HEADER DE NOVO PROTEIN 29-JUN-16 5LEA TITLE CRYSTAL STRUCTURE OF DARPIN-DARPIN RIGID FUSION, VARIANT TITLE 2 DD_OFF7_12_3G124 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DD_OFF7_12_3G124; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: XL1-BLUE KEYWDS DE NOVO PROTEIN, DESIGNED ANKYRIN REPEAT PROTEINS, PROTEIN DESIGN, KEYWDS 2 PROTEIN ENGINEERING, RIGID DOMAIN FUSIONS EXPDTA X-RAY DIFFRACTION AUTHOR A.BATYUK,Y.WU,P.R.MITTL,A.PLUECKTHUN REVDAT 3 10-JAN-24 5LEA 1 REMARK REVDAT 2 20-MAR-19 5LEA 1 JRNL REVDAT 1 02-AUG-17 5LEA 0 JRNL AUTH Y.WU,A.BATYUK,A.HONEGGER,F.BRANDL,P.R.E.MITTL,A.PLUCKTHUN JRNL TITL RIGIDLY CONNECTED MULTISPECIFIC ARTIFICIAL BINDERS WITH JRNL TITL 2 ADJUSTABLE GEOMETRIES. JRNL REF SCI REP V. 7 11217 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28894181 JRNL DOI 10.1038/S41598-017-11472-X REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2398) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 13281 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 665 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 36.4413 - 4.1025 0.98 2575 136 0.2037 0.2645 REMARK 3 2 4.1025 - 3.2569 0.98 2496 131 0.2322 0.2279 REMARK 3 3 3.2569 - 2.8454 1.00 2531 134 0.2759 0.3730 REMARK 3 4 2.8454 - 2.5853 1.00 2503 132 0.2960 0.3635 REMARK 3 5 2.5853 - 2.4001 0.99 2511 132 0.3207 0.3802 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.710 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) : 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 : 0.002 2447 REMARK 3 ANGLE : 0.460 3326 REMARK 3 CHIRALITY : 0.034 384 REMARK 3 PLANARITY : 0.003 434 REMARK 3 DIHEDRAL : 10.173 1448 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 12 THROUGH 182 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6960 -14.9185 20.3447 REMARK 3 T TENSOR REMARK 3 T11: 0.3581 T22: 0.3478 REMARK 3 T33: 0.3465 T12: 0.0173 REMARK 3 T13: -0.0056 T23: -0.0129 REMARK 3 L TENSOR REMARK 3 L11: 1.6991 L22: 6.7604 REMARK 3 L33: 4.3185 L12: -0.8238 REMARK 3 L13: 0.4974 L23: -3.8770 REMARK 3 S TENSOR REMARK 3 S11: -0.0160 S12: 0.0313 S13: 0.0717 REMARK 3 S21: 0.1409 S22: 0.2822 S23: 0.2675 REMARK 3 S31: -0.1729 S32: -0.1199 S33: -0.2233 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 183 THROUGH 327 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.2698 17.4589 10.1734 REMARK 3 T TENSOR REMARK 3 T11: 0.6423 T22: 1.0651 REMARK 3 T33: 0.7485 T12: 0.2473 REMARK 3 T13: -0.0398 T23: 0.0803 REMARK 3 L TENSOR REMARK 3 L11: 5.1474 L22: 1.5891 REMARK 3 L33: 3.1679 L12: -0.3146 REMARK 3 L13: -1.5688 L23: 1.9585 REMARK 3 S TENSOR REMARK 3 S11: -0.2308 S12: -1.0056 S13: -0.7797 REMARK 3 S21: -0.0395 S22: 0.0503 S23: 0.4127 REMARK 3 S31: -0.3784 S32: -0.8190 S33: 0.1407 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 5LEA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000593. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-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 : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13295 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 36.437 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.38100 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: 1SVX CHAIN A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD 32.3% V/V, SODIUM CHLORIDE 0.2 M, REMARK 280 SODIUM ACETATE TRIHYDRATE 0.1 M, PH 5.