HEADER DE NOVO PROTEIN 16-FEB-24 8S1X TITLE CRYSTAL STRUCTURE OF ACTINONIN-BOUND PDF1 AND THE COMPUTATIONALLY TITLE 2 DESIGNED DBACT553_1 PROTEIN BINDER COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PDF,POLYPEPTIDE DEFORMYLASE; COMPND 5 EC: 3.5.1.88; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: ACTIONIN; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DBACT553_1; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: ACTIONIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: DEF, PA0019; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACTINONIN, DE NOVO, COMPUTATIONAL, BINDER, CID, SWITCH, DEFORMYLASE, KEYWDS 2 DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.MARCHAND,M.PACESA,B.E.CORREIA REVDAT 3 29-JAN-25 8S1X 1 JRNL REVDAT 2 15-JAN-25 8S1X 1 JRNL REVDAT 1 30-OCT-24 8S1X 0 JRNL AUTH A.MARCHAND,S.BUCKLEY,A.SCHNEUING,M.PACESA,M.ELIA,P.GAINZA, JRNL AUTH 2 E.ELIZAROVA,R.M.NEESER,P.W.LEE,L.REYMOND,Y.MIAO,L.SCHELLER, JRNL AUTH 3 S.GEORGEON,J.SCHMIDT,P.SCHWALLER,S.J.MAERKL,M.BRONSTEIN, JRNL AUTH 4 B.E.CORREIA JRNL TITL TARGETING PROTEIN-LIGAND NEOSURFACES WITH A GENERALIZABLE JRNL TITL 2 DEEP LEARNING TOOL. JRNL REF NATURE 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 39814890 JRNL DOI 10.1038/S41586-024-08435-4 REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21_5184 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 24982 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1255 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 55.7000 - 3.9100 0.93 2721 111 0.1675 0.1874 REMARK 3 2 3.9100 - 3.1100 0.94 2557 151 0.1723 0.1775 REMARK 3 3 3.1100 - 2.7100 0.96 2626 139 0.1896 0.2045 REMARK 3 4 2.7100 - 2.4600 0.97 2646 134 0.1961 0.2393 REMARK 3 5 2.4600 - 2.2900 0.98 2638 146 0.1906 0.1866 REMARK 3 6 2.2900 - 2.1500 0.98 2598 147 0.1979 0.2435 REMARK 3 7 2.1500 - 2.0500 0.99 2647 145 0.2319 0.2773 REMARK 3 8 2.0500 - 1.9600 0.98 2642 133 0.2772 0.2812 REMARK 3 9 1.9600 - 1.8800 0.99 2652 149 0.3037 0.3416 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) : 0.237 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.488 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.21 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 : 0.006 1939 REMARK 3 ANGLE : 0.779 2604 REMARK 3 CHIRALITY : 0.051 289 REMARK 3 PLANARITY : 0.009 339 REMARK 3 DIHEDRAL : 15.631 777 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 8S1X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292136690. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87313 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24990 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 55.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 1.12500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FORMATE, 0.1 M SODIUM REMARK 280 PHOSPHATE PH 6.2, 20% (V/V) PEG SMEAR, 10% (V/V) GLYCEROL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291.15K 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 24.72000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.58000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.50500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.58000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.72000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.50500 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 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 TYR B 62 REMARK 465 GLY B 63 REMARK 465 SER B 64 REMARK 465 HIS B 65 REMARK 465 HIS B 66 REMARK 465 HIS B 67 REMARK 465 HIS B 68 REMARK 465 HIS B 69 REMARK 465 HIS B 70 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 PRO A 10 34.49 -95.