HEADER TRANSPORT PROTEIN 22-JAN-18 5Z6C TITLE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS SUGAR-BINDING PROTEIN YESO TITLE 2 INVOLVED IN IMPORT OF RHAMNOGALACTURONAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN YESO; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS (STRAIN 168); SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YESO, BSU06970; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS ABC TRANSPORTER SUBSTRATE-BINDING PROTEIN, SUGAR TRANSPORT, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.SUGIURA,S.OIKI,B.MIKAMI,K.MURATA,W.HASHIMOTO REVDAT 2 22-NOV-23 5Z6C 1 REMARK REVDAT 1 23-JAN-19 5Z6C 0 JRNL AUTH H.SUGIURA,S.OIKI,B.MIKAMI,K.MURATA,W.HASHIMOTO JRNL TITL CRYSTAL STRUCTURE OF BACILLUS SUBTILIS SUGAR-BINDING PROTEIN JRNL TITL 2 YESO INVOLVED IN IMPORT OF RHAMNOGALACTURONAN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 21481 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1095 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 37.2678 - 3.9304 0.98 2554 146 0.1707 0.2020 REMARK 3 2 3.9304 - 3.1202 0.99 2542 159 0.1884 0.2665 REMARK 3 3 3.1202 - 2.7259 0.99 2556 127 0.2225 0.2652 REMARK 3 4 2.7259 - 2.4767 0.99 2578 139 0.2214 0.2630 REMARK 3 5 2.4767 - 2.2992 1.00 2558 138 0.2189 0.3208 REMARK 3 6 2.2992 - 2.1637 1.00 2557 148 0.2253 0.3042 REMARK 3 7 2.1637 - 2.0553 1.00 2595 128 0.2159 0.3015 REMARK 3 8 2.0553 - 1.9659 0.94 2446 110 0.1987 0.2731 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.890 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 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 : 0.007 3098 REMARK 3 ANGLE : 0.970 4193 REMARK 3 CHIRALITY : 0.054 451 REMARK 3 PLANARITY : 0.006 541 REMARK 3 DIHEDRAL : 7.835 1875 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 5Z6C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006412. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-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 : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42265 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.27800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.060 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4R6K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 23.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MIB (SODIUM MALONATE, IMIDAZOLE, REMARK 280 BORIC ACID) BUFFER (PH 6.0), 25% (W/V) PEG-1500, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 54.28900 REMARK 290 SMTRY3 2 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: 16880 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 MET A -19 REMARK 465 LYS A -18 REMARK 465 LYS A -17 REMARK 465 ILE A -16 REMARK 465 CYS A -15 REMARK 465 TYR A -14 REMARK 465 VAL A -13 REMARK 465 LEU A -12 REMARK 465 LEU A -11 REMARK 465 SER A -10 REMARK 465 LEU A -9 REMARK 465 VAL A -8 REMARK 465 CYS A -7 REMARK 465 VAL A -6 REMARK 465 PHE A -5 REMARK 465 LEU A -4 REMARK 465 PHE A -3 REMARK 465 SER A -2 REMARK 465 GLY A -1 REMARK 465 CYS A 0 REMARK 465 SER A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 GLU A 4 REMARK 465 GLU A 5 REMARK 465 ALA A 6 REMARK 465 SER A 7 REMARK 465 GLY A 8 REMARK 465 LYS A 9 REMARK 465 LYS A 10 REMARK 465 GLU A 11 REMARK 465 ASP A 12 REMARK 465 VAL A 13 REMARK 465 PRO A 225 REMARK 465 THR A 226 REMARK 465 PRO A 227 REMARK 465 ASP A 228 REMARK 465 GLU A 229 REMARK 465 SER A 230 REMARK 465 ALA A 231 REMARK 465 GLN A 232 REMARK 465 ILE A 233 REMARK 465 LYS A 234 REMARK 465 GLY A 235 REMARK 465 MET A 236 REMARK 465 GLU A 237 REMARK 465 ASP A 238 REMARK 465 LYS A 243 REMARK 465 GLY A 244 REMARK 465 LYS A 245 REMARK 465 ASN A 407 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 GLN A 67 39.43 -143.65 REMARK 500 ASN A 149 44.59 -154.63 REMARK 500 MET A 287 168.28 178.71 REMARK 500 LYS A 319 52.33 36.72 REMARK 500 ARG A 405 4.90 -68.