HEADER TRANSPORT PROTEIN 15-MAY-13 4KQP TITLE CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS GLNP SUBSTRATE BINDING DOMAIN TITLE 2 2 (SBD2) IN COMPLEX WITH GLUTAMINE AT 0.95 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMINE ABC TRANSPORTER PERMEASE AND SUBSTRATE BINDING COMPND 3 PROTEIN PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: SUBSTRATE BINDING DOMAIN 2, UNP RESIDUES 255-484; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. LACTIS; SOURCE 3 ORGANISM_TAXID: 272623; SOURCE 4 STRAIN: IL1403; SOURCE 5 GENE: GLNP, L165, LL1759; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLUTAMINE/GLUTAMIC ACID BINDING, AMINO ACID TRANSPORT, TRANSPORT KEYWDS 2 PROTEIN, EXTRACELLULAR EXPDTA X-RAY DIFFRACTION AUTHOR A.VUJICIC ZAGAR,A.GUSKOV,G.K.SCHUURMAN-WOLTERS,D.J.SLOTBOOM,B.POOLMAN REVDAT 3 28-FEB-24 4KQP 1 REMARK SEQADV REVDAT 2 20-NOV-13 4KQP 1 JRNL REVDAT 1 11-SEP-13 4KQP 0 JRNL AUTH F.FULYANI,G.K.SCHUURMAN-WOLTERS,A.V.ZAGAR,A.GUSKOV, JRNL AUTH 2 D.J.SLOTBOOM,B.POOLMAN JRNL TITL FUNCTIONAL DIVERSITY OF TANDEM SUBSTRATE-BINDING DOMAINS IN JRNL TITL 2 ABC TRANSPORTERS FROM PATHOGENIC BACTERIA. JRNL REF STRUCTURE V. 21 1879 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23994008 JRNL DOI 10.1016/J.STR.2013.07.020 REMARK 2 REMARK 2 RESOLUTION. 0.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2) 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) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 119814 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.115 REMARK 3 R VALUE (WORKING SET) : 0.115 REMARK 3 FREE R VALUE : 0.120 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5990 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 0.9608 - 0.9500 0.96 3717 195 0.2073 0.2049 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) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 9.460 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 2085 REMARK 3 ANGLE : 1.281 2852 REMARK 3 CHIRALITY : 0.070 309 REMARK 3 PLANARITY : 0.007 375 REMARK 3 DIHEDRAL : 11.768 791 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 4KQP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079674. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 119821 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 44.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.240 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 (%): 36.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 6000, 100MM CACL2, 0.1M SODIUM REMARK 280 ACETATE BUFFER, PH 5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 281K 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 25.84500 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 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 GLY A 253 REMARK 465 MET A 254 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 HH TYR A 403 OD2 ASP A 416 1.57 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 PHE A 270 54.13 -154.08 REMARK 500 HIS A 319 -84.71 -96.33 REMARK 500 SER A 325 39.55 -156.63 REMARK 500 ASP A 356 -153.57 -132.00 REMARK 500 ASP A 357 12.15 -149.37 REMARK 500 ASP A 440 25.90 -142.19 REMARK 500 GLU A 481 145.72 27.