HEADER CELL ADHESION 01-AUG-22 8ALU TITLE CRYSTAL STRUCTURE OF THE TEICHOIC ACID BINDING DOMAIN OF SLPA, S-LAYER TITLE 2 PROTEIN FROM LACTOBACILLUS ACIDOPHILUS (AA. 314-444) COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-LAYER PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS ACIDOPHILUS; SOURCE 3 ORGANISM_TAXID: 1579; SOURCE 4 GENE: CXB72_00965; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS S-LAYER, SURFACE LAYER, CELL WALL BINDING, TEICHOIC ACIDS, CELL KEYWDS 2 ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR M.EDER,A.DORDIC,T.SAGMEISTER,D.VEJZOVIC,T.PAVKOV-KELLER REVDAT 2 19-JUN-24 8ALU 1 JRNL REVDAT 1 16-AUG-23 8ALU 0 JRNL AUTH T.SAGMEISTER,N.GUBENSAK,C.BUHLHELLER,C.GRININGER,M.EDER, JRNL AUTH 2 A.ÐORDIC,C.MILLAN,A.MEDINA,P.A.S.MURCIA,F.BERNI, JRNL AUTH 3 U.HYNONEN,D.VEJZOVIC,E.DAMISCH,N.KULMINSKAYA,L.PETROWITSCH, JRNL AUTH 4 M.OBERER,A.PALVA,N.MALANOVIC,J.CODEE,W.KELLER,I.USON, JRNL AUTH 5 T.PAVKOV-KELLER JRNL TITL THE MOLECULAR ARCHITECTURE OF LACTOBACILLUS S-LAYER: JRNL TITL 2 ASSEMBLY AND ATTACHMENT TO TEICHOIC ACIDS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 121 86121 2024 JRNL REFN ESSN 1091-6490 JRNL PMID 38838019 JRNL DOI 10.1073/PNAS.2401686121 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.3 REMARK 3 NUMBER OF REFLECTIONS : 12330 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1228 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 40.2100 - 4.3500 0.91 1403 150 0.1596 0.2165 REMARK 3 2 4.3500 - 3.4600 0.95 1459 168 0.1773 0.2234 REMARK 3 3 3.4600 - 3.0200 0.95 1433 151 0.2097 0.2853 REMARK 3 4 3.0200 - 2.7400 0.94 1485 163 0.2383 0.2978 REMARK 3 5 2.7400 - 2.5500 0.94 1437 170 0.2818 0.2876 REMARK 3 6 2.5500 - 2.4000 0.93 1418 165 0.2600 0.3105 REMARK 3 7 2.4000 - 2.2800 0.70 1066 115 0.2639 0.2991 REMARK 3 8 2.2800 - 2.1800 0.51 796 85 0.3045 0.3839 REMARK 3 9 2.1800 - 2.0900 0.39 605 61 0.3286 0.3721 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.312 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.641 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.63 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 : 0.002 1071 REMARK 3 ANGLE : 0.398 1444 REMARK 3 CHIRALITY : 0.045 159 REMARK 3 PLANARITY : 0.001 178 REMARK 3 DIHEDRAL : 2.288 640 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 8ALU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1292124709. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95 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 : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12330 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 40.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.5 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 44.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.55500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.530 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 7QEH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: INDEX SCREEN CONDITION #80 (0.2 M REMARK 280 AMMONIUM ACETATE, 0.1 M HEPES PH 7.5 AND 25 % PEG 3350) WITH A REMARK 280 PROTEIN STOCK SOLUTION OF 20 MG/ML IN 20 MM ADA PH 6.5 AND 100 REMARK 280 MM NACL., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 40.21500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.52500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.21500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.52500 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: 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 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 636 LIES ON A SPECIAL POSITION. 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 TYR A 343 57.81 -109.75 REMARK 500 ILE A 379 -58.52 -124.73 REMARK 500 ASN A 401 -155.48 -160.56 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8ALU A 314 444 UNP A0A809K9V2_LACAI DBREF2 8ALU A A0A809K9V2 316 446 SEQRES 1 A 131 VAL ALA SER VAL SER LYS ARG ILE MET HIS ASN ALA TYR SEQRES 2 A 131 TYR TYR ASP LYS ASP ALA LYS ARG VAL GLY THR ASP SER SEQRES 3 A 131 VAL LYS ARG TYR ASN SER VAL SER VAL LEU PRO ASN THR SEQRES 4 A 131 THR THR ILE ASN GLY LYS THR TYR TYR GLN VAL VAL GLU SEQRES 5 A 131 ASN GLY LYS ALA VAL ASP LYS TYR ILE ASN ALA ALA ASN SEQRES 6 A 131 ILE ASP GLY THR LYS ARG THR LEU LYS HIS ASN ALA TYR SEQRES 7 A 131 VAL TYR ALA SER SER LYS LYS ARG ALA ASN LYS VAL VAL SEQRES 8 A 131 LEU LYS LYS GLY GLU VAL VAL THR THR TYR GLY ALA SER SEQRES 9 A 131 TYR THR PHE LYS ASN GLY GLN LYS TYR TYR LYS ILE GLY SEQRES 10 A 131 ASP ASN THR ASP LYS THR TYR VAL LYS VAL ALA ASN PHE SEQRES 11 A 131 ARG HET PO4 A 501 5 HET PO4 A 502 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 2(O4 P 3-) FORMUL 4 HOH *45(H2 O) HELIX 1 AA1 ALA A 377 ILE A 379 5 3 HELIX 2 AA2 ALA A 441 PHE A 443 5 3 SHEET 1 AA1 2 VAL A 317 ARG A 320 0 SHEET 2 AA1 2 SER A 345 VAL A 348 -1 O VAL A 346 N LYS A 319 SHEET 1 AA2 3 THR A 353 ILE A 355 0 SHEET 2 AA2 3 LYS A 358 GLU A 365 -1 O TYR A 360 N THR A 353 SHEET 3 AA2 3 LYS A 368 ASN A 375 -1 O LYS A 372 N VAL A 363 SHEET 1 AA3 2 THR A 382 THR A 385 0 SHEET 2 AA3 2 VAL A 410 THR A 413 -1 O VAL A 411 N ARG A 384 SHEET 1 AA4 2 ALA A 390 TYR A 393 0 SHEET 2 AA4 2 ARG A 399 LEU A 405 -1 O LEU A 405 N ALA A 390 SHEET 1 AA5 3 TYR A 418 THR A 419 0 SHEET 2 AA5 3 LYS A 425 LYS A 428 -1 O TYR A 426 N TYR A 418 SHEET 3 AA5 3 TYR A 437 LYS A 439 -1 O VAL A 438 N TYR A 427 CISPEP 1 ARG A 342 TYR A 343 0 -0.11 CRYST1 80.430 27.050 61.890 90.00 91.05 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 0.012433 0.000000 0.000227 0.00000 SCALE2 0.000000 0.036969 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016160 0.00000