HEADER GLYCINE BETAINE-BINDING PROTEIN 23-DEC-09 3L6G TITLE CRYSTAL STRUCTURE OF LACTOCOCCAL OPUAC IN ITS OPEN CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETAINE ABC TRANSPORTER PERMEASE AND SUBSTRATE BINDING COMPND 3 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: SUBSTRATE BINDING DOMAIN (UNP RESIDUES 320-573); COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS; SOURCE 3 ORGANISM_COMMON: STREPTOCOCCUS LACTIS; SOURCE 4 ORGANISM_TAXID: 1358; SOURCE 5 STRAIN: NZ9000; SOURCE 6 GENE: BUSAB, LL1451, L724, L72477; SOURCE 7 EXPRESSION_SYSTEM: LACTOCOCCUS LACTIS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1358; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: NZ9000; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PNZ9000 KEYWDS GLYCINE BETAINE BINDING, SUBSTRATE BINDING DOMAIN, VENUS FLY-TRAP, KEYWDS 2 CELL MEMBRANE, MEMBRANE, TRANSMEMBRANE, TRANSPORT, GLYCINE BETAINE- KEYWDS 3 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.P.A.BERNTSSON,J.C.WOLTERS,N.GUL,A.KARASAWA,A.M.W.H.THUNNISSEN, AUTHOR 2 D.J.SLOTBOOM,B.POOLMAN REVDAT 1 19-MAY-10 3L6G 0 JRNL AUTH J.C.WOLTERS,R.P.BERNTSSON,N.GUL,A.KARASAWA,A.M.THUNNISSEN, JRNL AUTH 2 D.J.SLOTBOOM,B.POOLMAN JRNL TITL LIGAND BINDING AND CRYSTAL STRUCTURES OF THE JRNL TITL 2 SUBSTRATE-BINDING DOMAIN OF THE ABC TRANSPORTER OPUA. JRNL REF PLOS ONE V. 5 E1036 2010 JRNL REFN ESSN 1932-6203 JRNL PMID 20454456 JRNL DOI 10.1371/JOURNAL.PONE.0010361 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 20914 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1046 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 44.0850 - 3.6320 0.99 3005 159 0.1800 0.1890 REMARK 3 2 3.6320 - 2.8830 1.00 2881 152 0.1600 0.1890 REMARK 3 3 2.8830 - 2.5180 1.00 2832 149 0.1620 0.2180 REMARK 3 4 2.5180 - 2.2880 1.00 2817 148 0.1510 0.1980 REMARK 3 5 2.2880 - 2.1240 1.00 2813 148 0.1490 0.1900 REMARK 3 6 2.1240 - 1.9990 1.00 2777 146 0.1580 0.2110 REMARK 3 7 1.9990 - 1.8990 0.99 2743 144 0.1910 0.2630 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 : 0.42 REMARK 3 B_SOL : 40.99 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04500 REMARK 3 B22 (A**2) : -0.04500 REMARK 3 B33 (A**2) : 0.08900 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 : 0.017 2095 REMARK 3 ANGLE : 1.428 2842 REMARK 3 CHIRALITY : 0.103 309 REMARK 3 PLANARITY : 0.007 358 REMARK 3 DIHEDRAL : 18.805 781 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 3L6G COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-10. REMARK 100 THE RCSB ID CODE IS RCSB056892. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.872 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 : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20918 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 44.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 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: 2B4L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM IODIDE, 0.1 M BIS-TRIS REMARK 280 PROPANE PH 8.5, 20% W/V PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 54.57150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.06550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.06550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.28575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.06550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.06550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 81.85725 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.06550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.06550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.28575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.06550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.06550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 