HEADER DE NOVO PROTEIN 05-JAN-11 3Q7X TITLE CRYSTAL STRUCTURE OF SYMFOIL-4P/PV1: DE NOVO DESIGNED BETA-TREFOIL TITLE 2 ARCHITECTURE WITH SYMMETRIC PRIMARY STRUCTURE, PRIMITIVE VERSION 1 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: SYNTHETIC SEQUENCE DERIVED FROM HUMAN ACIDIC SOURCE 4 FIBROBLAST GROWTH FACTOR WITH A SYMMETRIC DECONSTRUCTION METHOD. THE SOURCE 5 PROTEIN PRODUCED BY THIS SEQUENCE ADOPTS A BETA-TREFOIL ARCHITECTURE SOURCE 6 WITH SYMMETRIC PRIMARY STRUCTURE. KEYWDS BETA-TREFOIL, BETA-TERFOIL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.BLABER,J.LEE REVDAT 4 20-FEB-13 3Q7X 1 JRNL REVDAT 3 06-FEB-13 3Q7X 1 JRNL REVDAT 2 23-JAN-13 3Q7X 1 JRNL REVDAT 1 11-JAN-12 3Q7X 0 JRNL AUTH L.M.LONGO,J.LEE,M.BLABER JRNL TITL SIMPLIFIED PROTEIN DESIGN BIASED FOR PREBIOTIC AMINO ACIDS JRNL TITL 2 YIELDS A FOLDABLE, HALOPHILIC PROTEIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 2135 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23341608 JRNL DOI 10.1073/PNAS.1219530110 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 4.520 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 28966 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1437 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 30.1704 - 3.0164 0.99 3099 169 0.1727 0.1717 REMARK 3 2 3.0164 - 2.3945 1.00 2979 157 0.1962 0.2380 REMARK 3 3 2.3945 - 2.0919 0.99 2941 157 0.1734 0.1962 REMARK 3 4 2.0919 - 1.9007 0.99 2911 156 0.1886 0.2177 REMARK 3 5 1.9007 - 1.7645 0.97 2847 150 0.1867 0.2107 REMARK 3 6 1.7645 - 1.6605 0.95 2786 144 0.1819 0.2345 REMARK 3 7 1.6605 - 1.5773 0.93 2688 135 0.1816 0.2107 REMARK 3 8 1.5773 - 1.5086 0.89 2576 140 0.1867 0.2199 REMARK 3 9 1.5086 - 1.4506 0.85 2477 127 0.1867 0.2505 REMARK 3 10 1.4506 - 1.4000 0.77 2225 102 0.1950 0.2117 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.49 REMARK 3 K_SOL : 0.43 REMARK 3 B_SOL : 55.41 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) : 12.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.67460 REMARK 3 B22 (A**2) : -0.30600 REMARK 3 B33 (A**2) : -0.36860 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 1069 REMARK 3 ANGLE : 1.095 1464 REMARK 3 CHIRALITY : 0.069 158 REMARK 3 PLANARITY : 0.005 206 REMARK 3 DIHEDRAL : 13.728 441 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 3Q7X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-11. REMARK 100 THE RCSB ID CODE IS RCSB063306. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-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 : 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) : 0.9795 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 : 28966 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 (%) : 93.4 REMARK 200 DATA REDUNDANCY : 12.800 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 65.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.90 REMARK 200 R MERGE FOR SHELL (I) : 0.30100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.000 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 (%): 53.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M AMMONIUM SULFATE, 0.1M LITHIUM REMARK 280 SULFATE, 0.1M TRIS, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 23.36250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.79950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.33300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.79950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.36250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.33300 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 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 SO4 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 141 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 REMARK 900 WITH AMINO TERMINAL HIS TAG REMARK 900 RELATED ID: 3O4D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SYMFOIL-4P: DE NOVO DESIGNED BETA- REMARK 900 TREFOIL ARCHITECTURE WITH SYMMETRIC PRIMARY STRUCTURE REMARK 900 RELATED ID: 3Q7W RELATED DB: PDB REMARK 900 RELATED ID: 3Q7Y RELATED DB: PDB DBREF 3Q7X A -5 140 PDB 3Q7X 3Q7X -5 140 SEQRES 1 A 132 HIS HIS HIS HIS HIS HIS GLU VAL LEU LEU ARG SER THR SEQRES 2 A 132 GLU THR GLY GLN PHE LEU ARG ILE ASN PRO ASP GLY THR SEQRES 3 A 132 VAL ASP GLY THR ARG ASP ARG SER ASP PRO GLY ILE GLN SEQRES 4 A 132 PHE GLN ILE SER PRO GLU GLY ASN GLY GLU VAL LEU LEU SEQRES 5 A 132 ARG SER THR GLU THR GLY GLN PHE LEU ARG ILE ASN PRO SEQRES 6 A 132 ASP GLY THR VAL ASP GLY THR ARG ASP ARG SER ASP PRO SEQRES 7 A 132 GLY ILE GLN PHE GLN ILE SER PRO GLU GLY ASN GLY GLU SEQRES 8 A 132 VAL LEU LEU ARG SER THR GLU THR GLY GLN PHE LEU ARG SEQRES 9 A 132 ILE ASN PRO ASP GLY THR VAL ASP GLY THR ARG ASP ARG SEQRES 10 A 132 SER ASP PRO GLY ILE GLN PHE GLN ILE SER PRO GLU GLY SEQRES 11 A 132 ASN GLY HET SO4 A 1 5 HET TRS A 141 8 HETNAM SO4 SULFATE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 SO4 O4 S 2- FORMUL 3 TRS C4 H12 N O3 1+ FORMUL 4 HOH *217(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 4 VAL A 12 SER A 16 0 SHEET 2 A 4 PHE A 132 PRO A 136 -1 O GLN A 133 N ARG A 15 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 GLY A 91 -1 N GLU A 90 O GLU A 94 SHEET 1 B 2 PHE A 22 ILE A 25 0 SHEET 2 B 2 VAL A 31 THR A 34 -1 O THR A 34 N PHE A 22 SHEET 1 C 2 PHE A 44 GLY A 50 0 SHEET 2 C 2 GLU A 53 SER A 58 -1 O GLU A 53 N GLU A 49 SHEET 1 D 2 PHE A 64 ILE A 67 0 SHEET 2 D 2 VAL A 73 THR A 76 -1 O THR A 76 N PHE A 64 SHEET 1 E 2 PHE A 108 ILE A 111 0 SHEET 2 E 2 VAL A 117 THR A 123 -1 O THR A 123 N PHE A 108 SITE 1 AC1 9 THR A 76 ARG A 76A ASP A 77 THR A 123 SITE 2 AC1 9 ARG A 123A ASP A 124 HOH A 223 HOH A 284 SITE 3 AC1 9 HOH A 321 SITE 1 AC2 9 THR A 30 VAL A 31 THR A 72 VAL A 73 SITE 2 AC2 9 THR A 116 VAL A 117 HOH A 195 HOH A 230 SITE 3 AC2 9 HOH A 240 CRYST1 46.725 48.666 67.599 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 0.021402 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020548 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014793 0.00000 MASTER 233 0 2 3 12 0 6 6 0 0 0 11 END