HEADER DE NOVO PROTEIN 11-OCT-10 3P6J TITLE CRYSTAL STRUCTURE OF SYMFOIL-4T PERMUTATION #3: 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 3P6J 1 REMARK REVDAT 1 12-OCT-11 3P6J 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. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 4.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 33256 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1647 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 36.3879 - 2.9080 0.98 0 192 0.1664 0.1877 REMARK 3 2 2.9080 - 2.3083 0.99 0 180 0.1657 0.1741 REMARK 3 3 2.3083 - 2.0165 0.98 0 181 0.1460 0.1751 REMARK 3 4 2.0165 - 1.8321 0.96 0 181 0.1339 0.1436 REMARK 3 5 1.8321 - 1.7008 0.94 0 171 0.1200 0.1270 REMARK 3 6 1.7008 - 1.6005 0.90 0 165 0.1052 0.1297 REMARK 3 7 1.6005 - 1.5204 0.88 0 159 0.0997 0.1337 REMARK 3 8 1.5204 - 1.4542 0.82 0 152 0.1101 0.1548 REMARK 3 9 1.4542 - 1.3982 0.77 0 147 0.1237 0.1667 REMARK 3 10 1.3982 - 1.3500 0.69 0 119 0.1409 0.1617 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 41.11 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 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) : -0.08670 REMARK 3 B22 (A**2) : -1.17340 REMARK 3 B33 (A**2) : 1.26010 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 1111 REMARK 3 ANGLE : 1.109 1538 REMARK 3 CHIRALITY : 0.072 173 REMARK 3 PLANARITY : 0.006 215 REMARK 3 DIHEDRAL : 13.684 465 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 3P6J 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_1000062018. 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 : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : 33256 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 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 (%) : 91.9 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 61.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 11.80 REMARK 200 R MERGE FOR SHELL (I) : 0.37200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.300 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 (%): 52.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M SODIUM CITRATE, 0.1M SODIUM REMARK 280 CACODYLATE, 10MG/ML PROTEIN CONCENTRATION, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING 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 23.43000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.70600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.84900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.70600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.43000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.84900 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ASP A 236 REMARK 465 ARG A 237 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 51 23.16 48.37 REMARK 500 REMARK 500 REMARK: NULL 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: 3P6I RELATED DB: PDB DBREF 3P6J A -5 237 PDB 3P6J 3P6J -5 237 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 ASP THR HIS ILE GLN PHE GLN ILE SER SEQRES 3 A 142 PRO GLU GLY ASN GLY GLU VAL LEU LEU LYS SER THR GLU SEQRES 4 A 142 THR GLY GLN TYR LEU ARG ILE ASN PRO ASP GLY THR VAL SEQRES 5 A 142 ASP GLY THR ARG ASP ARG SER ASP THR HIS ILE GLN PHE SEQRES 6 A 142 GLN ILE SER PRO GLU GLY ASN GLY GLU VAL LEU LEU LYS SEQRES 7 A 142 SER THR GLU THR GLY GLN TYR LEU ARG ILE ASN PRO ASP SEQRES 8 A 142 GLY THR VAL ASP GLY THR ARG ASP ARG SER ASP THR HIS SEQRES 9 A 142 ILE GLN PHE GLN ILE SER PRO GLU GLY ASN GLY GLU VAL SEQRES 10 A 142 LEU LEU LYS SER THR GLU THR GLY GLN TYR LEU ARG ILE SEQRES 11 A 142 ASN PRO ASP GLY THR VAL ASP GLY THR ARG ASP ARG FORMUL 2 HOH *181(H2 O) HELIX 1 1 ASP A 80 ILE A 83 5 4 HELIX 2 2 ASP A 127 ILE A 130 5 4 SHEET 1 A 2 PHE A 44 PRO A 48 0 SHEET 2 A 2 VAL A 54 SER A 58 -1 O LYS A 57 N GLN A 45 SHEET 1 B 2 TYR A 64 ILE A 67 0 SHEET 2 B 2 VAL A 73 THR A 76 -1 O THR A 76 N TYR A 64 SHEET 1 C 4 PHE A 85 GLY A 91 0 SHEET 2 C 4 GLU A 94 SER A 99 -1 O GLU A 94 N GLU A 90 SHEET 3 C 4 GLN A 107 ILE A 111 -1 O GLN A 107 N SER A 99 SHEET 4 C 4 VAL A 117 THR A 123 -1 O THR A 123 N TYR A 108 SHEET 1 D 2 PHE A 132 PRO A 136 0 SHEET 2 D 2 VAL A 212 SER A 216 -1 O LEU A 213 N SER A 135 SHEET 1 E 2 TYR A 222 ILE A 225 0 SHEET 2 E 2 VAL A 231 THR A 234 -1 O THR A 234 N TYR A 222 CRYST1 46.860 57.698 61.412 90.00 90.00 90.00 P 21 21 21 4 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 0.021340 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017332 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016283 0.00000