81.85725 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 54.57150 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 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 422 -75.14 -138.05 REMARK 500 ILE A 432 -143.79 -124.05 REMARK 500 SER A 460 -98.79 -151.40 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 B3P A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3L6H RELATED DB: PDB DBREF 3L6G A 320 573 UNP Q7DAU8 Q7DAU8_LACLA 320 573 SEQADV 3L6G GLY A 574 UNP Q7DAU8 EXPRESSION TAG SEQADV 3L6G SER A 575 UNP Q7DAU8 EXPRESSION TAG SEQRES 1 A 256 ASP LYS LYS VAL ASP LEU VAL TYR MET ASN TRP ASP SER SEQRES 2 A 256 GLU VAL ALA SER ILE ASN VAL LEU THR GLN ALA MET LYS SEQRES 3 A 256 GLU HIS GLY PHE ASP VAL LYS THR THR ALA LEU ASP ASN SEQRES 4 A 256 ALA VAL ALA TRP GLN THR VAL ALA ASN GLY GLN ALA ASP SEQRES 5 A 256 GLY MET VAL SER ALA TRP LEU PRO ASN THR HIS LYS THR SEQRES 6 A 256 GLN TRP GLN LYS TYR GLY LYS SER VAL ASP LEU LEU GLY SEQRES 7 A 256 PRO ASN LEU LYS GLY ALA LYS VAL GLY PHE VAL VAL PRO SEQRES 8 A 256 SER TYR MET ASN VAL ASN SER ILE GLU ASP LEU THR ASN SEQRES 9 A 256 GLN ALA ASN LYS THR ILE THR GLY ILE GLU PRO GLY ALA SEQRES 10 A 256 GLY VAL MET ALA ALA SER GLU LYS THR LEU ASN SER TYR SEQRES 11 A 256 ASP ASN LEU LYS ASP TRP LYS LEU VAL PRO SER SER SER SEQRES 12 A 256 GLY ALA MET THR VAL ALA LEU GLY GLU ALA ILE LYS GLN SEQRES 13 A 256 HIS LYS ASP ILE VAL ILE THR GLY TRP SER PRO HIS TRP SEQRES 14 A 256 MET PHE ASN LYS TYR ASP LEU LYS TYR LEU ALA ASP PRO SEQRES 15 A 256 LYS GLY THR MET GLY THR SER GLU ASN ILE ASN THR ILE SEQRES 16 A 256 VAL ARG LYS GLY LEU LYS LYS GLU ASN PRO GLU ALA TYR SEQRES 17 A 256 LYS VAL LEU ASP LYS PHE ASN TRP THR THR LYS ASP MET SEQRES 18 A 256 GLU ALA VAL MET LEU ASP ILE GLN ASN GLY LYS THR PRO SEQRES 19 A 256 GLU GLU ALA ALA LYS ASN TRP ILE LYS ASP HIS GLN LYS SEQRES 20 A 256 GLU VAL ASP LYS TRP PHE LYS GLY SER HET B3P A 1 19 HETNAM B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)- HETNAM 2 B3P PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL FORMUL 2 B3P C11 H26 N2 O6 FORMUL 3 HOH *280(H2 O) HELIX 1 1 TRP A 330 HIS A 347 1 18 HELIX 2 2 ASP A 357 ASN A 367 1 11 HELIX 3 3 HIS A 382 GLY A 390 1 9 HELIX 4 4 SER A 417 LEU A 421 5 5 HELIX 5 5 ASN A 423 ASN A 426 5 4 HELIX 6 6 ALA A 436 ASN A 447 1 12 HELIX 7 7 TYR A 449 LYS A 453 5 5 HELIX 8 8 SER A 461 GLN A 475 1 15 HELIX 9 9 TRP A 488 TYR A 493 1 6 HELIX 10 10 GLY A 518 ASN A 523 1 6 HELIX 11 11 ASN A 523 PHE A 533 1 11 HELIX 12 12 THR A 536 ASN A 549 1 14 HELIX 13 13 THR A 552 HIS A 564 1 13 HELIX 14 14 HIS A 564 LYS A 570 1 7 HELIX 15 15 TRP A 571 LYS A 573 5 3 SHEET 1 A 2 LYS A 321 TYR A 327 0 SHEET 2 A 2 PHE A 349 ALA A 355 1 O LYS A 352 N LEU A 325 SHEET 1 B 4 GLY A 372 LEU A 378 0 SHEET 2 B 4 GLU A 509 ARG A 516 -1 O ASN A 512 N ALA A 376 SHEET 3 B 4 VAL A 393 PRO A 410 -1 N ASN A 399 O ILE A 511 SHEET 4 B 4 ILE A 481 SER A 485 -1 O ILE A 481 N VAL A 408 SHEET 1 C 4 GLY A 372 LEU A 378 0 SHEET 2 C 4 GLU A 509 ARG A 516 -1 O ASN A 512 N ALA A 376 SHEET 3 C 4 VAL A 393 PRO A 410 -1 N ASN A 399 O ILE A 511 SHEET 4 C 4 LEU A 495 TYR A 497 -1 O LYS A 496 N VAL A 409 SHEET 1 D 2 THR A 428 THR A 430 0 SHEET 2 D 2 LYS A 456 VAL A 458 1 O LYS A 456 N ILE A 429 CISPEP 1 LEU A 378 PRO A 379 0 8.97 CISPEP 2 SER A 485 PRO A 486 0 0.62 SITE 1 AC1 12 HOH A 70 HOH A 83 HOH A 103 HOH A 123 SITE 2 AC1 12 HOH A 229 LEU A 395 LEU A 396 PRO A 398 SITE 3 AC1 12 GLU A 433 ASP A 531 LYS A 532 ASN A 534 CRYST1 68.131 68.131 109.143 90.00 90.00 90.00 P 41 21 2 8 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 0.014678 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014678 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009162 0.00000 MASTER 241 0 1 15 12 0 3 6 0 0 0 20 END