HEADER PROTEIN BINDING 13-JUN-22 8DA8 TITLE COEVOLVED AFFIBODY-Z DOMAIN PAIR LL2.C1 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.FIIK; 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 2 09-AUG-23 8DA8 1 JRNL REVDAT 1 26-JUL-23 8DA8 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. 1.29 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) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 22123 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1129 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 26.4600 - 2.5800 0.96 2712 147 0.1762 0.2012 REMARK 3 2 2.5800 - 2.0500 0.93 2569 142 0.2029 0.2027 REMARK 3 3 2.0500 - 1.7900 0.96 2689 136 0.2315 0.2650 REMARK 3 4 1.7900 - 1.6300 0.97 2689 137 0.2470 0.3315 REMARK 3 5 1.6300 - 1.5100 0.90 2472 142 0.2598 0.2780 REMARK 3 6 1.5100 - 1.4200 0.95 2641 142 0.2903 0.3091 REMARK 3 7 1.4200 - 1.3500 0.95 2616 139 0.3330 0.3535 REMARK 3 8 1.3500 - 1.2900 0.95 2606 144 0.3505 0.3695 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) : 0.179 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.60 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 : 0.012 940 REMARK 3 ANGLE : 1.161 1276 REMARK 3 CHIRALITY : 0.081 139 REMARK 3 PLANARITY : 0.008 173 REMARK 3 DIHEDRAL : 14.736 362 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 8DA8 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_1000266208. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.82653 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, XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22160 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 26.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.06021 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 1.30400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.860 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 (%): 19.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5 M AMMONIUM SULFATE 100 MM HEPES PH REMARK 280 7.0 CRYOPROTECTED WITH 30% GLYCEROL, VAPOR DIFFUSION, SITTING REMARK 280 DROP, 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 25.12550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.27800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.12550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.27800 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: 1550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 143 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 PRO A 57 REMARK 465 LYS A 58 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 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 B 7 CD CE NZ REMARK 470 GLU B 8 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 15 O HOH A 101 2.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 201 O HOH B 228 2657 2.09 REMARK 500 REMARK 500 REMARK: NULL 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: 8DA9 RELATED DB: PDB REMARK 900 RELATED ID: 8DAA RELATED DB: PDB REMARK 900 RELATED ID: 8DAB RELATED DB: PDB REMARK 900 RELATED ID: 8DAC RELATED DB: PDB DBREF 8DA8 A 2 58 UNP P38507 SPA_STAAU 213 269 DBREF 8DA8 B 0 66 PDB 8DA8 8DA8 0 66 SEQADV 8DA8 ALA A 0 UNP P38507 EXPRESSION TAG SEQADV 8DA8 VAL A 1 UNP P38507 EXPRESSION TAG SEQADV 8DA8 LEU A 9 UNP P38507 GLN 220 ENGINEERED MUTATION SEQADV 8DA8 VAL A 13 UNP P38507 PHE 224 ENGINEERED MUTATION SEQADV 8DA8 ALA A 29 UNP P38507 GLY 240 ENGINEERED MUTATION SEQADV 8DA8 PHE A 31 UNP P38507 ILE 242 ENGINEERED MUTATION SEQADV 8DA8 LEU A 59 UNP P38507 EXPRESSION TAG SEQADV 8DA8 GLU A 60 UNP P38507 EXPRESSION TAG SEQADV 8DA8 HIS A 61 UNP P38507 EXPRESSION TAG SEQADV 8DA8 HIS A 62 UNP P38507 EXPRESSION TAG SEQADV 8DA8 HIS A 63 UNP P38507 EXPRESSION TAG SEQADV 8DA8 HIS A 64 UNP P38507 EXPRESSION TAG SEQADV 8DA8 HIS A 65 UNP P38507 EXPRESSION TAG SEQADV 8DA8 HIS A 66 UNP P38507 EXPRESSION TAG SEQRES 1 A 67 ALA VAL ASP ASN LYS PHE ASN LYS GLU LEU GLN ASN ALA SEQRES 2 A 67 VAL TYR GLU ILE LEU HIS LEU PRO ASN LEU ASN GLU GLU SEQRES 3 A 67 GLN ARG ASN ALA PHE PHE GLN SER LEU LYS ASP ASP PRO SEQRES 4 A 67 SER GLN SER ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU SEQRES 5 A 67 ASN ASP ALA GLN ALA PRO LYS 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 PHE SER VAL ALA SEQRES 2 B 67 GLY ARG GLU ILE ILE THR LEU PRO ASN LEU ASN ASP PRO SEQRES 3 B 67 GLN MLY MLY ALA PHE ILE MLY SER LEU TRP ASP ASP PRO SEQRES 4 B 67 SER GLN SER ALA ASN LEU LEU ALA GLU ALA MLY LYS LEU SEQRES 5 B 67 ASN ASP ALA GLN ALA PRO LYS LEU GLU HIS HIS HIS HIS SEQRES 6 B 67 HIS HIS HET MLY B 27 27 HET MLY B 28 27 HET MLY B 32 27 HET MLY B 49 27 HET GOL B 101 14 HETNAM MLY N-DIMETHYL-LYSINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MLY 4(C8 H18 N2 O2) FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *97(H2 O) HELIX 1 AA1 PHE A 5 LEU A 19 1 15 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 GLN B 26 N MLY B 27 1555 1555 1.32 LINK C MLY B 27 N MLY B 28 1555 1555 1.34 LINK C MLY B 28 N ALA B 29 1555 1555 1.34 LINK C ILE B 31 N MLY B 32 1555 1555 1.34 LINK C MLY B 32 N SER B 33 1555 1555 1.33 LINK C ALA B 48 N MLY B 49 1555 1555 1.35 LINK C MLY B 49 N LYS B 50 1555 1555 1.31 CRYST1 50.251 54.556 34.721 90.00 97.64 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 0.019900 0.000000 0.002669 0.00000 SCALE2 0.000000 0.018330 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029059 0.00000