HEADER DE NOVO PROTEIN 20-MAR-22 7UDJ TITLE CRYSTAL STRUCTURE OF DESIGNED HELICAL REPEAT PROTEIN RPB_PEW3_R4 BOUND TITLE 2 TO PAWX4 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4XPAW PEPTIDE; COMPND 3 CHAIN: G; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DE NOVO DESIGNED HELICAL REPEAT PROTEIN RPB_PEW3_R4; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 7 ORGANISM_TAXID: 32630; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 37762 KEYWDS SYNTHETIC PROTEIN, DESIGNED HELICAL REPEAT PROTEIN, PEPTIDE BINDER, KEYWDS 2 DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.L.REDLER,Y.CHANG,G.BHABHA,D.EKIERT REVDAT 4 03-APR-24 7UDJ 1 REMARK REVDAT 3 03-MAY-23 7UDJ 1 JRNL REVDAT 2 19-APR-23 7UDJ 1 JRNL REVDAT 1 22-MAR-23 7UDJ 0 JRNL AUTH K.WU,H.BAI,Y.T.CHANG,R.REDLER,K.E.MCNALLY,W.SHEFFLER, JRNL AUTH 2 T.J.BRUNETTE,D.R.HICKS,T.E.MORGAN,T.J.STEVENS,A.BROERMAN, JRNL AUTH 3 I.GORESHNIK,M.DEWITT,C.M.CHOW,Y.SHEN,L.STEWART,E.DERIVERY, JRNL AUTH 4 D.A.SILVA,G.BHABHA,D.C.EKIERT,D.BAKER JRNL TITL DE NOVO DESIGN OF MODULAR PEPTIDE-BINDING PROTEINS BY JRNL TITL 2 SUPERHELICAL MATCHING. JRNL REF NATURE V. 616 581 2023 JRNL REFN ESSN 1476-4687 JRNL PMID 37020023 JRNL DOI 10.1038/S41586-023-05909-9 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16-3549-0000 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 6373 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 316 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 38.3000 - 3.4000 1.00 3091 162 0.2307 0.2601 REMARK 3 2 3.4000 - 2.7000 1.00 2966 154 0.3224 0.3305 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.449 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.249 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 92.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 114.9 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 1627 REMARK 3 ANGLE : 0.406 2198 REMARK 3 CHIRALITY : 0.029 252 REMARK 3 PLANARITY : 0.002 290 REMARK 3 DIHEDRAL : 10.896 1004 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -4.6907 10.8001 -15.7001 REMARK 3 T TENSOR REMARK 3 T11: 0.9370 T22: 0.8789 REMARK 3 T33: 0.9900 T12: 0.0527 REMARK 3 T13: 0.1078 T23: -0.0380 REMARK 3 L TENSOR REMARK 3 L11: 2.8773 L22: 2.4139 REMARK 3 L33: 2.2873 L12: 0.9900 REMARK 3 L13: 0.5448 L23: 0.6410 REMARK 3 S TENSOR REMARK 3 S11: -0.0781 S12: 0.0536 S13: -0.0480 REMARK 3 S21: -0.3543 S22: -0.0027 S23: 0.0144 REMARK 3 S31: -0.2702 S32: -0.0705 S33: -0.0002 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 7UDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000261958. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03318 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6383 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 38.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06972 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 1.05600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: PREDICTED MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 5, 30% W/V PEG6000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 22.70000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.65000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.65000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.70000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.80000 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: 1690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H 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: 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 H 97 2.25 -66.73 REMARK 500 GLU H 151 -3.10 66.27 REMARK 500 REMARK 500 REMARK: NULL DBREF 7UDJ G 11 22 PDB 7UDJ 7UDJ 11 22 DBREF 7UDJ H 6 197 PDB 7UDJ 7UDJ 6 197 SEQRES 1 G 12 ALA TRP PRO ALA TRP PRO ALA TRP PRO ALA TRP PRO SEQRES 1 H 192 LYS LYS GLU ALA GLU GLU VAL ALA ALA HIS VAL GLU GLN SEQRES 2 H 192 ILE ALA PHE ILE ALA LYS GLU GLN GLY ASN GLU GLU VAL SEQRES 3 H 192 ALA LYS LEU ALA LYS ARG LEU ALA GLU THR ILE LYS ARG SEQRES 4 H 192 LEU ASN GLU GLY THR GLU GLU GLU VAL LYS ARG LEU LEU SEQRES 5 H 192 GLU ALA ALA GLU VAL ALA ALA HIS VAL LEU GLN ILE ALA SEQRES 6 H 192 PHE ILE ALA HIS GLU GLN GLY ASN GLU GLU VAL ALA LYS SEQRES 7 H 192 LEU ALA LEU GLU LEU ALA GLU SER ILE LEU ARG LEU ILE SEQRES 8 H 192 GLU GLY THR GLU GLU GLU VAL LYS ARG LEU LEU GLU ALA SEQRES 9 H 192 ALA GLU VAL ALA ALA HIS VAL LEU GLN ILE ALA PHE ILE SEQRES 10 H 192 ALA HIS GLU GLN GLY ASN GLU GLU VAL ALA LYS LEU ALA SEQRES 11 H 192 LEU GLU LEU ALA GLU SER ILE LEU ARG LEU ILE GLU GLY SEQRES 12 H 192 THR GLU GLU GLU VAL LYS GLU LEU LEU GLU ARG ALA GLU SEQRES 13 H 192 GLU ALA ALA HIS VAL LEU GLN HIS ALA PHE ILE ALA THR SEQRES 14 H 192 GLU GLN GLY ASN GLU GLU ASP ALA LYS GLU ALA LEU ARG SEQRES 15 H 192 LYS ALA GLU GLU ILE LEU ARG ARG ASN ALA HELIX 1 AA1 LYS H 7 GLY H 27 1 21 HELIX 2 AA2 ASN H 28 LEU H 45 1 18 HELIX 3 AA3 THR H 49 GLN H 76 1 28 HELIX 4 AA4 ASN H 78 ILE H 96 1 19 HELIX 5 AA5 THR H 99 GLN H 126 1 28 HELIX 6 AA6 ASN H 128 GLY H 148 1 21 HELIX 7 AA7 GLU H 152 GLY H 177 1 26 HELIX 8 AA8 ASN H 178 ARG H 195 1 18 CRYST1 45.400 67.600 71.300 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 0.022026 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014025 0.00000