PDB Short entry for 3O4D HEADER DE NOVO PROTEIN 26-JUL-10 3O4D TITLE CRYSTAL STRUCTURE OF SYMFOIL-4P: 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 3O4D 1 REMARK REVDAT 3 22-JUN-11 3O4D 1 SOURCE REVDAT 2 19-JAN-11 3O4D 1 JRNL REVDAT 1 22-DEC-10 3O4D 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. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.140 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 13224 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 667 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 42.4040 - 2.8160 0.99 2770 150 0.1780 0.1973 REMARK 3 2 2.8160 - 2.2352 0.99 2650 142 0.1915 0.2443 REMARK 3 3 2.2352 - 1.9526 0.97 2599 136 0.1912 0.2372 REMARK 3 4 1.9526 - 1.7741 0.94 2507 127 0.2110 0.2606 REMARK 3 5 1.7741 - 1.6500 0.78 2031 112 0.2296 0.3205 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 : 46.96 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) : 8.23350 REMARK 3 B22 (A**2) : -5.59880 REMARK 3 B33 (A**2) : -2.63470 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 1035 REMARK 3 ANGLE : 1.124 1415 REMARK 3 CHIRALITY : 0.074 154 REMARK 3 PLANARITY : 0.004 193 REMARK 3 DIHEDRAL : 15.437 405 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 3O4D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060649. 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) : 0.97950 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 : 13224 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 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 (%) : 97.6 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 59.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.33300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.500 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 (%): 31.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 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 25.18600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.57550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.39000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.18600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.57550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.39000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.18600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 26.57550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.39000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.18600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 26.57550 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.39000 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 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: 3O4B RELATED DB: PDB REMARK 900 RELATED ID: 3O4C RELATED DB: PDB REMARK 900 RELATED ID: 3O4E RELATED DB: PDB DBREF 3O4D A -5 140 PDB 3O4D 3O4D -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 PRO 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 PRO 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 PRO 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 *93(H2 O) HELIX 1 1 ASP A 39 ILE A 42 5 4 HELIX 2 2 ASP A 80 ILE A 83 5 4 HELIX 3 3 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 -3.37 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 149 SITE 3 AC1 10 HOH A 150 HOH A 153 SITE 1 AC2 4 ARG A 110 THR A 123 HOH A 184 HOH A 211 SITE 1 AC3 3 ARG A 66 THR A 76 HOH A 228 SITE 1 AC4 2 PRO A 113 ASP A 114 CRYST1 50.372 53.151 84.780 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 0.019852 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018814 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011795 0.00000