HEADER PROTEIN BINDING 13-JUN-22 8DAB TITLE COEVOLVED AFFIBODY-Z DOMAIN PAIR LL2.C17 COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN G-BINDING PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IGG-BINDING PROTEIN A,STAPHYLOCOCCAL PROTEIN A,SPA; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: AFFIBODY LL2.IVVY; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: SPA; 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 AFFIBODY, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR K.M.JUDE,A.YANG,K.C.GARCIA REVDAT 3 22-NOV-23 8DAB 1 TITLE REVDAT 2 09-AUG-23 8DAB 1 JRNL REVDAT 1 26-JUL-23 8DAB 0 JRNL AUTH A.YANG,K.M.JUDE,B.LAI,M.MINOT,A.M.KOCYLA,C.R.GLASSMAN, JRNL AUTH 2 D.NISHIMIYA,Y.S.KIM,S.T.REDDY,A.A.KHAN,K.C.GARCIA JRNL TITL DEPLOYING SYNTHETIC COEVOLUTION AND MACHINE LEARNING TO JRNL TITL 2 ENGINEER PROTEIN-PROTEIN INTERACTIONS. JRNL REF SCIENCE V. 381 H1720 2023 JRNL REFN ESSN 1095-9203 JRNL PMID 37499032 JRNL DOI 10.1126/SCIENCE.ADH1720 REMARK 2 REMARK 2 RESOLUTION. 1.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 60.8 REMARK 3 NUMBER OF REFLECTIONS : 27307 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1528 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 31.6500 - 2.5200 0.98 3892 233 0.1635 0.1800 REMARK 3 2 2.5200 - 2.0000 0.97 3782 225 0.1515 0.1752 REMARK 3 3 2.0000 - 1.7500 0.99 3799 227 0.1624 0.1910 REMARK 3 4 1.7500 - 1.5900 0.96 3715 221 0.1785 0.2302 REMARK 3 5 1.5900 - 1.4800 0.80 3089 184 0.1850 0.2464 REMARK 3 6 1.4800 - 1.3900 0.65 2492 158 0.2207 0.2656 REMARK 3 7 1.3900 - 1.3200 0.53 2031 120 0.2582 0.2719 REMARK 3 8 1.3200 - 1.2600 0.39 1509 83 0.2853 0.2859 REMARK 3 9 1.2600 - 1.2100 0.25 954 46 0.3201 0.4086 REMARK 3 10 1.2100 - 1.1700 0.11 414 25 0.3918 0.4714 REMARK 3 11 1.1700 - 1.1340 0.03 102 6 0.3784 0.4824 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) : 0.107 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.777 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.88 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 : 0.007 905 REMARK 3 ANGLE : 0.828 1238 REMARK 3 CHIRALITY : 0.056 134 REMARK 3 PLANARITY : 0.009 167 REMARK 3 DIHEDRAL : 12.638 352 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 8DAB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1000266212. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.77488 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 : DIALS, XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27318 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.134 REMARK 200 RESOLUTION RANGE LOW (A) : 31.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 60.8 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.09152 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 3.1 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 4.14100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.210 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: 5DJT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.3 M AMM2HPO4, 100 MM TRIS PH 8.2 REMARK 280 CRYOPROTECTED IN 30% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 38.54550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.76600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.54550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.76600 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: 1680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 147 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 171 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 108 LIES ON A SPECIAL POSITION. 