HEADER STRUCTURAL PROTEIN 02-DEC-21 7QEC TITLE CRYSTAL STRUCTURE OF SLPA - DOMAIN II, DOMAIN THAT IS INVOLVED IN THE TITLE 2 SELF-ASSEMBLY OF THE S-LAYER FROM LACTOBACILLUS AMYLOVORUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-LAYER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS AMYLOVORUS (STRAIN GRL 1112); SOURCE 3 ORGANISM_TAXID: 695560; SOURCE 4 STRAIN: GRL 1112; SOURCE 5 GENE: LA2_00970; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS S-LAYER, SELF-ASSEMBLY, LACTOBACILLUS AMYLOVORUS, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.EDER,A.DORDIC,C.MILLAN,T.SAGMEISTER,I.USON,T.PAVKOV-KELLER REVDAT 2 19-JUN-24 7QEC 1 JRNL REVDAT 1 14-DEC-22 7QEC 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. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 14654 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1469 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 35.6100 - 4.2000 1.00 1346 146 0.1695 0.2601 REMARK 3 2 4.2000 - 3.3400 1.00 1353 158 0.1736 0.1944 REMARK 3 3 3.3400 - 2.9100 1.00 1358 148 0.1810 0.2526 REMARK 3 4 2.9100 - 2.6500 1.00 1355 149 0.1837 0.2211 REMARK 3 5 2.6500 - 2.4600 1.00 1324 154 0.1921 0.2680 REMARK 3 6 2.4600 - 2.3100 1.00 1355 145 0.2022 0.2593 REMARK 3 7 2.3100 - 2.2000 1.00 1361 158 0.2070 0.2311 REMARK 3 8 2.2000 - 2.1000 1.00 1321 144 0.2121 0.3403 REMARK 3 9 2.1000 - 2.0200 1.00 1347 149 0.2310 0.2829 REMARK 3 10 2.0200 - 1.9500 0.78 1065 118 0.2311 0.2617 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) : 0.234 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.908 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.76 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 : 0.008 786 REMARK 3 ANGLE : 0.779 1072 REMARK 3 CHIRALITY : 0.059 135 REMARK 3 PLANARITY : 0.005 139 REMARK 3 DIHEDRAL : 2.714 628 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 7QEC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1292119478. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-12 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 : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14655 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 35.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 18.90 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.90000 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: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS SCREEN CONDITION #1-24 (30 MM REMARK 280 OF EACH HALOGEN (SODIUM FLUORIDE, SODIUM BROMIDE AND SODIUM REMARK 280 IODIDE), 0.1 M BICINE/TRIZMA BASE PH 8.5 WITH 12.5% V/V MPD, REMARK 280 12.5 % PEG 1000 AND 12.5 % W/V PEG 3350). PROTEIN STOCK SOLUTION REMARK 280 OF 4.18 MG/ML IN 10 MM HEPES PH 7 AND 50 MM NACL. DROPS: 0.5 + REMARK 280 0.5UL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 71.22050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 19.31650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 19.31650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.61025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 19.31650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 19.31650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 106.83075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 19.31650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.31650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.61025 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 19.31650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.31650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 106.83075 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 71.22050 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: 1770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 401 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 413 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 443 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 ASN A 261 REMARK 465 GLY A 262 REMARK 465 ALA A 263 REMARK 465 SER A 264 REMARK 465 ALA A 310 REMARK 465 GLN A 311 REMARK 465 ASN A 312 REMARK 465 ALA A 313 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 OG1 THR A 233 OD1 ASN A 265 5555 1.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 7QEC A 213 326 UNP E4SK47 E4SK47_LACAR 213 326 SEQRES 1 A 114 SER VAL SER PHE TYR GLU ILE ALA ASN GLY ASN GLU VAL SEQRES 2 A 114 HIS THR GLY SER LEU ASN MET THR ALA ASN PRO THR SER SEQRES 3 A 114 HIS GLU LEU ASN VAL SER ALA VAL LEU ALA ALA ALA LYS SEQRES 4 A 114 ALA LYS TYR ALA ALA HIS GLN LEU GLU ASN GLY ALA SER SEQRES 5 A 114 ASN GLY ALA SER VAL ALA VAL THR THR ASP VAL LYS ASP SEQRES 6 A 114 LEU THR ASP GLN LEU THR LYS ALA GLY ILE LYS VAL ASP SEQRES 7 A 114 PRO LEU GLY ASN PHE GLN ALA GLN ALA SER PHE SER PHE SEQRES 8 A 114 ASN LEU ALA ALA LYS SER ALA GLN ASN ALA ALA THR ALA SEQRES 9 A 114 THR LEU PRO ILE THR VAL SER VAL ALA ASN FORMUL 2 HOH *45(H2 O) HELIX 1 AA1 VAL A 243 LYS A 253 1 11 HELIX 2 AA2 ASP A 274 LYS A 284 1 11 SHEET 1 AA1 7 GLU A 224 VAL A 225 0 SHEET 2 AA1 7 VAL A 214 GLU A 218 -1 N PHE A 216 O VAL A 225 SHEET 3 AA1 7 TYR A 254 GLN A 258 -1 O HIS A 257 N SER A 215 SHEET 4 AA1 7 ALA A 267 VAL A 271 -1 O ALA A 267 N GLN A 258 SHEET 5 AA1 7 SER A 300 LYS A 308 -1 O LYS A 308 N ALA A 270 SHEET 6 AA1 7 ALA A 316 VAL A 324 -1 O VAL A 322 N PHE A 301 SHEET 7 AA1 7 GLY A 228 MET A 232 1 N GLY A 228 O PRO A 319 SHEET 1 AA2 2 GLU A 240 ASN A 242 0 SHEET 2 AA2 2 ASN A 294 GLN A 296 -1 O PHE A 295 N LEU A 241 CRYST1 38.633 38.633 142.441 90.00 90.00 90.00 P 41 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 0.025885 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025885 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007020 0.00000