HEADER DE NOVO PROTEIN 14-OCT-13 4N6T TITLE ADHIRON: A STABLE AND VERSATILE PEPTIDE DISPLAY SCAFFOLD - FULL LENGTH TITLE 2 ADHIRON COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADHIRON; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTIFICIAL GENE; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 GENE: PHYTOCYSTATIN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS PROTEIN SCAFFOLD, CONSENSUS PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.MCPHERSON,D.TOMLINSON,R.L.OWEN,J.E.NETTLESHIP,R.J.OWENS REVDAT 3 28-FEB-24 4N6T 1 REMARK REVDAT 2 14-MAY-14 4N6T 1 JRNL REVDAT 1 09-APR-14 4N6T 0 JRNL AUTH C.TIEDE,A.A.TANG,S.E.DEACON,U.MANDAL,J.E.NETTLESHIP, JRNL AUTH 2 R.L.OWEN,S.E.GEORGE,D.J.HARRISON,R.J.OWENS,D.C.TOMLINSON, JRNL AUTH 3 M.J.MCPHERSON JRNL TITL ADHIRON: A STABLE AND VERSATILE PEPTIDE DISPLAY SCAFFOLD FOR JRNL TITL 2 MOLECULAR RECOGNITION APPLICATIONS. JRNL REF PROTEIN ENG.DES.SEL. V. 27 145 2014 JRNL REFN ISSN 1741-0126 JRNL PMID 24668773 JRNL DOI 10.1093/PROTEIN/GZU007 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 15115 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 696 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 35.8627 - 2.9924 1.00 2966 115 0.1710 0.1829 REMARK 3 2 2.9924 - 2.3753 0.99 2940 161 0.2030 0.2850 REMARK 3 3 2.3753 - 2.0751 0.99 2927 151 0.2225 0.2729 REMARK 3 4 2.0751 - 1.8854 0.98 2889 127 0.2438 0.2405 REMARK 3 5 1.8854 - 1.7503 0.91 2697 142 0.2801 0.2811 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 33.08 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.81830 REMARK 3 B22 (A**2) : 1.81830 REMARK 3 B33 (A**2) : -3.63660 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 : 0.007 664 REMARK 3 ANGLE : 1.072 892 REMARK 3 CHIRALITY : 0.079 96 REMARK 3 PLANARITY : 0.003 112 REMARK 3 DIHEDRAL : 15.275 252 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 32:62) REMARK 3 ORIGIN FOR THE GROUP (A): 11.0901 -2.6426 7.0550 REMARK 3 T TENSOR REMARK 3 T11: 0.2360 T22: 0.3050 REMARK 3 T33: 0.2069 T12: 0.0391 REMARK 3 T13: 0.0752 T23: -0.0545 REMARK 3 L TENSOR REMARK 3 L11: 4.2328 L22: 9.0723 REMARK 3 L33: 4.6167 L12: 0.8387 REMARK 3 L13: -0.4273 L23: -1.5737 REMARK 3 S TENSOR REMARK 3 S11: -0.1851 S12: -0.4415 S13: 0.3173 REMARK 3 S21: 0.6623 S22: 0.4383 S23: 0.0164 REMARK 3 S31: -0.2885 S32: -0.1137 S33: -0.1647 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 63:96) REMARK 3 ORIGIN FOR THE GROUP (A): 15.5261 -7.1726 2.2596 REMARK 3 T TENSOR REMARK 3 T11: 0.2270 T22: 0.1951 REMARK 3 T33: 0.2199 T12: -0.0252 REMARK 3 T13: 0.0756 T23: -0.0698 REMARK 3 L TENSOR REMARK 3 L11: 6.9661 L22: 7.7890 REMARK 3 L33: 6.6976 L12: 0.2545 REMARK 3 L13: 0.4132 L23: -0.7193 REMARK 3 S TENSOR REMARK 3 S11: -0.3659 S12: 0.0764 S13: -0.0753 REMARK 3 S21: 0.0490 S22: 0.3184 S23: -0.6818 REMARK 3 S31: 0.1424 S32: 0.0443 S33: -0.0246 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 97:110) REMARK 3 ORIGIN FOR THE GROUP (A): 21.0738 -5.3805 8.5881 REMARK 3 T TENSOR REMARK 3 T11: 0.3509 T22: 0.3167 REMARK 3 T33: 0.4949 T12: 0.0162 REMARK 3 T13: -0.0551 T23: -0.1296 REMARK 3 L TENSOR REMARK 3 L11: 5.1068 L22: 6.6330 REMARK 3 L33: 9.1300 L12: -0.7071 REMARK 3 L13: 1.4326 L23: -3.9185 REMARK 3 S TENSOR REMARK 3 S11: -0.1645 S12: -0.3438 S13: -0.2186 REMARK 3 S21: 0.4913 S22: -0.0474 S23: -1.1029 REMARK 3 S31: 0.0210 S32: 1.3563 S33: -0.0755 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 4N6T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000082824. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7889 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 36.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.89700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS (H05), 0.02 M GLYCINE, 0.02 M REMARK 280 SODIUM L-GLUTAMATE, 0.02 M DL-ALANINE, 0.02 M DL-LYSINE REMARK 280 HYDROCHLORIDE, 0.02 M DL-SERINE, 0.1 M MOPS PH=7.50, 0.1 M HEPES REMARK 280 SODIUM SALT PH=7.50, 10.0% W/V POLYETHYLENE GLYCOL 20000, 20.0% REMARK 280 W/V POLYETHYLENE GLYCOL 550 MME, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 280K, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 30.92350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.46175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.38525 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 32 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N GLU A 32 O HOH A 237 3545 1.90 REMARK 500 REMARK 500 REMARK: NULL 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 LEU A 55 42.75 -142.75 REMARK 500 VAL A 69 -139.36 -137.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4N6U RELATED DB: PDB DBREF 4N6T A 32 110 PDB 4N6T 4N6T 32 110 SEQRES 1 A 79 GLU ASN SER LEU GLU ILE GLU GLU LEU ALA ARG PHE ALA SEQRES 2 A 79 VAL ASP GLU HIS ASN LYS LYS GLU ASN ALA LEU LEU GLU SEQRES 3 A 79 PHE VAL ARG VAL VAL LYS ALA LYS GLU GLN VAL VAL ALA SEQRES 4 A 79 GLY THR MET TYR TYR LEU THR LEU GLU ALA LYS ASP GLY SEQRES 5 A 79 GLY LYS LYS LYS LEU TYR GLU ALA LYS VAL TRP VAL LYS SEQRES 6 A 79 PRO TRP GLU ASN PHE LYS GLU LEU GLN GLU PHE LYS PRO SEQRES 7 A 79 VAL FORMUL 2 HOH *43(H2 O) HELIX 1 1 GLU A 32 ASN A 53 1 22 SHEET 1 A 4 GLU A 57 VAL A 68 0 SHEET 2 A 4 THR A 72 ASP A 82 -1 O MET A 73 N GLN A 67 SHEET 3 A 4 LYS A 85 LYS A 96 -1 O LYS A 85 N ASP A 82 SHEET 4 A 4 PHE A 101 PRO A 109 -1 O LYS A 108 N GLU A 90 CRYST1 35.855 35.855 61.847 90.00 90.00 90.00 P 41 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 0.027890 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027890 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016169 0.00000