HEADER TRANSPORT PROTEIN 26-JUL-22 7YLE TITLE RNDMPX IN COMPLEX WITH DMSP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCINE BETAINE/PROLINE ABC TRANSPORTER, PERIPLASMIC COMPND 3 GLYCINEBETAINE/PROLINE-BINDING PROTEIN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ROSEOVARIUS NUBINHIBENS ISM; SOURCE 3 ORGANISM_TAXID: 89187; SOURCE 4 GENE: ISM_12265; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ABC TRANSPORTER, SUBSTRATE BINDING PROTEIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.LI REVDAT 3 05-APR-23 7YLE 1 JRNL REVDAT 2 22-FEB-23 7YLE 1 JRNL REVDAT 1 25-JAN-23 7YLE 0 JRNL AUTH C.Y.LI,M.A.MAUSZ,A.MURPHY,N.ZHANG,X.L.CHEN,S.Y.WANG,C.GAO, JRNL AUTH 2 M.M.AGUILO-FERRETJANS,E.SILVANO,I.D.E.A.LIDBURY,H.H.FU, JRNL AUTH 3 J.D.TODD,Y.CHEN,Y.Z.ZHANG JRNL TITL UBIQUITOUS OCCURRENCE OF A DIMETHYLSULFONIOPROPIONATE ABC JRNL TITL 2 TRANSPORTER IN ABUNDANT MARINE BACTERIA. JRNL REF ISME J V. 17 579 2023 JRNL REFN ESSN 1751-7370 JRNL PMID 36707613 JRNL DOI 10.1038/S41396-023-01375-3 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 28311 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1439 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 31.0880 - 4.4162 1.00 2899 134 0.1535 0.1699 REMARK 3 2 4.4162 - 3.5068 0.99 2836 158 0.1540 0.1988 REMARK 3 3 3.5068 - 3.0640 0.99 2824 171 0.1944 0.2056 REMARK 3 4 3.0640 - 2.7840 0.99 2796 152 0.2143 0.2726 REMARK 3 5 2.7840 - 2.5846 0.98 2749 156 0.2215 0.2496 REMARK 3 6 2.5846 - 2.4323 0.96 2738 129 0.2105 0.2468 REMARK 3 7 2.4323 - 2.3105 0.94 2651 144 0.2180 0.2651 REMARK 3 8 2.3105 - 2.2100 0.89 2514 136 0.2471 0.2818 REMARK 3 9 2.2100 - 2.1249 0.86 2441 124 0.2209 0.3133 REMARK 3 10 2.1249 - 2.0520 0.86 2424 135 0.2263 0.3118 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 42.84 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.07430 REMARK 3 B22 (A**2) : -3.07430 REMARK 3 B33 (A**2) : 6.14850 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 2325 REMARK 3 ANGLE : 1.054 3185 REMARK 3 CHIRALITY : 0.069 356 REMARK 3 PLANARITY : 0.005 416 REMARK 3 DIHEDRAL : 13.429 794 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 7YLE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.989 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29829 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.51400 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM CHLORIDE, 0.1M BIS-TRIS REMARK 280 (PH 5.5), 25% (WT/VOL) POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 43.89400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.94700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.84100 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 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 1 REMARK 465 THR A 2 REMARK 465 LYS A 3 REMARK 465 ILE A 4 REMARK 465 ASN A 5 REMARK 465 LEU A 6 REMARK 465 ALA A 7 REMARK 465 THR A 8 REMARK 465 LEU A 9 REMARK 465 SER A 10 REMARK 465 VAL A 11 REMARK 465 ILE A 12 REMARK 465 GLY A 13 REMARK 465 PHE A 14 REMARK 465 LEU A 15 REMARK 465 GLY A 16 REMARK 465 SER A 17 REMARK 465 ALA A 18 REMARK 465 SER A 19 REMARK 465 ILE A 20 REMARK 465 ALA A 21 REMARK 465 GLN A 22 REMARK 465 ALA A 23 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 81 142.56 -170.37 REMARK 500 LEU A 88 73.06 -115.