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.20000 REMARK 290 SMTRY3 2 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 TOTAL BURIED SURFACE AREA: 380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 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 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 O ASN A 102 O HOH A 501 2.15 REMARK 500 OD1 ASP A 151 NH2 ARG A 154 2.18 REMARK 500 O VAL A 139 O HOH A 502 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 GLU A 219 -34.35 82.33 REMARK 500 HIS A 293 45.04 -101.21 REMARK 500 ASP A 301 -165.04 -70.07 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 MPD A 402 DBREF 5LEA A 1 327 PDB 5LEA 5LEA 1 327 SEQRES 1 A 327 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ASP SEQRES 2 A 327 LEU GLY LYS LYS LEU LEU GLU ALA ALA ARG ALA GLY GLN SEQRES 3 A 327 ASP ASP GLU VAL ARG ILE LEU MET ALA ASN GLY ALA ASP SEQRES 4 A 327 VAL ASN ALA ALA ASP ASN THR GLY THR THR PRO LEU HIS SEQRES 5 A 327 LEU ALA ALA TYR SER GLY HIS LEU GLU ILE VAL GLU VAL SEQRES 6 A 327 LEU LEU LYS HIS GLY ALA ASP VAL ASP ALA SER ASP VAL SEQRES 7 A 327 PHE GLY TYR THR PRO LEU HIS LEU ALA ALA TYR TRP GLY SEQRES 8 A 327 HIS LEU GLU ILE VAL GLU VAL LEU LEU LYS ASN GLY ALA SEQRES 9 A 327 ASP VAL ASN ALA MET ASP SER ASP GLY MET THR PRO LEU SEQRES 10 A 327 HIS LEU ALA ALA LYS TRP GLY TYR LEU GLU ILE VAL GLU SEQRES 11 A 327 VAL LEU LEU LYS HIS GLY ALA ALA VAL GLY ALA GLN ASP SEQRES 12 A 327 LYS PHE GLY LYS THR PRO LYS ASP LEU ALA ARG ASP ASN SEQRES 13 A 327 GLY ASN GLN TRP ILE TYR GLU LEU LEU GLU LYS ALA GLU SEQRES 14 A 327 LYS ASP LEU ARG ARG LYS LEU LEU GLU ALA ALA ARG ALA SEQRES 15 A 327 GLY HIS ARG GLU GLU VAL GLU LYS LEU ILE LYS LEU GLY SEQRES 16 A 327 ALA ASP VAL ASN ALA ALA ASP ASP VAL GLY VAL THR PRO SEQRES 17 A 327 LEU HIS LEU ALA ALA GLN ARG GLY HIS LEU GLU ILE VAL SEQRES 18 A 327 GLU VAL LEU LEU LYS CYS GLY ALA ASP VAL ASN ALA ALA SEQRES 19 A 327 ASP LEU TRP GLY GLN THR PRO LEU HIS LEU ALA ALA THR SEQRES 20 A 327 ALA GLY HIS LEU GLU ILE VAL GLU VAL LEU LEU LYS ASN SEQRES 21 A 327 GLY ALA ASP VAL ASN ALA ARG ASP ASN ILE GLY HIS THR SEQRES 22 A 327 PRO LEU HIS LEU ALA ALA TRP ALA GLY HIS LEU GLU ILE SEQRES 23 A 327 VAL GLU VAL LEU LEU LYS HIS GLY ALA ASP VAL ASN ALA SEQRES 24 A 327 GLN ASP LYS PHE GLY LYS THR PRO PHE ASP LEU ALA ILE SEQRES 25 A 327 ASP ASN GLY ASN GLU ASP ILE ALA GLU VAL LEU GLN LYS SEQRES 26 A 327 ALA ALA HET MPD A 401 22 HET MPD A 402 22 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 MPD 2(C6 H14 O2) FORMUL 4 HOH *17(H2 O) HELIX 1 AA1 SER A 12 GLY A 25 1 14 HELIX 2 AA2 GLN A 26 ASN A 36 1 11 HELIX 3 AA3 THR A 49 GLY A 58 1 10 HELIX 4 AA4 HIS A 59 HIS 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 GLY A 124 1 10 HELIX 8 AA8 TYR A 125 HIS A 135 1 11 HELIX 9 AA9 THR A 148 ASN A 156 1 9 HELIX 10 AB1 ASN A 158 GLY A 183 1 26 HELIX 11 AB2 HIS A 184 LEU A 194 1 11 HELIX 12 AB3 THR A 207 GLY A 216 1 10 HELIX 13 AB4 GLU A 219 GLY A 228 1 10 HELIX 14 AB5 THR A 240 GLY A 249 1 10 HELIX 15 AB6 HIS A 250 ASN A 260 1 11 HELIX 16 AB7 THR A 273 GLY A 282 1 10 HELIX 17 AB8 HIS A 283 HIS A 293 1 11 HELIX 18 AB9 THR A 306 ASN A 314 1 9 HELIX 19 AC1 ASN A 316 ALA A 326 1 11 SITE 1 AC1 1 ASP A 171 CRYST1 62.410 46.400 63.080 90.00 111.10 90.00 P 1 21 1 2 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 0.016023 0.000000 0.006182 0.00000 SCALE2 0.000000 0.021552 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016992 0.00000