HEADER DE NOVO PROTEIN 28-AUG-24 9DEA TITLE CRYSTAL STRUCTURE OF C3-THREADED COMPND MOL_ID: 1; COMPND 2 MOLECULE: C3_THREADED; 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; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO PROTEIN, DESIGN MODEL, BARCODING, MASS SPEC. EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,J.SIMS,D.BAKER REVDAT 1 26-MAR-25 9DEA 0 JRNL AUTH D.FELDMAN,J.N.SIMS,X.LI,R.JOHNSON,S.GERBEN,D.E.KIM, JRNL AUTH 2 C.RICHARDSON,B.KOEPNICK,H.EISENACH,D.R.HICKS,E.C.YANG, JRNL AUTH 3 B.I.M.WICKY,L.F.MILLES,A.K.BERA,A.KANG,E.BRACKENBROUGH, JRNL AUTH 4 E.JOYCE,B.SANKARAN,J.M.LUBNER,I.GORESHNIK,D.VAFEADOS, JRNL AUTH 5 A.ALLEN,L.STEWART,M.J.MACCOSS,D.BAKER JRNL TITL MASSIVELY PARALLEL ASSESSMENT OF DESIGNED PROTEIN SOLUTION JRNL TITL 2 PROPERTIES USING MASS SPECTROMETRY AND PEPTIDE BARCODING. JRNL REF BIORXIV 2025 JRNL REFN ISSN 2692-8205 JRNL PMID 40060547 JRNL DOI 10.1101/2025.02.24.639402 REMARK 2 REMARK 2 RESOLUTION. 2.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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) : 2.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 1539 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.270 REMARK 3 FREE R VALUE TEST SET COUNT : 158 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 3.0000 - 2.8700 1.00 1381 158 0.2376 0.2722 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 : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.299 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 87.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 80.77 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 : 0.004 613 REMARK 3 ANGLE : 0.685 826 REMARK 3 CHIRALITY : 0.045 107 REMARK 3 PLANARITY : 0.004 101 REMARK 3 DIHEDRAL : 25.838 241 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 9DEA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1000287928. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.00005 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1542 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.870 REMARK 200 RESOLUTION RANGE LOW (A) : 36.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 38.00 REMARK 200 R MERGE (I) : 0.17200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 38.00 REMARK 200 R MERGE FOR SHELL (I) : 1.82600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 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 (%): 32.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 % V/V PEG 400, 0.05 M MES PH 6, 0.1 REMARK 280 M POTASSIUM CHLORIDE AND 2 MM MAGNESIUM CHLORIDE HEXAHYDRATE, PH REMARK 280 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 36.32450 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 36.32450 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 36.32450 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 36.32450 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 36.32450 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 36.32450 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 36.32450 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 36.32450 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 36.32450 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 36.32450 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 36.32450 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 36.32450 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 36.32450 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 36.32450 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 36.32450 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 36.32450 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 36.32450 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 36.32450 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 36.32450 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 36.32450 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 36.32450 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 36.32450 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 36.32450 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 36.32450 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 36.32450 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 36.32450 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 36.32450 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 36.32450 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 36.32450 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 36.32450 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 36.32450 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 36.32450 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 36.32450 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 36.32450 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 36.32450 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 36.32450 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 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 SER A 1 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 16 56.77 -103.83 REMARK 500 LYS A 79 -43.40 -130.99 REMARK 500 REMARK 500 REMARK: NULL DBREF 9DEA A 1 80 PDB 9DEA 9DEA 1 80 SEQRES 1 A 80 SER ALA LEU LEU GLU LYS ILE GLU LYS GLU ALA GLU ARG SEQRES 2 A 80 LEU LEU ASP LYS ASP GLU ALA LYS LEU LEU ILE LEU ALA SEQRES 3 A 80 GLU LYS PHE SER GLY TYR ALA PRO ALA CYS LEU LEU ALA SEQRES 4 A 80 LEU VAL ARG GLN GLY ALA ASP SER LEU SER LEU LEU ILE SEQRES 5 A 80 ALA LEU GLU ILE LEU LEU LYS VAL LEU THR PRO GLU ASN SEQRES 6 A 80 GLU PRO ILE ILE LEU LEU GLY LEU LYS ALA ILE LEU GLU SEQRES 7 A 80 LYS GLU HELIX 1 AA1 ALA A 2 LEU A 15 1 14 HELIX 2 AA2 ASP A 18 PHE A 29 1 12 HELIX 3 AA3 TYR A 32 GLN A 43 1 12 HELIX 4 AA4 ASP A 46 LYS A 59 1 14 HELIX 5 AA5 VAL A 60 LEU A 61 5 2 HELIX 6 AA6 THR A 62 GLU A 64 5 3 HELIX 7 AA7 ASN A 65 GLU A 78 1 14 CRYST1 72.649 72.649 72.649 90.00 90.00 90.00 I 2 3 24 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 0.013765 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013765 0.00000