HEADER TRANSPORT PROTEIN 09-MAY-18 6GHU TITLE CRYSTAL STRUCTURE OF THE PERIPLASMIC DOMAIN OF XCPY, OP CRYSTAL FORM. COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE II SECRETION SYSTEM PROTEIN L; COMPND 3 CHAIN: B, A; COMPND 4 FRAGMENT: PERIPLASMIC DOMAIN; COMPND 5 SYNONYM: T2SS PROTEIN L; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: XCPY, PAMH19_1972; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSF 1B KEYWDS FERREDOXIN FOLD, DIMER, GSPL, TYPE II SECRETION SYSTEM, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.FULARA,S.N.SAVVIDES REVDAT 3 17-JAN-24 6GHU 1 REMARK REVDAT 2 28-NOV-18 6GHU 1 JRNL REVDAT 1 21-NOV-18 6GHU 0 SPRSDE 21-NOV-18 6GHU 5N7S JRNL AUTH A.FULARA,I.VANDENBERGHE,R.J.READ,B.DEVREESE,S.N.SAVVIDES JRNL TITL STRUCTURE AND OLIGOMERIZATION OF THE PERIPLASMIC DOMAIN OF JRNL TITL 2 GSPL FROM THE TYPE II SECRETION SYSTEM OF PSEUDOMONAS JRNL TITL 3 AERUGINOSA. JRNL REF SCI REP V. 8 16760 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 30425318 JRNL DOI 10.1038/S41598-018-34956-W REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 10691 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1066 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 39.3279 - 3.9985 0.97 1278 142 0.2056 0.2284 REMARK 3 2 3.9985 - 3.1741 0.99 1232 135 0.1944 0.2346 REMARK 3 3 3.1741 - 2.7730 1.00 1215 134 0.2169 0.3118 REMARK 3 4 2.7730 - 2.5195 0.99 1191 132 0.2316 0.2632 REMARK 3 5 2.5195 - 2.3390 0.99 1171 130 0.2243 0.3304 REMARK 3 6 2.3390 - 2.2011 0.99 1196 134 0.2311 0.2823 REMARK 3 7 2.2011 - 2.0909 1.00 1169 129 0.2717 0.3087 REMARK 3 8 2.0909 - 1.9998 0.98 1173 130 0.3162 0.3607 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.00 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 : 0.004 1188 REMARK 3 ANGLE : 0.681 1617 REMARK 3 CHIRALITY : 0.047 195 REMARK 3 PLANARITY : 0.005 219 REMARK 3 DIHEDRAL : 18.430 723 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 6GHU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1200009973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10733 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 39.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.050 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 2W7V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M L-PROLINE, 0.1 M HEPES, PH=7.5, REMARK 280 PEG 3350, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 11.69750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.47450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.39300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.47450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.69750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.39300 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 GLN B 304 CG CD OE1 NE2 REMARK 470 LEU B 306 CG CD1 CD2 REMARK 470 LEU A 306 CG CD1 CD2 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 OE1 GLN A 326 O HOH A 401 2.09 REMARK 500 OE1 GLN B 326 O HOH B 401 2.16 REMARK 500 OE2 GLU B 357 O HOH B 402 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 418 O HOH A 407 2554 2.02 REMARK 500 O HOH B 427 O HOH A 418 2554 2.18 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 LEU A 305 37.40 -82.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5N7L RELATED DB: PDB REMARK 900 THE OTHER CRYSTAL FORM OF THE SAME MOLECULE DBREF1 6GHU B 304 381 UNP A0A0A8RGG2_PSEAI DBREF2 6GHU B A0A0A8RGG2 304 381 DBREF1 6GHU A 304 381 UNP A0A0A8RGG2_PSEAI DBREF2 6GHU A A0A0A8RGG2 304 381 SEQRES 1 B 78 GLN LEU LEU GLY LEU LEU GLY GLN ALA ALA THR VAL ILE SEQRES 2 B 78 GLY GLY GLU PRO THR VAL SER VAL GLU GLN LEU ASP PHE SEQRES 3 B 78 SER ALA ALA ARG GLY ASP VAL ALA LEU GLN VAL ARG ALA SEQRES 4 B 78 PRO GLY PHE ASP VAL LEU GLU ARG LEU ARG SER ARG LEU SEQRES 5 B 78 SER GLU SER GLY LEU ALA VAL GLN LEU GLY SER ALA SER SEQRES 6 B 78 ARG ASP GLY SER THR VAL SER ALA ARG LEU VAL ILE GLY SEQRES 1 A 78 GLN LEU LEU GLY LEU LEU GLY GLN ALA ALA THR VAL ILE SEQRES 2 A 78 GLY GLY GLU PRO THR VAL SER VAL GLU GLN LEU ASP PHE SEQRES 3 A 78 SER ALA ALA ARG GLY ASP VAL ALA LEU GLN VAL ARG ALA SEQRES 4 A 78 PRO GLY PHE ASP VAL LEU GLU ARG LEU ARG SER ARG LEU SEQRES 5 A 78 SER GLU SER GLY LEU ALA VAL GLN LEU GLY SER ALA SER SEQRES 6 A 78 ARG ASP GLY SER THR VAL SER ALA ARG LEU VAL ILE GLY FORMUL 3 HOH *97(H2 O) HELIX 1 AA1 LEU B 305 GLY B 318 1 14 HELIX 2 AA2 GLY B 344 SER B 358 1 15 HELIX 3 AA3 LEU A 305 GLY A 318 1 14 HELIX 4 AA4 GLY A 344 SER A 358 1 15 SHEET 1 AA1 8 VAL B 362 LEU B 364 0 SHEET 2 AA1 8 THR B 373 ILE B 380 -1 O VAL B 379 N GLN B 363 SHEET 3 AA1 8 ASP B 335 ALA B 342 -1 N LEU B 338 O LEU B 378 SHEET 4 AA1 8 SER B 323 SER B 330 -1 N GLN B 326 O GLN B 339 SHEET 5 AA1 8 SER A 323 SER A 330 -1 O LEU A 327 N PHE B 329 SHEET 6 AA1 8 VAL A 336 ALA A 342 -1 O ALA A 337 N ASP A 328 SHEET 7 AA1 8 THR A 373 ILE A 380 -1 O VAL A 374 N ALA A 342 SHEET 8 AA1 8 VAL A 362 LEU A 364 -1 N GLN A 363 O VAL A 379 SHEET 1 AA2 8 SER B 368 ASP B 370 0 SHEET 2 AA2 8 THR B 373 ILE B 380 -1 O THR B 373 N ASP B 370 SHEET 3 AA2 8 ASP B 335 ALA B 342 -1 N LEU B 338 O LEU B 378 SHEET 4 AA2 8 SER B 323 SER B 330 -1 N GLN B 326 O GLN B 339 SHEET 5 AA2 8 SER A 323 SER A 330 -1 O LEU A 327 N PHE B 329 SHEET 6 AA2 8 VAL A 336 ALA A 342 -1 O ALA A 337 N ASP A 328 SHEET 7 AA2 8 THR A 373 ILE A 380 -1 O VAL A 374 N ALA A 342 SHEET 8 AA2 8 SER A 368 ASP A 370 -1 N ASP A 370 O THR A 373 CRYST1 23.395 64.786 98.949 90.00 90.00 90.00 P 21 21 21 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 0.042744 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015435 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010106 0.00000