HEADER DE NOVO PROTEIN 14-OCT-13 4N6U TITLE ADHIRON: A STABLE AND VERSATILE PEPTIDE DISPLAY SCAFFOLD - TRUNCATED 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 4N6U 1 REMARK REVDAT 2 14-MAY-14 4N6U 1 JRNL REVDAT 1 09-APR-14 4N6U 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. 2.25 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.240 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 6985 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.640 REMARK 3 FREE R VALUE TEST SET COUNT : 324 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 36.3777 - 2.8364 0.97 3360 144 0.1601 0.2136 REMARK 3 2 2.8364 - 2.2514 0.97 3301 180 0.2551 0.3351 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 38.22 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.71180 REMARK 3 B22 (A**2) : -1.71180 REMARK 3 B33 (A**2) : 3.42360 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 : 0.009 668 REMARK 3 ANGLE : 1.284 897 REMARK 3 CHIRALITY : 0.088 96 REMARK 3 PLANARITY : 0.003 113 REMARK 3 DIHEDRAL : 16.929 255 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): 2.9610 24.8928 -7.3724 REMARK 3 T TENSOR REMARK 3 T11: 0.2464 T22: 0.3396 REMARK 3 T33: 0.2463 T12: 0.0013 REMARK 3 T13: -0.0167 T23: 0.0963 REMARK 3 L TENSOR REMARK 3 L11: 8.7712 L22: 2.3076 REMARK 3 L33: 3.8431 L12: 2.2937 REMARK 3 L13: -1.3726 L23: 0.1019 REMARK 3 S TENSOR REMARK 3 S11: -0.3380 S12: 0.5714 S13: 0.2150 REMARK 3 S21: -0.1799 S22: 0.3167 S23: 0.2020 REMARK 3 S31: -0.1179 S32: -0.3838 S33: 0.0802 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 63:96) REMARK 3 ORIGIN FOR THE GROUP (A): 7.2567 20.5703 -2.6964 REMARK 3 T TENSOR REMARK 3 T11: 0.2282 T22: 0.2349 REMARK 3 T33: 0.2629 T12: -0.0157 REMARK 3 T13: -0.0241 T23: 0.0584 REMARK 3 L TENSOR REMARK 3 L11: 5.3599 L22: 4.7128 REMARK 3 L33: 6.6644 L12: 0.5091 REMARK 3 L13: -2.0963 L23: 0.7263 REMARK 3 S TENSOR REMARK 3 S11: 0.0124 S12: -0.0794 S13: 0.0747 REMARK 3 S21: 0.2774 S22: -0.0770 S23: -0.3370 REMARK 3 S31: 0.1091 S32: 0.1122 S33: -0.0697 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 97:110) REMARK 3 ORIGIN FOR THE GROUP (A): 5.6232 14.8622 -8.9636 REMARK 3 T TENSOR REMARK 3 T11: 0.2722 T22: 0.3059 REMARK 3 T33: 0.3019 T12: -0.1001 REMARK 3 T13: 0.0014 T23: -0.0100 REMARK 3 L TENSOR REMARK 3 L11: 7.8298 L22: 4.5539 REMARK 3 L33: 6.2929 L12: -3.1557 REMARK 3 L13: -6.6845 L23: 4.0977 REMARK 3 S TENSOR REMARK 3 S11: -0.4928 S12: 0.5534 S13: -0.5742 REMARK 3 S21: 0.2449 S22: -0.4504 S23: 0.1431 REMARK 3 S31: 0.9094 S32: -0.8306 S33: 0.6906 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 4N6U 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_1000082825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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 : 3709 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.72200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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 (%): 41.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PACTPREMIER (D02), 0.1 M MMT SYSTEM PH REMARK 280 5.0, 25.0% W/V POLYETHYLENE GLYCOL 1500, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 280K 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 29.62150 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 14.81075 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 44.43225 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 46 O HOH A 218 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 OE1 GLU A 39 OH TYR A 75 4564 2.19 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 VAL A 59 -64.27 -105.17 REMARK 500 VAL A 69 -134.07 -140.51 REMARK 500 ASP A 82 -90.80 -79.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4N6T RELATED DB: PDB DBREF 4N6U A 32 110 PDB 4N6U 4N6U 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 *33(H2 O) HELIX 1 1 ASN A 33 ASN A 53 1 21 SHEET 1 A 4 GLU A 57 VAL A 68 0 SHEET 2 A 4 THR A 72 LYS A 81 -1 O THR A 77 N VAL A 62 SHEET 3 A 4 LYS A 86 LYS A 96 -1 O VAL A 95 N THR A 72 SHEET 4 A 4 PHE A 101 PRO A 109 -1 O LYS A 108 N GLU A 90 CRYST1 36.373 36.373 59.243 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 0.027493 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016880 0.00000