HEADER TRANSPORT PROTEIN 26-NOV-20 7DLA TITLE CRYSTAL STRUCTURE OF NUCLEOSIDE TRANSPORTER NUPG (D323A MUTANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE PERMEASE NUPG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEOSIDE-TRANSPORT SYSTEM PROTEIN NUPG; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: NUPG, B2964, JW2932; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MFS, NUCLEOSIDE, TRANSPORTER, MEMBRANE PROTEIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.WANG,Q.J.XIAO,D.DENG REVDAT 4 03-APR-24 7DLA 1 REMARK REVDAT 3 27-MAR-24 7DLA 1 REMARK REVDAT 2 21-JUL-21 7DLA 1 JRNL REVDAT 1 07-APR-21 7DLA 0 JRNL AUTH C.WANG,Q.XIAO,H.DUAN,J.LI,J.ZHANG,Q.WANG,L.GUO,J.HU,B.SUN, JRNL AUTH 2 D.DENG JRNL TITL MOLECULAR BASIS FOR SUBSTRATE RECOGNITION BY THE BACTERIAL JRNL TITL 2 NUCLEOSIDE TRANSPORTER NUPG. JRNL REF J.BIOL.CHEM. V. 296 00479 2021 JRNL REFN ESSN 1083-351X JRNL PMID 33640454 JRNL DOI 10.1016/J.JBC.2021.100479 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 8717 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 869 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 19.7660 - 5.4201 1.00 1356 148 0.1858 0.2354 REMARK 3 2 5.4201 - 4.3168 1.00 1311 149 0.2255 0.2637 REMARK 3 3 4.3168 - 3.7755 0.99 1295 146 0.2292 0.2759 REMARK 3 4 3.7755 - 3.4322 1.00 1293 141 0.2549 0.3118 REMARK 3 5 3.4322 - 3.1873 1.00 1303 144 0.3366 0.3517 REMARK 3 6 3.1873 - 3.0001 1.00 1290 141 0.2908 0.3287 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.96 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7DLA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300019590. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-20 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8747 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 19.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.17300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.98300 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PREDICT MODEL FROM ROBETTA WEBISTE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NACL, 0.1 M MGCL2, 0.1M MES REMARK 280 PH6.0, 30% PEG550MME, LIPIDIC CUBIC PHASE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 72.66600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.54800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 72.66600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.54800 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 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 TYR A 404 REMARK 465 LYS A 405 REMARK 465 HIS A 406 REMARK 465 VAL A 407 REMARK 465 ARG A 408 REMARK 465 VAL A 409 REMARK 465 PRO A 410 REMARK 465 THR A 411 REMARK 465 GLY A 412 REMARK 465 THR A 413 REMARK 465 GLN A 414 REMARK 465 THR A 415 REMARK 465 VAL A 416 REMARK 465 SER A 417 REMARK 465 HIS A 418 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 4 CG CD CE NZ REMARK 470 GLU A 334 CG CD OE1 OE2 REMARK 470 GLN A 374 CG CD OE1 NE2 REMARK 470 LYS A 403 CG CD CE NZ 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 LEU A 157 3.79 -69.60 REMARK 500 HIS A 159 -7.51 -59.11 REMARK 500 ALA A 189 -61.83 -143.63 REMARK 500 LEU A 204 -9.93 -56.01 REMARK 500 REMARK 500 REMARK: NULL DBREF 7DLA A 1 418 UNP P0AFF4 NUPG_ECOLI 1 418 SEQADV 7DLA ALA A 323 UNP P0AFF4 ASP 323 ENGINEERED