HEADER STRUCTURAL PROTEIN 08-MAR-25 9M6Y TITLE CRYSTAL STRUCTURE OF C1 DOMAIN FROM SURFACE PROTEIN SLPM OF TITLE 2 LACTOBACILLUS BREVIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SURFACE LAYER PROTEIN SLPM; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C1 DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: IT WAS EXPRESSED WITH SUMO TAG, AND AFTER CLEAVAGE, AN COMPND 7 N-TERMINAL SER IS LEFT. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEVILACTOBACILLUS BREVIS; SOURCE 3 ORGANISM_TAXID: 1580; SOURCE 4 GENE: SLPM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28A-SUMO KEYWDS SELF-ASSEMBLY, SURFACE PROTEIN, S-LAYER PROTEIN, DIMERIZATION, KEYWDS 2 STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.XUE,X.KANG REVDAT 1 11-JUN-25 9M6Y 0 JRNL AUTH Y.XUE,X.KANG JRNL TITL CRYSTAL STRUCTURE OF THE C1 DOMAIN OF THE SURFACE-LAYER JRNL TITL 2 PROTEIN SLPM FROM LACTOBACILLUS BREVIS: A MODULE INVOLVED IN JRNL TITL 3 PROTEIN SELF-ASSEMBLY. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 81 255 2025 JRNL REFN ESSN 2053-230X JRNL PMID 40371669 JRNL DOI 10.1107/S2053230X25004194 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18625 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 927 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 27.6000 - 3.2500 1.00 2572 105 0.1454 0.1809 REMARK 3 2 3.2500 - 2.5800 1.00 2536 111 0.1728 0.2152 REMARK 3 3 2.5800 - 2.2500 1.00 2488 174 0.1759 0.2287 REMARK 3 4 2.2500 - 2.0500 1.00 2541 142 0.1700 0.2194 REMARK 3 5 2.0500 - 1.9000 1.00 2512 118 0.2001 0.2292 REMARK 3 6 1.9000 - 1.7900 1.00 2540 135 0.2471 0.3079 REMARK 3 7 1.7900 - 1.7000 0.99 2509 142 0.3212 0.3548 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1379 REMARK 3 ANGLE : 0.519 1894 REMARK 3 CHIRALITY : 0.039 229 REMARK 3 PLANARITY : 0.002 256 REMARK 3 DIHEDRAL : 5.471 199 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 235 THROUGH 326) REMARK 3 ORIGIN FOR THE GROUP (A): -0.3336 -0.3462 -0.0380 REMARK 3 T TENSOR REMARK 3 T11: 0.0235 T22: 0.0306 REMARK 3 T33: 0.0327 T12: -0.0063 REMARK 3 T13: -0.0099 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.2265 L22: 0.1909 REMARK 3 L33: 0.4081 L12: -0.1447 REMARK 3 L13: -0.2959 L23: 0.2342 REMARK 3 S TENSOR REMARK 3 S11: 0.0123 S12: -0.0038 S13: -0.0115 REMARK 3 S21: 0.0288 S22: 0.0033 S23: -0.0209 REMARK 3 S31: 0.0343 S32: 0.0304 S33: 0.0043 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 235 THROUGH 326) REMARK 3 ORIGIN FOR THE GROUP (A): -5.0358 20.0219 20.5897 REMARK 3 T TENSOR REMARK 3 T11: 0.0514 T22: 0.0337 REMARK 3 T33: 0.0348 T12: 0.0003 REMARK 3 T13: 0.0014 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.5175 L22: 0.1858 REMARK 3 L33: 0.4726 L12: -0.1161 REMARK 3 L13: -0.3969 L23: 0.2557 REMARK 3 S TENSOR REMARK 3 S11: -0.0077 S12: -0.0458 S13: 0.0280 REMARK 3 S21: -0.0101 S22: 0.0398 S23: 0.0069 REMARK 3 S31: -0.0092 S32: 0.0641 S33: 0.0022 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 9M6Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 11-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057292. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-25 REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER D8 QUEST REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON III REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18676 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 27.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 19.00 REMARK 200 R MERGE (I) : 0.23290 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 REMARK 200 R MERGE FOR SHELL (I) : 1.76300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.910 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2 0.1 M TRIS PH 8.5 30% PEG REMARK 280 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 236 CD CE NZ REMARK 470 LYS A 301 CG CD CE NZ REMARK 470 LYS B 236 CG CD CE NZ REMARK 470 LYS B 248 CD CE NZ REMARK 470 LYS B 301 CG CD CE NZ 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 OE2 GLU A 281 O HOH A 401 1.90 REMARK 500 O HOH A 428 O HOH A 432 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 THR A 272 -73.20 -87.59 REMARK 500 THR B 272 -70.15 -86.46 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 608 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 609 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH A 610 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH B 600 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH B 601 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH B 602 DISTANCE = 6.79 ANGSTROMS DBREF 9M6Y A 236 326 UNP H9BQS1 H9BQS1_LEVBR 236 326 DBREF 9M6Y B 236 326 UNP H9BQS1 H9BQS1_LEVBR 236 326 SEQADV 9M6Y SER A 235 UNP H9BQS1 EXPRESSION TAG SEQADV 9M6Y SER B 235 UNP H9BQS1 EXPRESSION TAG SEQRES 1 A 92 SER LYS ALA SER GLN VAL LYS VAL ASN ILE ASN ASN LEU SEQRES 2 A 92 LYS GLY GLU THR LEU LYS SER PHE ASN TYR ASN VAL GLY SEQRES 3 A 92 THR ASN ALA THR ASN THR ASN ALA VAL ASP GLY THR VAL SEQRES 4 A 92 TYR ASN SER THR ALA THR PRO GLU HIS PHE ALA GLN GLY SEQRES 5 A 92 PHE ALA ASP THR VAL ASN ASN ALA LEU ALA GLY THR GLY SEQRES 6 A 92 TYR LYS VAL ASP GLY ASP ASN ALA LEU ASN HIS VAL ALA SEQRES 7 A 92 ASN LEU LYS SER GLY SER THR LEU THR ILE TYR ALA THR SEQRES 8 A 92 GLU SEQRES 1 B 92 SER LYS ALA SER GLN VAL LYS VAL ASN ILE ASN ASN LEU SEQRES 2 B 92 LYS GLY GLU THR LEU LYS SER PHE ASN TYR ASN VAL GLY SEQRES 3 B 92 THR ASN ALA THR ASN THR ASN ALA VAL ASP GLY THR VAL SEQRES 4 B 92 TYR ASN SER THR ALA THR PRO GLU HIS PHE ALA GLN GLY SEQRES 5 B 92 PHE ALA ASP THR VAL ASN ASN ALA LEU ALA GLY THR GLY SEQRES 6 B 92 TYR LYS VAL ASP GLY ASP ASN ALA LEU ASN HIS VAL ALA SEQRES 7 B 92 ASN LEU LYS SER GLY SER THR LEU THR ILE TYR ALA THR SEQRES 8 B 92 GLU FORMUL 3 HOH *412(H2 O) HELIX 1 AA1 ALA A 284 LEU A 295 1 12 HELIX 2 AA2 ASN A 306 HIS A 310 5 5 HELIX 3 AA3 ALA B 284 LEU B 295 1 12 HELIX 4 AA4 ASN B 306 HIS B 310 5 5 SHEET 1 AA1 3 THR A 251 ASN A 258 0 SHEET 2 AA1 3 GLN A 239 ASN A 245 -1 N ILE A 244 O LEU A 252 SHEET 3 AA1 3 THR A 319 TYR A 323 1 O LEU A 320 N LYS A 241 SHEET 1 AA2 3 THR B 251 ASN B 258 0 SHEET 2 AA2 3 GLN B 239 ASN B 245 -1 N ILE B 244 O LEU B 252 SHEET 3 AA2 3 THR B 319 TYR B 323 1 O LEU B 320 N LYS B 241 CRYST1 30.065 37.804 42.058 85.85 84.92 66.91 P 1 2 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 0.033261 -0.014178 -0.002377 0.00000 SCALE2 0.000000 0.028755 -0.001182 0.00000 SCALE3 0.000000 0.000000 0.023891 0.00000 MASTER 277 0 0 4 6 0 0 6 1752 2 0 16 END