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLN A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KR5 RELATED DB: PDB REMARK 900 RELATED ID: 4KPT RELATED DB: PDB REMARK 900 SUBSTRATE BINDING DOMAIN 1 (SBD1) DBREF 4KQP A 255 484 UNP Q9CES5 Q9CES5_LACLA 255 484 SEQADV 4KQP GLY A 253 UNP Q9CES5 EXPRESSION TAG SEQADV 4KQP MET A 254 UNP Q9CES5 EXPRESSION TAG SEQRES 1 A 232 GLY MET ALA THR PRO LYS LYS ASP VAL TYR THR ILE ALA SEQRES 2 A 232 SER ASP ASN SER PHE ALA PRO PHE GLU PHE GLN ASN ASP SEQRES 3 A 232 ASP LYS GLN PHE THR GLY ILE ASP VAL ASP LEU LEU ASN SEQRES 4 A 232 ALA ILE ALA LYS ASN GLN GLY PHE LYS LEU LYS TRP ASN SEQRES 5 A 232 PHE ILE GLY PHE GLN ALA ALA VAL ASP SER VAL GLN SER SEQRES 6 A 232 GLY HIS ALA ASP GLY MET MET SER GLY MET SER ILE THR SEQRES 7 A 232 ASP ALA ARG LYS GLN VAL PHE ASP TYR GLY SER PRO TYR SEQRES 8 A 232 TYR SER SER ASN LEU THR ILE ALA THR SER SER THR ASP SEQRES 9 A 232 ASP SER ILE LYS SER TRP LYS ASP LEU LYS GLY LYS THR SEQRES 10 A 232 LEU GLY ALA LYS ASN GLY THR ALA SER PHE ASP TYR LEU SEQRES 11 A 232 ASN ALA HIS ALA LYS GLU TYR GLY TYR THR VAL LYS THR SEQRES 12 A 232 PHE THR ASP ALA THR THR MET TYR SER SER LEU ASN ASN SEQRES 13 A 232 GLY SER ILE ASN ALA LEU MET ASP ASP GLU PRO VAL ILE SEQRES 14 A 232 LYS TYR ALA ILE LYS GLN GLY GLN LYS PHE ALA THR PRO SEQRES 15 A 232 ILE LYS PRO ILE PRO ASP GLY GLN TYR GLY PHE ALA VAL SEQRES 16 A 232 LYS LYS GLY SER ASN PRO GLU LEU ILE GLU MET PHE ASN SEQRES 17 A 232 ASN GLY LEU ALA ASN LEU ARG ALA ASN GLY GLU TYR ASP SEQRES 18 A 232 LYS ILE ILE ASP LYS TYR LEU GLU SER ASP ALA HET GLN A 501 19 HETNAM GLN GLUTAMINE FORMUL 2 GLN C5 H10 N2 O3 FORMUL 3 HOH *440(H2 O) HELIX 1 1 GLY A 284 GLY A 298 1 15 HELIX 2 2 GLY A 307 SER A 317 1 11 HELIX 3 3 ALA A 332 GLN A 335 5 4 HELIX 4 4 SER A 361 LYS A 366 5 6 HELIX 5 5 THR A 376 GLY A 390 1 15 HELIX 6 6 ASP A 398 ASN A 408 1 11 HELIX 7 7 GLU A 418 GLY A 428 1 11 HELIX 8 8 ASN A 452 GLY A 470 1 19 HELIX 9 9 GLY A 470 LEU A 480 1 11 SHEET 1 A 3 LEU A 301 PHE A 305 0 SHEET 2 A 3 TYR A 262 SER A 266 1 N ILE A 264 O LYS A 302 SHEET 3 A 3 GLY A 322 MET A 323 1 O GLY A 322 N ALA A 265 SHEET 1 B 2 PHE A 275 GLN A 276 0 SHEET 2 B 2 PHE A 282 THR A 283 -1 O THR A 283 N PHE A 275 SHEET 1 C 2 PHE A 337 TYR A 339 0 SHEET 2 C 2 ALA A 446 LYS A 448 -1 O VAL A 447 N ASP A 338 SHEET 1 D 5 THR A 392 PHE A 396 0 SHEET 2 D 5 THR A 369 LYS A 373 1 N LEU A 370 O THR A 392 SHEET 3 D 5 ALA A 413 ASP A 417 1 O ALA A 413 N GLY A 371 SHEET 4 D 5 TYR A 344 SER A 353 -1 N THR A 349 O ASP A 416 SHEET 5 D 5 PHE A 431 ALA A 432 -1 O ALA A 432 N THR A 352 SHEET 1 E 5 THR A 392 PHE A 396 0 SHEET 2 E 5 THR A 369 LYS A 373 1 N LEU A 370 O THR A 392 SHEET 3 E 5 ALA A 413 ASP A 417 1 O ALA A 413 N GLY A 371 SHEET 4 E 5 TYR A 344 SER A 353 -1 N THR A 349 O ASP A 416 SHEET 5 E 5 ILE A 438 TYR A 443 -1 O ILE A 438 N LEU A 348 CISPEP 1 ALA A 271 PRO A 272 0 12.52 SITE 1 AC1 13 ASP A 267 PHE A 270 PHE A 308 SER A 325 SITE 2 AC1 13 GLY A 326 MET A 327 SER A 328 ARG A 333 SITE 3 AC1 13 LYS A 373 THR A 376 ALA A 377 ASP A 417 SITE 4 AC1 13 HOH A1039 CRYST1 42.990 51.690 44.230 90.00 91.10 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 0.023261 0.000000 0.000446 0.00000 SCALE2 0.000000 0.019346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022613 0.00000