HEADER DE NOVO PROTEIN 26-APR-24 9BK7 TITLE STRUCTURE OF SHRT_BINDER COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHRT_BINDER; 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 SHRT_BINDER, PROTEIN DESIGN, DIFFUSION, DEEP LEARNING, DE NOVO KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,S.V.TORRES,A.KANG,D.BAKER REVDAT 4 12-MAR-25 9BK7 1 JRNL REVDAT 3 29-JAN-25 9BK7 1 JRNL REVDAT 2 15-JAN-25 9BK7 1 JRNL REVDAT 1 09-OCT-24 9BK7 0 JRNL AUTH S.VAZQUEZ TORRES,M.BENARD VALLE,S.P.MACKESSY,S.K.MENZIES, JRNL AUTH 2 N.R.CASEWELL,S.AHMADI,N.J.BURLET,E.MURATSPAHIC,I.SAPPINGTON, JRNL AUTH 3 M.D.OVERATH,E.RIVERA-DE-TORRE,J.LEDERGERBER,A.H.LAUSTSEN, JRNL AUTH 4 K.BODDUM,A.K.BERA,A.KANG,E.BRACKENBROUGH,I.A.CARDOSO, JRNL AUTH 5 E.P.CRITTENDEN,R.J.EDGE,J.DECARREAU,R.J.RAGOTTE,A.S.PILLAI, JRNL AUTH 6 M.ABEDI,H.L.HAN,S.R.GERBEN,A.MURRAY,R.SKOTHEIM,L.STUART, JRNL AUTH 7 L.STEWART,T.J.A.FRYER,T.P.JENKINS,D.BAKER JRNL TITL DE NOVO DESIGNED PROTEINS NEUTRALIZE LETHAL SNAKE VENOM JRNL TITL 2 TOXINS. JRNL REF NATURE V. 639 225 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 39814879 JRNL DOI 10.1038/S41586-024-08393-X REMARK 2 REMARK 2 RESOLUTION. 2.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_4761 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) : 2.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 5179 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 518 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 32.1700 - 4.1000 1.00 1226 142 0.1740 0.1822 REMARK 3 2 4.0900 - 3.2500 1.00 1159 121 0.1885 0.2450 REMARK 3 3 3.2500 - 2.8400 1.00 1139 130 0.2366 0.2685 REMARK 3 4 2.8400 - 2.5800 1.00 1137 125 0.2951 0.3562 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) : 0.324 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.347 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.50 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 : 0.004 746 REMARK 3 ANGLE : 0.608 1006 REMARK 3 CHIRALITY : 0.041 114 REMARK 3 PLANARITY : 0.004 137 REMARK 3 DIHEDRAL : 3.782 107 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 9BK7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1000283565. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9201 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : KB BIMORPH MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5179 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.580 REMARK 200 RESOLUTION RANGE LOW (A) : 32.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 24.60 REMARK 200 R MERGE (I) : 0.24600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 25.20 REMARK 200 R MERGE FOR SHELL (I) : 1.06900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.130 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 (%): 59.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08 M SODIUM ACETATE TRIHYDRATE PH REMARK 280 4.6, 1.6 M AMMONIUM SULFATE AND 20% (V/V) GLYCEROL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+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 37.66700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 37.66700 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.17200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.66700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.08600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.66700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 81.25800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.66700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 81.25800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.66700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.08600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 37.66700 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 37.66700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 54.17200 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 37.66700 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 37.66700 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 54.17200 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 37.66700 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 81.25800 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 37.66700 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 27.08600 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 37.66700 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 27.08600 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 37.66700 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 81.25800 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 37.66700 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 37.66700 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 54.17200 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 MET A -3 REMARK 465 SER A -2 REMARK 465 GLY A -1 REMARK 465 GLY A 0 REMARK 465 SER A 103 REMARK 465 GLY A 104 REMARK 465 SER A 105 REMARK 465 HIS A 106 REMARK 465 HIS A 107 REMARK 465 TRP A 108 REMARK 465 GLY A 109 REMARK 465 SER A 110 REMARK 465 THR A 111 REMARK 465 HIS A 112 REMARK 465 HIS A 113 REMARK 465 HIS A 114 REMARK 465 HIS A 115 REMARK 465 HIS A 116 REMARK 465 HIS A 117 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 84 -167.61 -70.00 REMARK 500 REMARK 500 REMARK: NULL DBREF 9BK7 A -3 117 PDB 9BK7 9BK7 -3 117 SEQRES 1 A 121 MET SER GLY GLY PRO LYS THR VAL VAL VAL ARG LEU SER SEQRES 2 A 121 PRO SER MET ASN GLU GLU GLN ALA ALA GLU ILE GLY ARG SEQRES 3 A 121 GLU ALA GLY LYS ALA ALA LEU ALA ALA GLY ASP ARG LEU SEQRES 4 A 121 VAL PHE VAL GLY PRO ALA ASP GLN SER TYR ALA ALA MET SEQRES 5 A 121 LYS ALA ALA MET GLU ALA GLY LEU PRO GLU VAL THR MET SEQRES 6 A 121 TYR ALA LEU ASP PHE SER ASP ALA GLU SER ALA LEU LYS SEQRES 7 A 121 ALA ALA GLU VAL ALA GLU ASP GLU GLY ASP GLU GLU VAL SEQRES 8 A 121 ALA GLU VAL ALA ARG GLU ILE ALA GLU GLU ILE LYS ALA SEQRES 9 A 121 GLY GLY SER GLY SER HIS HIS TRP GLY SER THR HIS HIS SEQRES 10 A 121 HIS HIS HIS HIS HELIX 1 AA1 ASN A 13 GLY A 32 1 20 HELIX 2 AA2 ALA A 41 ALA A 54 1 14 HELIX 3 AA3 ASP A 68 GLU A 82 1 15 HELIX 4 AA4 ASP A 84 GLY A 101 1 18 SHEET 1 AA1 3 THR A 3 ARG A 7 0 SHEET 2 AA1 3 ARG A 34 PRO A 40 1 O ARG A 34 N VAL A 4 SHEET 3 AA1 3 THR A 60 LEU A 64 1 O TYR A 62 N PHE A 37 CRYST1 75.334 75.334 108.344 90.00 90.00 90.00 I 41 2 2 16 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 0.013274 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013274 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009230 0.00000 TER 740 GLY A 102 MASTER 283 0 0 4 3 0 0 6 739 1 0 10 END