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 7YLE A 1 322 UNP A3SME7 A3SME7_ROSNI 1 322 SEQRES 1 A 322 MET THR LYS ILE ASN LEU ALA THR LEU SER VAL ILE GLY SEQRES 2 A 322 PHE LEU GLY SER ALA SER ILE ALA GLN ALA GLU CYS GLY SEQRES 3 A 322 GLU VAL SER ILE THR GLU MET ASN TRP ALA SER ALA SER SEQRES 4 A 322 VAL VAL THR THR VAL ALA THR PHE LEU MET GLU GLN GLY SEQRES 5 A 322 TYR GLY CYS ALA VAL THR VAL VAL PRO SER SER THR VAL SEQRES 6 A 322 PRO ALA VAL THR SER VAL SER GLU THR GLY GLU PRO ASP SEQRES 7 A 322 ILE LEU THR GLU LEU TRP LEU SER SER LEU PRO ASN TYR SEQRES 8 A 322 ALA LYS LEU GLU ALA GLN GLY THR VAL ARG THR LEU THR SEQRES 9 A 322 GLU VAL LEU SER ASP GLY GLY GLN GLU GLY TRP TRP VAL SEQRES 10 A 322 PRO GLN TYR LEU ALA GLU ALA HIS PRO GLU VAL THR THR SEQRES 11 A 322 ILE GLU GLY ILE LEU ALA ASN PRO ASP LEU VAL GLY GLY SEQRES 12 A 322 ARG PHE HIS ARG SER PRO ASP GLY TRP ALA ALA ALA ILE SEQRES 13 A 322 VAL ASP SER SER LEU ALA LYS ALA TRP ASP LEU GLU GLY SEQRES 14 A 322 ASN GLY ILE GLU VAL PHE ALA HIS GLY SER GLY GLU THR SEQRES 15 A 322 LEU ALA THR SER ILE ALA ALA ALA TYR ALA ASP ARG GLU SEQRES 16 A 322 PRO TRP PHE GLY TYR TYR TRP ALA PRO THR SER VAL LEU SEQRES 17 A 322 GLY LYS PHE PRO MET VAL MET VAL ASP LEU GLY GLU PHE SEQRES 18 A 322 ASP ALA ASP ILE HIS ALA CYS ASN SER LYS ALA ASP CYS SEQRES 19 A 322 ALA ASN VAL GLY LYS SER PRO TYR PRO ARG ALA ARG VAL SEQRES 20 A 322 ILE THR ALA VAL THR PRO GLY PHE ALA GLU GLU ASN PRO SEQRES 21 A 322 GLU ILE ILE GLU MET LEU SER ASN LEU SER PHE THR ASN SEQRES 22 A 322 ASP GLN MET GLY ALA ILE LEU ALA TRP GLN GLU GLU ASN SEQRES 23 A 322 GLY ALA SER SER GLU GLU ALA ALA VAL TRP PHE LEU SER SEQRES 24 A 322 ASN ASN SER ASP ILE TRP ALA GLY TRP VAL ASN ASP ALA SEQRES 25 A 322 ALA ARG GLU ASN LEU ALA ALA LEU ILE PRO HET DQY A 401 8 HETNAM DQY 3-(DIMETHYL-LAMBDA~4~-SULFANYL)PROPANOIC ACID FORMUL 2 DQY C5 H12 O2 S FORMUL 3 HOH *265(H2 O) HELIX 1 AA1 TRP A 35 GLY A 54 1 20 HELIX 2 AA2 SER A 63 GLY A 75 1 13 HELIX 3 AA3 ASN A 90 GLN A 97 1 8 HELIX 4 AA4 GLN A 119 HIS A 125 1 7 HELIX 5 AA5 PRO A 126 THR A 129 5 4 HELIX 6 AA6 THR A 130 ASN A 137 1 8 HELIX 7 AA7 PRO A 138 GLY A 142 5 5 HELIX 8 AA8 TRP A 152 TRP A 165 1 14 HELIX 9 AA9 LEU A 167 GLY A 171 5 5 HELIX 10 AB1 SER A 179 ASP A 193 1 15 HELIX 11 AB2 THR A 205 PHE A 211 1 7 HELIX 12 AB3 ASP A 222 SER A 230 1 9 HELIX 13 AB4 THR A 252 ASN A 259 1 8 HELIX 14 AB5 ASN A 259 SER A 267 1 9 HELIX 15 AB6 THR A 272 ASN A 286 1 15 HELIX 16 AB7 SER A 289 ASN A 301 1 13 HELIX 17 AB8 ASN A 301 ALA A 306 1 6 HELIX 18 AB9 GLY A 307 VAL A 309 5 3 HELIX 19 AC1 ASN A 310 ILE A 321 1 12 SHEET 1 AA1 2 GLU A 27 MET A 33 0 SHEET 2 AA1 2 ALA A 56 SER A 62 1 O THR A 58 N VAL A 28 SHEET 1 AA2 3 ILE A 79 TRP A 84 0 SHEET 2 AA2 3 VAL A 247 VAL A 251 -1 O ALA A 250 N LEU A 80 SHEET 3 AA2 3 ARG A 101 GLU A 105 -1 N ARG A 101 O VAL A 251 SHEET 1 AA3 3 GLY A 199 ALA A 203 0 SHEET 2 AA3 3 GLY A 111 PRO A 118 -1 N TRP A 116 O GLY A 199 SHEET 3 AA3 3 MET A 213 MET A 215 -1 O VAL A 214 N VAL A 117 SHEET 1 AA4 3 GLY A 199 ALA A 203 0 SHEET 2 AA4 3 GLY A 111 PRO A 118 -1 N TRP A 116 O GLY A 199 SHEET 3 AA4 3 ARG A 244 ALA A 245 -1 O ALA A 245 N GLY A 111 SHEET 1 AA5 2 ARG A 144 ARG A 147 0 SHEET 2 AA5 2 GLU A 173 ALA A 176 1 O PHE A 175 N PHE A 145 SSBOND 1 CYS A 25 CYS A 55 1555 1555 2.03 SSBOND 2 CYS A 228 CYS A 234 1555 1555 2.03 CISPEP 1 GLU A 76 PRO A 77 0 -3.27 CISPEP 2 THR A 81 GLU A 82 0 -9.58 CISPEP 3 ALA A 203 PRO A 204 0 0.63 CRYST1 74.332 74.332 87.788 90.00 90.00 90.00 P 41 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 0.013453 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011391 0.00000