HEADER STRUCTURAL PROTEIN 24-SEP-19 6SX1 TITLE STRUCTURE OF RIB STANDARD, A RIB DOMAIN FROM LACTOBACILLUS ACIDOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SURFACE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: RIB STANDARD (RESIDUES 1269-1351) FROM LACTOBACILLUS COMPND 6 ACIDOPHILUS, RECOMBINANTLY OVEREXPRESSED AND PURIFIED USING THE COMPND 7 PET_FPP1 VECTOR IN ESCHERICHIA COLI SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS ACIDOPHILUS (STRAIN ATCC 700396 / SOURCE 3 NCK56 / N2 / NCFM); SOURCE 4 ORGANISM_TAXID: 272621; SOURCE 5 STRAIN: ATCC 700396 / NCK56 / N2 / NCFM; SOURCE 6 GENE: LBA1633; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET_FPP1 KEYWDS RIB DOMAIN, BACTERIAL CELL SURFACE, IMMUNOGLOBULIN FOLD, PROFILE-HMM, KEYWDS 2 DOMAIN ATROPHY, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.E.M.COOPER,S.C.GRIFFITHS,J.P.TURKENBURG,A.BATEMAN,J.R.POTTS REVDAT 3 19-JUN-24 6SX1 1 REMARK REVDAT 2 21-DEC-22 6SX1 1 JRNL REVDAT 1 18-DEC-19 6SX1 0 JRNL AUTH F.WHELAN,A.LAFITA,S.C.GRIFFITHS,R.E.M.COOPER, JRNL AUTH 2 J.L.WHITTINGHAM,J.P.TURKENBURG,I.W.MANFIELD,A.N.ST JOHN, JRNL AUTH 3 E.PACI,A.BATEMAN,J.R.POTTS JRNL TITL DEFINING THE REMARKABLE STRUCTURAL MALLEABILITY OF A JRNL TITL 2 BACTERIAL SURFACE PROTEIN RIB DOMAIN IMPLICATED IN JRNL TITL 3 INFECTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 116 26540 2019 JRNL REFN ESSN 1091-6490 JRNL PMID 31818940 JRNL DOI 10.1073/PNAS.1911776116 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 17665 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 585 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6SX1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1292104016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-19 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17774 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 31.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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 (%): 30.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULPHATE, 2M SODIUM REMARK 280 CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 15.09150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.40550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.32200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.40550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.09150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.32200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 1348 REMARK 465 THR A 1349 REMARK 465 THR A 1350 REMARK 465 PRO A 1351 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 O HOH A 1403 O HOH A 1430 1.58 REMARK 500 O HOH A 1454 O HOH A 1456 1.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 6SX1 A 1269 1351 UNP Q5FIM8 Q5FIM8_LACAC 1269 1351 SEQRES 1 A 83 GLY GLN THR ASP ALA ASP LYS TYR THR PRO GLU ALA LYS SEQRES 2 A 83 ASP ILE THR VAL THR PRO GLY PRO THR PRO ASP PRO ALA SEQRES 3 A 83 GLU GLY ILE GLY ASN LYS ASP THR LEU PRO SER GLY THR SEQRES 4 A 83 LYS TYR GLU TRP LYS ASP PRO VAL ASP THR THR THR PRO SEQRES 5 A 83 GLY ASP LYS THR GLY THR ILE VAL VAL SER TYR PRO ASP SEQRES 6 A 83 GLY SER THR ASP GLU ILE GLN VAL THR VAL LYS VAL THR SEQRES 7 A 83 ASP PRO THR THR PRO FORMUL 2 HOH *75(H2 O) HELIX 1 AA1 THR A 1271 LYS A 1275 5 5 HELIX 2 AA2 ASP A 1292 ILE A 1297 5 6 HELIX 3 AA3 ASN A 1299 LEU A 1303 5 5 SHEET 1 AA1 4 ILE A1283 VAL A1285 0 SHEET 2 AA1 4 THR A1336 VAL A1345 1 O LYS A1344 N ILE A1283 SHEET 3 AA1 4 GLY A1321 SER A1330 -1 N ILE A1327 O ILE A1339 SHEET 4 AA1 4 LYS A1308 TRP A1311 -1 N GLU A1310 O VAL A1328 CRYST1 30.183 32.644 62.811 90.00 90.00 90.00 P 21 21 21 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 0.033131 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015921 0.00000