90.00 90.00 P 21 21 21 12 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 0.020194 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018699 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015182 0.00000