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 5Z6C A -19 407 UNP O31518 YESO_BACSU 1 427 SEQRES 1 A 427 MET LYS LYS ILE CYS TYR VAL LEU LEU SER LEU VAL CYS SEQRES 2 A 427 VAL PHE LEU PHE SER GLY CYS SER ALA GLY GLU GLU ALA SEQRES 3 A 427 SER GLY LYS LYS GLU ASP VAL THR LEU ARG ILE ALA TRP SEQRES 4 A 427 TRP GLY GLY GLN PRO ARG HIS ASP TYR THR THR LYS VAL SEQRES 5 A 427 ILE GLU LEU TYR GLU LYS LYS ASN PRO HIS VAL HIS ILE SEQRES 6 A 427 GLU ALA GLU PHE ALA ASN TRP ASP ASP TYR TRP LYS LYS SEQRES 7 A 427 LEU ALA PRO MET SER ALA ALA GLY GLN LEU PRO ASP VAL SEQRES 8 A 427 ILE GLN MET ASP THR ALA TYR LEU ALA GLN TYR GLY LYS SEQRES 9 A 427 LYS ASN GLN LEU GLU ASP LEU THR PRO TYR THR LYS ASP SEQRES 10 A 427 GLY THR ILE ASP VAL SER SER ILE ASP GLU ASN MET LEU SEQRES 11 A 427 SER GLY GLY LYS ILE ASP ASN LYS LEU TYR GLY PHE THR SEQRES 12 A 427 LEU GLY VAL ASN VAL LEU SER VAL ILE ALA ASN GLU ASP SEQRES 13 A 427 LEU LEU LYS LYS ALA GLY VAL SER ILE ASN GLN GLU ASN SEQRES 14 A 427 TRP THR TRP GLU ASP TYR GLU LYS LEU ALA TYR ASP LEU SEQRES 15 A 427 GLN GLU LYS ALA GLY VAL TYR GLY SER ASN GLY MET HIS SEQRES 16 A 427 PRO PRO ASP ILE PHE PHE PRO TYR TYR LEU ARG THR LYS SEQRES 17 A 427 GLY GLU ARG PHE TYR LYS GLU ASP GLY THR GLY LEU ALA SEQRES 18 A 427 TYR GLN ASP ASP GLN LEU PHE VAL ASP TYR PHE GLU ARG SEQRES 19 A 427 GLN LEU ARG LEU VAL LYS ALA LYS THR SER PRO THR PRO SEQRES 20 A 427 ASP GLU SER ALA GLN ILE LYS GLY MET GLU ASP ASP PHE SEQRES 21 A 427 ILE VAL LYS GLY LYS SER ALA ILE THR TRP ASN TYR SER SEQRES 22 A 427 ASN GLN TYR LEU GLY PHE ALA ARG LEU THR ASP SER PRO SEQRES 23 A 427 LEU SER LEU TYR LEU PRO PRO GLU GLN MET GLN GLU LYS SEQRES 24 A 427 ALA LEU THR LEU LYS PRO SER MET LEU PHE SER ILE PRO SEQRES 25 A 427 LYS SER SER GLU HIS LYS LYS GLU ALA ALA LYS PHE ILE SEQRES 26 A 427 ASN PHE PHE VAL ASN ASN GLU GLU ALA ASN GLN LEU ILE SEQRES 27 A 427 LYS GLY GLU ARG GLY VAL PRO VAL SER ASP LYS VAL ALA SEQRES 28 A 427 ASP ALA ILE LYS PRO LYS LEU ASN GLU GLU GLU THR ASN SEQRES 29 A 427 ILE VAL GLU TYR VAL GLU THR ALA SER LYS ASN ILE SER SEQRES 30 A 427 LYS ALA ASP PRO PRO GLU PRO VAL GLY SER ALA GLU VAL SEQRES 31 A 427 ILE LYS LEU LEU LYS ASP THR SER ASP GLN ILE LEU TYR SEQRES 32 A 427 GLN LYS VAL SER PRO GLU LYS ALA ALA LYS THR PHE ARG SEQRES 33 A 427 LYS LYS ALA ASN GLU ILE LEU GLU ARG ASN ASN FORMUL 2 HOH *116(H2 O) HELIX 1 AA1 GLY A 22 ASN A 40 1 19 HELIX 2 AA2 ASN A 51 GLY A 66 1 16 HELIX 3 AA3 ASP A 75 GLY A 83 1 9 HELIX 4 AA4 LYS A 84 GLN A 87 5 4 HELIX 5 AA5 LEU A 91 ASP A 97 1 7 HELIX 6 AA6 ASP A 106 GLY A 112 5 7 HELIX 7 AA7 GLU A 135 ALA A 141 1 7 HELIX 8 AA8 THR A 151 GLY A 167 1 17 HELIX 9 AA9 PRO A 176 LYS A 188 1 13 HELIX 10 AB1 ASP A 204 LYS A 220 1 17 HELIX 11 AB2 GLN A 255 THR A 263 1 9 HELIX 12 AB3 HIS A 297 ASN A 311 1 15 HELIX 13 AB4 ASN A 311 LYS A 319 1 9 HELIX 14 AB5 SER A 327 LYS A 335 1 9 HELIX 15 AB6 PRO A 336 LEU A 338 5 3 HELIX 16 AB7 ASN A 339 SER A 353 1 15 HELIX 17 AB8 LYS A 354 ILE A 356 5 3 HELIX 18 AB9 GLY A 366 TYR A 383 1 18 HELIX 19 AC1 SER A 387 GLU A 404 1 18 SHEET 1 AA1 5 ILE A 45 ALA A 50 0 SHEET 2 AA1 5 LEU A 15 TRP A 20 1 N LEU A 15 O GLU A 46 SHEET 3 AA1 5 VAL A 71 MET A 74 1 O VAL A 71 N ALA A 18 SHEET 4 AA1 5 LYS A 284 SER A 290 -1 O LEU A 288 N MET A 74 SHEET 5 AA1 5 PHE A 122 ASN A 127 -1 N PHE A 122 O PHE A 289 SHEET 1 AA2 2 LYS A 114 ILE A 115 0 SHEET 2 AA2 2 LYS A 118 LEU A 119 -1 O LYS A 118 N ILE A 115 SHEET 1 AA3 3 ILE A 248 TYR A 252 0 SHEET 2 AA3 3 LEU A 129 ASN A 134 -1 N ILE A 132 O THR A 249 SHEET 3 AA3 3 LEU A 267 TYR A 270 -1 O SER A 268 N ALA A 133 CISPEP 1 HIS A 175 PRO A 176 0 -0.73 CRYST1 36.184 108.578 40.494 90.00 101.58 90.00 P 1 21 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 0.027637 0.000000 0.005661 0.00000 SCALE2 0.000000 0.009210 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025208 0.00000