HEADER DE NOVO PROTEIN 09-AUG-17 5OP1 TITLE DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) A4 IN COMPLEX WITH LYSOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: DARPIN A4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DARPIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: LYSOZYME C; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: LYSOZYME; COMPND 11 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C,ALLERGEN GAL D IV; COMPND 12 EC: 3.2.1.17 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI M15; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 1007065; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PQE30; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 10 ORGANISM_COMMON: CHICKEN; SOURCE 11 ORGANISM_TAXID: 9031; SOURCE 12 OTHER_DETAILS: EGG WHITE KEYWDS DARPIN, DIRECTED EVOLUTION, DESIGNED PROTEIN, PROTEIN PROTEIN KEYWDS 2 COMPLEX, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.FISCHER,B.J.HOGAN,G.HOULIHAN,S.EDMOND,T.T.K.HUOVINEN,F.HOLLFELDER, AUTHOR 2 M.HYVONEN REVDAT 2 17-JAN-24 5OP1 1 REMARK REVDAT 1 29-AUG-18 5OP1 0 JRNL AUTH G.FISCHER,M.HYVONEN JRNL TITL DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) A4 IN COMPLEX WITH JRNL TITL 2 LYSOZYME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 13618 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 683 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 51.4460 - 3.9047 1.00 2733 155 0.1685 0.1850 REMARK 3 2 3.9047 - 3.0994 0.96 2525 124 0.2092 0.2589 REMARK 3 3 3.0994 - 2.7076 1.00 2572 140 0.2584 0.3449 REMARK 3 4 2.7076 - 2.4600 1.00 2571 132 0.2583 0.3569 REMARK 3 5 2.4600 - 2.2837 1.00 2534 132 0.2654 0.3507 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.003 2166 REMARK 3 ANGLE : 0.533 2936 REMARK 3 CHIRALITY : 0.037 333 REMARK 3 PLANARITY : 0.003 386 REMARK 3 DIHEDRAL : 13.415 1295 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 5OP1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006157. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 0.96858 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13626 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.284 REMARK 200 RESOLUTION RANGE LOW (A) : 55.916 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.30 REMARK 200 R MERGE FOR SHELL (I) : 0.77600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 3OOS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M (NH4)2 TART, 20 %W/V PEG 3350, REMARK 280 PH 8.0, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z 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 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 27.95800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.43300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.95800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.43300 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1 REMARK 465 ARG A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 GLY A 11 REMARK 465 SER A 12 REMARK 465 LEU A 168 REMARK 465 PRO B 70 REMARK 465 GLY B 71 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 ASP A 13 CG OD1 OD2 REMARK 470 GLU A 20 CD OE1 OE2 REMARK 470 GLU A 159 CG CD OE1 OE2 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 B 18 O HOH B 301 2.00 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 ASP A 44 -164.34 -100.98 REMARK 500 ASN B 19 36.46 -148.37 REMARK 500 ARG B 68 51.57 -150.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 201 DBREF 5OP1 A 1 168 PDB 5OP1 5OP1 1 168 DBREF 5OP1 B 1 129 UNP P00698 LYSC_CHICK 19 147 SEQRES 1 A 168 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ASP SEQRES 2 A 168 LEU GLY LYS LYS LEU LEU GLU ALA ALA ARG ALA GLY GLN SEQRES 3 A 168 ASP ASP GLU VAL ARG ILE LEU MET ALA ASN GLY ALA ASP SEQRES 4 A 168 VAL ASN ALA ASN ASP GLU TYR GLY SER THR PRO LEU HIS SEQRES 5 A 168 LEU ALA ALA LEU MET GLY HIS LEU GLU ILE VAL GLU VAL SEQRES 6 A 168 LEU LEU LYS ASN GLY ALA ASP VAL ASN ALA GLU ASP THR SEQRES 7 A 168 VAL GLY ASP THR PRO LEU HIS LEU ALA ALA SER LEU GLY SEQRES 8 A 168 HIS LEU GLU ILE VAL GLU VAL LEU LEU LYS ASN GLY ALA SEQRES 9 A 168 ASP VAL ASN ALA GLN ASP PHE VAL GLY ALA THR PRO LEU SEQRES 10 A 168 HIS LEU ALA ALA ASN LEU GLY HIS LEU GLU ILE VAL GLU SEQRES 11 A 168 VAL LEU LEU LYS HIS GLY ALA ASP VAL ASN ALA GLN ASP SEQRES 12 A 168 LYS PHE GLY LYS THR ALA PHE ASP ILE SER ILE ASP ASN SEQRES 13 A 168 GLY ASN GLU ASP LEU ALA GLU ILE LEU GLN LYS LEU SEQRES 1 B 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 B 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 B 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 B 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 B 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 B 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 B 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 B 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 B 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 B 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU HET CL B 201 1 HETNAM CL CHLORIDE ION FORMUL 3 CL CL 1- FORMUL 4 HOH *81(H2 O) HELIX 1 AA1 LEU A 14 ALA A 24 1 11 HELIX 2 AA2 GLN A 26 ASN A 36 1 11 HELIX 3 AA3 THR A 49 MET A 57 1 9 HELIX 4 AA4 HIS A 59 ASN A 69 1 11 HELIX 5 AA5 THR A 82 GLY A 91 1 10 HELIX 6 AA6 HIS A 92 ASN A 102 1 11 HELIX 7 AA7 THR A 115 LEU A 123 1 9 HELIX 8 AA8 HIS A 125 HIS A 135 1 11 HELIX 9 AA9 THR A 148 ASN A 156 1 9 HELIX 10 AB1 ASN A 158 GLN A 166 1 9 HELIX 11 AB2 GLY B 4 HIS B 15 1 12 HELIX 12 AB3 SER B 24 ASN B 37 1 14 HELIX 13 AB4 PRO B 79 SER B 85 5 7 HELIX 14 AB5 ILE B 88 SER B 100 1 13 HELIX 15 AB6 ASP B 101 GLY B 102 5 2 HELIX 16 AB7 ASN B 103 ALA B 107 5 5 HELIX 17 AB8 TRP B 108 CYS B 115 1 8 HELIX 18 AB9 ASP B 119 ILE B 124 5 6 SHEET 1 AA1 3 THR B 43 ARG B 45 0 SHEET 2 AA1 3 THR B 51 TYR B 53 -1 O ASP B 52 N ASN B 44 SHEET 3 AA1 3 ILE B 58 ASN B 59 -1 O ILE B 58 N TYR B 53 SSBOND 1 CYS B 6 CYS B 127 1555 1555 2.04 SSBOND 2 CYS B 30 CYS B 115 1555 1555 2.03 SSBOND 3 CYS B 64 CYS B 80 1555 1555 2.03 SSBOND 4 CYS B 76 CYS B 94 1555 1555 2.04 SITE 1 AC1 4 LYS A 101 ASN A 140 ARG B 21 HOH B 333 CRYST1 55.916 102.866 50.277 90.00 90.00 90.00 P 21 21 2 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 0.017884 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009721 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019890 0.00000