HEADER DE NOVO PROTEIN 09-NOV-22 8BL3 TITLE DE NOVO SINGLE-CHAIN IMMUNOGLOBULIN DIMER SCIG12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCIG12; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 4 ORGANISM_TAXID: 562 KEYWDS DE NOVO, IMMUNOGLOBULIN, SINGLE-CHAIN DIMER, SANDWICH, BETA, DE NOVO KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.NADAL,J.ROEL-TOURIS,E.MARCOS REVDAT 1 04-OCT-23 8BL3 0 JRNL AUTH J.ROEL-TOURIS,M.NADAL,E.MARCOS JRNL TITL SINGLE-CHAIN DIMERS FROM DE NOVO IMMUNOGLOBULINS AS ROBUST JRNL TITL 2 SCAFFOLDS FOR MULTIPLE BINDING LOOPS. JRNL REF NAT COMMUN V. 14 5939 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37741853 JRNL DOI 10.1038/S41467-023-41717-5 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.4 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 6712 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 678 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.51 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4343 REMARK 3 BIN FREE R VALUE : 0.5924 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 20 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1137 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 104.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.67930 REMARK 3 B22 (A**2) : -0.67930 REMARK 3 B33 (A**2) : 1.35850 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.410 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.512 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.334 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.470 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.331 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1165 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1572 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 552 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 205 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1165 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 143 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 822 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.25 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.75 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 3.61 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8BL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126604. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JAN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6749 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 48.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: PREDICTION REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45% V/V 2-METHYL-2,4-PENTANEDIOL REMARK 280 (MPD), 0.2 M CALCIUM CHLORIDE, 0.1 M BIS-TRIS AT PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.53350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.00650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.00650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 72.80025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.00650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.00650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.26675 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.00650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.00650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 72.80025 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.00650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.00650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.26675 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 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 48.53350 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: 270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 21 38.10 -99.06 REMARK 500 PRO A 56 7.57 -62.30 REMARK 500 ASP A 92 58.27 -102.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 317 DISTANCE = 5.87 ANGSTROMS DBREF 8BL3 A 0 140 PDB 8BL3 8BL3 0 140 SEQRES 1 A 141 MET GLY ARG VAL GLU VAL ARG VAL GLU PHE GLU GLY ASP SEQRES 2 A 141 LYS MET ARG VAL ARG LEU ARG ASN ASP SER SER THR PRO SEQRES 3 A 141 VAL GLU VAL HIS ILE LYS VAL GLY ASP GLU LYS ARG THR SEQRES 4 A 141 VAL THR VAL ASN PRO GLY GLU GLU VAL GLU VAL THR PHE SEQRES 5 A 141 SER ALA ASN ASP PRO HIS LYS PHE ASN ARG PRO GLN PHE SEQRES 6 A 141 THR ILE GLU TRP GLY GLY GLY GLY ARG VAL GLU VAL ARG SEQRES 7 A 141 VAL GLU PHE GLU GLY ASP LYS MET ARG VAL ARG LEU ARG SEQRES 8 A 141 ASN ASP SER SER THR PRO VAL GLU VAL HIS ILE LYS VAL SEQRES 9 A 141 GLY ASP GLU LYS ARG THR VAL THR VAL ASN PRO GLY GLU SEQRES 10 A 141 GLU VAL GLU VAL THR PHE SER ALA ASN ASP PRO HIS LYS SEQRES 11 A 141 PHE ASN ARG PRO GLN PHE THR ILE GLU TRP GLY HET GOL A 201 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *17(H2 O) HELIX 1 AA1 HIS A 57 ARG A 61 5 5 HELIX 2 AA2 ASP A 126 ASN A 131 5 6 SHEET 1 AA1 6 GLU A 46 SER A 52 0 SHEET 2 AA1 6 LYS A 13 ASP A 21 -1 N LEU A 18 O VAL A 47 SHEET 3 AA1 6 ARG A 2 GLU A 10 -1 N ARG A 6 O ARG A 17 SHEET 4 AA1 6 GLN A 134 TRP A 139 -1 O PHE A 135 N VAL A 5 SHEET 5 AA1 6 VAL A 97 VAL A 103 -1 N HIS A 100 O THR A 136 SHEET 6 AA1 6 GLU A 106 VAL A 112 -1 O ARG A 108 N ILE A 101 SHEET 1 AA2 6 GLU A 35 VAL A 41 0 SHEET 2 AA2 6 VAL A 26 VAL A 32 -1 N ILE A 30 O ARG A 37 SHEET 3 AA2 6 GLN A 63 TRP A 68 -1 O GLU A 67 N GLU A 27 SHEET 4 AA2 6 GLY A 72 GLU A 81 -1 O VAL A 76 N PHE A 64 SHEET 5 AA2 6 LYS A 84 ASP A 92 -1 O ASP A 92 N ARG A 73 SHEET 6 AA2 6 GLU A 117 SER A 123 -1 O VAL A 118 N LEU A 89 CRYST1 72.013 72.013 97.067 90.00 90.00 90.00 P 43 21 2 8 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 0.013886 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013886 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010302 0.00000