MUTATION SEQRES 1 A 418 MET ASN LEU LYS LEU GLN LEU LYS ILE LEU SER PHE LEU SEQRES 2 A 418 GLN PHE CYS LEU TRP GLY SER TRP LEU THR THR LEU GLY SEQRES 3 A 418 SER TYR MET PHE VAL THR LEU LYS PHE ASP GLY ALA SER SEQRES 4 A 418 ILE GLY ALA VAL TYR SER SER LEU GLY ILE ALA ALA VAL SEQRES 5 A 418 PHE MET PRO ALA LEU LEU GLY ILE VAL ALA ASP LYS TRP SEQRES 6 A 418 LEU SER ALA LYS TRP VAL TYR ALA ILE CYS HIS THR ILE SEQRES 7 A 418 GLY ALA ILE THR LEU PHE MET ALA ALA GLN VAL THR THR SEQRES 8 A 418 PRO GLU ALA MET PHE LEU VAL ILE LEU ILE ASN SER PHE SEQRES 9 A 418 ALA TYR MET PRO THR LEU GLY LEU ILE ASN THR ILE SER SEQRES 10 A 418 TYR TYR ARG LEU GLN ASN ALA GLY MET ASP ILE VAL THR SEQRES 11 A 418 ASP PHE PRO PRO ILE ARG ILE TRP GLY THR ILE GLY PHE SEQRES 12 A 418 ILE MET ALA MET TRP VAL VAL SER LEU SER GLY PHE GLU SEQRES 13 A 418 LEU SER HIS MET GLN LEU TYR ILE GLY ALA ALA LEU SER SEQRES 14 A 418 ALA ILE LEU VAL LEU PHE THR LEU THR LEU PRO HIS ILE SEQRES 15 A 418 PRO VAL ALA LYS GLN GLN ALA ASN GLN SER TRP THR THR SEQRES 16 A 418 LEU LEU GLY LEU ASP ALA PHE ALA LEU PHE LYS ASN LYS SEQRES 17 A 418 ARG MET ALA ILE PHE PHE ILE PHE SER MET LEU LEU GLY SEQRES 18 A 418 ALA GLU LEU GLN ILE THR ASN MET PHE GLY ASN THR PHE SEQRES 19 A 418 LEU HIS SER PHE ASP LYS ASP PRO MET PHE ALA SER SER SEQRES 20 A 418 PHE ILE VAL GLN HIS ALA SER ILE ILE MET SER ILE SER SEQRES 21 A 418 GLN ILE SER GLU THR LEU PHE ILE LEU THR ILE PRO PHE SEQRES 22 A 418 PHE LEU SER ARG TYR GLY ILE LYS ASN VAL MET MET ILE SEQRES 23 A 418 SER ILE VAL ALA TRP ILE LEU ARG PHE ALA LEU PHE ALA SEQRES 24 A 418 TYR GLY ASP PRO THR PRO PHE GLY THR VAL LEU LEU VAL SEQRES 25 A 418 LEU SER MET ILE VAL TYR GLY CYS ALA PHE ALA PHE PHE SEQRES 26 A 418 ASN ILE SER GLY SER VAL PHE VAL GLU LYS GLU VAL SER SEQRES 27 A 418 PRO ALA ILE ARG ALA SER ALA GLN GLY MET PHE LEU MET SEQRES 28 A 418 MET THR ASN GLY PHE GLY CYS ILE LEU GLY GLY ILE VAL SEQRES 29 A 418 SER GLY LYS VAL VAL GLU MET TYR THR GLN ASN GLY ILE SEQRES 30 A 418 THR ASP TRP GLN THR VAL TRP LEU ILE PHE ALA GLY TYR SEQRES 31 A 418 SER VAL VAL LEU ALA PHE ALA PHE MET ALA MET PHE LYS SEQRES 32 A 418 TYR LYS HIS VAL ARG VAL PRO THR GLY THR GLN THR VAL SEQRES 33 A 418 SER HIS HELIX 1 AA1 ASN A 2 SER A 20 1 19 HELIX 2 AA2 THR A 24 VAL A 31 1 8 HELIX 3 AA3 ASP A 36 TRP A 65 1 30 HELIX 4 AA4 SER A 67 ALA A 87 1 21 HELIX 5 AA5 THR A 91 ASN A 123 1 33 HELIX 6 AA6 ASP A 127 PHE A 132 1 6 HELIX 7 AA7 ILE A 137 SER A 153 1 17 HELIX 8 AA8 HIS A 159 THR A 178 1 20 HELIX 9 AA9 SER A 192 GLY A 198 1 7 HELIX 10 AB1 LEU A 199 LEU A 204 1 6 HELIX 11 AB2 ASN A 207 GLU A 223 1 17 HELIX 12 AB3 GLN A 225 SER A 237 1 13 HELIX 13 AB4 PHE A 238 ASP A 241 5 4 HELIX 14 AB5 SER A 247 HIS A 252 1 6 HELIX 15 AB6 HIS A 252 TYR A 300 1 49 HELIX 16 AB7 THR A 304 GLU A 336 1 33 HELIX 17 AB8 SER A 338 ALA A 340 5 3 HELIX 18 AB9 ILE A 341 GLY A 355 1 15 HELIX 19 AC1 GLY A 355 TYR A 372 1 18 HELIX 20 AC2 ASP A 379 LYS A 403 1 25 SHEET 1 AA1 2 THR A 373 GLN A 374 0 SHEET 2 AA1 2 ILE A 377 THR A 378 -1 O ILE A 377 N GLN A 374 CRYST1 145.332 47.096 63.383 90.00 94.90 90.00 C 1 2 1 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 0.006881 0.000000 0.000590 0.00000 SCALE2 0.000000 0.021233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015835 0.00000