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 ALA A 0 REMARK 465 VAL A 1 REMARK 465 ASP A 2 REMARK 465 ASN A 3 REMARK 465 LYS A 4 REMARK 465 PHE A 5 REMARK 465 ASN A 6 REMARK 465 LEU A 59 REMARK 465 GLU A 60 REMARK 465 HIS A 61 REMARK 465 HIS A 62 REMARK 465 HIS A 63 REMARK 465 HIS A 64 REMARK 465 HIS A 65 REMARK 465 HIS A 66 REMARK 465 ALA B 0 REMARK 465 VAL B 1 REMARK 465 ASP B 2 REMARK 465 LYS B 58 REMARK 465 LEU B 59 REMARK 465 GLU B 60 REMARK 465 HIS B 61 REMARK 465 HIS B 62 REMARK 465 HIS B 63 REMARK 465 HIS B 64 REMARK 465 HIS B 65 REMARK 465 HIS B 66 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 7 CG CD CE NZ REMARK 470 ASN B 3 CG OD1 ND2 REMARK 470 LYS B 4 CG CD CE NZ REMARK 470 GLU B 8 CG CD OE1 OE2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8DA3 RELATED DB: PDB REMARK 900 RELATED ID: 8DA4 RELATED DB: PDB REMARK 900 RELATED ID: 8DA5 RELATED DB: PDB REMARK 900 RELATED ID: 8DA6 RELATED DB: PDB REMARK 900 RELATED ID: 8DA7 RELATED DB: PDB REMARK 900 RELATED ID: 8DA8 RELATED DB: PDB REMARK 900 RELATED ID: 8DA9 RELATED DB: PDB REMARK 900 RELATED ID: 8DAC RELATED DB: PDB DBREF 8DAB A 2 58 UNP P38507 SPA_STAAU 213 269 DBREF 8DAB B 0 66 PDB 8DAB 8DAB 0 66 SEQADV 8DAB ALA A 0 UNP P38507 EXPRESSION TAG SEQADV 8DAB VAL A 1 UNP P38507 EXPRESSION TAG SEQADV 8DAB VAL A 9 UNP P38507 GLN 220 ENGINEERED MUTATION SEQADV 8DAB ALA A 29 UNP P38507 GLY 240 ENGINEERED MUTATION SEQADV 8DAB VAL A 31 UNP P38507 ILE 242 ENGINEERED MUTATION SEQADV 8DAB LEU A 59 UNP P38507 EXPRESSION TAG SEQADV 8DAB GLU A 60 UNP P38507 EXPRESSION TAG SEQADV 8DAB HIS A 61 UNP P38507 EXPRESSION TAG SEQADV 8DAB HIS A 62 UNP P38507 EXPRESSION TAG SEQADV 8DAB HIS A 63 UNP P38507 EXPRESSION TAG SEQADV 8DAB HIS A 64 UNP P38507 EXPRESSION TAG SEQADV 8DAB HIS A 65 UNP P38507 EXPRESSION TAG SEQADV 8DAB HIS A 66 UNP P38507 EXPRESSION TAG SEQRES 1 A 67 ALA VAL ASP ASN LYS PHE ASN LYS GLU VAL GLN ASN ALA SEQRES 2 A 67 PHE TYR GLU ILE LEU HIS LEU PRO ASN LEU ASN GLU GLU SEQRES 3 A 67 GLN ARG ASN ALA PHE VAL GLN SER LEU MLY ASP ASP PRO SEQRES 4 A 67 SER GLN SER ALA ASN LEU LEU ALA GLU ALA MLY MLY LEU SEQRES 5 A 67 ASN ASP ALA GLN ALA PRO MLY LEU GLU HIS HIS HIS HIS SEQRES 6 A 67 HIS HIS SEQRES 1 B 67 ALA VAL ASP ASN LYS PHE ASN LYS GLU ILE SER VAL ALA SEQRES 2 B 67 GLY ARG GLU ILE VAL THR LEU PRO ASN LEU ASN ASP PRO SEQRES 3 B 67 GLN MLY LYS ALA PHE VAL TYR SER LEU TRP ASP ASP PRO SEQRES 4 B 67 SER GLN SER ALA ASN LEU LEU ALA GLU ALA MLY MLY LEU SEQRES 5 B 67 ASN ASP ALA GLN ALA PRO LYS LEU GLU HIS HIS HIS HIS SEQRES 6 B 67 HIS HIS MODRES 8DAB MLY A 35 LYS MODIFIED RESIDUE MODRES 8DAB MLY A 49 LYS MODIFIED RESIDUE MODRES 8DAB MLY A 50 LYS MODIFIED RESIDUE MODRES 8DAB MLY A 58 LYS MODIFIED RESIDUE HET MLY A 35 27 HET MLY A 49 27 HET MLY A 50 27 HET MLY A 58 26 HET MLY B 27 27 HET MLY B 49 49 HET MLY B 50 27 HETNAM MLY N-DIMETHYL-LYSINE FORMUL 1 MLY 7(C8 H18 N2 O2) FORMUL 3 HOH *148(H2 O) HELIX 1 AA1 LYS A 7 LEU A 19 1 13 HELIX 2 AA2 ASN A 23 ASP A 37 1 15 HELIX 3 AA3 GLN A 40 GLN A 55 1 16 HELIX 4 AA4 LYS B 4 THR B 18 1 15 HELIX 5 AA5 ASN B 23 ASP B 37 1 15 HELIX 6 AA6 GLN B 40 GLN B 55 1 16 LINK C LEU A 34 N MLY A 35 1555 1555 1.33 LINK C MLY A 35 N ASP A 36 1555 1555 1.33 LINK C ALA A 48 N MLY A 49 1555 1555 1.33 LINK C MLY A 49 N MLY A 50 1555 1555 1.33 LINK C MLY A 50 N LEU A 51 1555 1555 1.32 LINK C PRO A 57 N MLY A 58 1555 1555 1.33 LINK C GLN B 26 N MLY B 27 1555 1555 1.33 LINK C MLY B 27 N LYS B 28 1555 1555 1.33 LINK C ALA B 48 N MLY B 49 1555 1555 1.34 LINK C MLY B 49 N MLY B 50 1555 1555 1.32 LINK C MLY B 50 N LEU B 51 1555 1555 1.32 CRYST1 77.091 35.532 49.433 90.00 115.42 90.00 C 1 2 1 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 0.012972 0.000000 0.006165 0.00000 SCALE2 0.000000 0.028144 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022398 0.00000