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 92 SG REMARK 620 2 HIS A 134 NE2 104.4 REMARK 620 3 HIS A 138 NE2 91.6 98.9 REMARK 620 4 BB2 A 202 O2 158.8 95.8 91.5 REMARK 620 5 BB2 A 202 O4 91.2 111.8 147.4 75.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 99 O REMARK 620 2 HOH A 314 O 67.8 REMARK 620 N 1 DBREF 8S1X A 1 168 UNP Q9I7A8 DEF_PSEAE 1 168 DBREF 8S1X B 1 70 PDB 8S1X 8S1X 1 70 SEQRES 1 A 168 MET ALA ILE LEU ASN ILE LEU GLU PHE PRO ASP PRO ARG SEQRES 2 A 168 LEU ARG THR ILE ALA LYS PRO VAL GLU VAL VAL ASP ASP SEQRES 3 A 168 ALA VAL ARG GLN LEU ILE ASP ASP MET PHE GLU THR MET SEQRES 4 A 168 TYR GLU ALA PRO GLY ILE GLY LEU ALA ALA THR GLN VAL SEQRES 5 A 168 ASN VAL HIS LYS ARG ILE VAL VAL MET ASP LEU SER GLU SEQRES 6 A 168 ASP LYS SER GLU PRO ARG VAL PHE ILE ASN PRO GLU PHE SEQRES 7 A 168 GLU PRO LEU THR GLU ASP MET ASP GLN TYR GLN GLU GLY SEQRES 8 A 168 CYS LEU SER VAL PRO GLY PHE TYR GLU ASN VAL ASP ARG SEQRES 9 A 168 PRO GLN LYS VAL ARG ILE LYS ALA LEU ASP ARG ASP GLY SEQRES 10 A 168 ASN PRO PHE GLU GLU VAL ALA GLU GLY LEU LEU ALA VAL SEQRES 11 A 168 CYS ILE GLN HIS GLU CYS ASP HIS LEU ASN GLY LYS LEU SEQRES 12 A 168 PHE VAL ASP TYR LEU SER THR LEU LYS ARG ASP ARG ILE SEQRES 13 A 168 ARG LYS LYS LEU GLU LYS GLN HIS ARG GLN GLN ALA SEQRES 1 B 70 ASP TYR ILE ARG GLU LEU ARG ALA ALA LEU ILE LEU LEU SEQRES 2 B 70 ALA LEU LYS LYS GLN HIS ALA GLU ASP PRO ASP ALA GLN SEQRES 3 B 70 ARG VAL ALA ASP GLU LEU MET LYS LYS LEU PHE ASP ALA SEQRES 4 B 70 ALA HIS ARG ASN ASP LYS ASP LYS VAL LYS LYS VAL VAL SEQRES 5 B 70 GLU GLU ALA LYS LYS VAL VAL SER THR TYR GLY SER HIS SEQRES 6 B 70 HIS HIS HIS HIS HIS HET ZN A 201 1 HET BB2 A 202 62 HET FMT A 203 4 HET FMT A 204 4 HET FMT A 205 4 HET FMT A 206 4 HET FMT A 207 4 HET FMT A 208 4 HET FMT A 209 4 HET FMT A 210 4 HET PO4 A 211 5 HET PO4 A 212 5 HET PO4 A 213 5 HET PO4 A 214 5 HET K B 101 1 HETNAM ZN ZINC ION HETNAM BB2 ACTINONIN HETNAM FMT FORMIC ACID HETNAM PO4 PHOSPHATE ION HETNAM K POTASSIUM ION HETSYN BB2 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2- HETSYN 2 BB2 HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL- HETSYN 3 BB2 PROPYL]-AMIDE FORMUL 3 ZN ZN 2+ FORMUL 4 BB2 C19 H35 N3 O5 FORMUL 5 FMT 8(C H2 O2) FORMUL 13 PO4 4(O4 P 3-) FORMUL 17 K K 1+ FORMUL 18 HOH *76(H2 O) HELIX 1 AA1 ASP A 11 THR A 16 5 6 HELIX 2 AA2 ASP A 25 ALA A 42 1 18 HELIX 3 AA3 THR A 50 ASN A 53 5 4 HELIX 4 AA4 GLY A 126 ASN A 140 1 15 HELIX 5 AA5 LEU A 143 LEU A 148 5 6 HELIX 6 AA6 SER A 149 ALA A 168 1 20 HELIX 7 AA7 TYR B 2 ALA B 20 1 19 HELIX 8 AA8 ASP B 22 ARG B 42 1 21 HELIX 9 AA9 ASP B 44 SER B 60 1 17 SHEET 1 AA1 5 GLY A 46 ALA A 48 0 SHEET 2 AA1 5 ILE A 58 ASP A 62 -1 O VAL A 60 N LEU A 47 SHEET 3 AA1 5 PRO A 70 PRO A 80 -1 O ARG A 71 N MET A 61 SHEET 4 AA1 5 LYS A 107 LEU A 113 -1 O ARG A 109 N GLU A 79 SHEET 5 AA1 5 PRO A 119 GLU A 125 -1 O GLU A 122 N ILE A 110 SHEET 1 AA2 2 ASP A 86 GLU A 90 0 SHEET 2 AA2 2 GLU A 100 ARG A 104 -1 O ARG A 104 N ASP A 86 LINK SG CYS A 92 ZN ZN A 201 1555 1555 2.27 LINK O TYR A 99 K K B 101 1555 1555 3.28 LINK NE2 HIS A 134 ZN ZN A 201 1555 1555 2.17 LINK NE2 HIS A 138 ZN ZN A 201 1555 1555 2.22 LINK ZN ZN A 201 O2 BB2 A 202 1555 1555 2.20 LINK ZN ZN A 201 O4 BB2 A 202 1555 1555 2.20 LINK O HOH A 314 K K B 101 1555 1555 3.09 CISPEP 1 PHE A 9 PRO A 10 0 5.34 CISPEP 2 ALA A 42 PRO A 43 0 -7.64 CRYST1 49.440 75.010 83.160 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 0.020227 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013332 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012025 0.00000