HEADER TRANSPORT PROTEIN 21-FEB-17 5N7S OBSLTE 21-NOV-18 5N7S 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,GENERAL SECRETION PATHWAY PROTEIN L; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 GENE: XCPY, PA3096; 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 FERRODOXIN FOLD, DIMER, GSPL, TYPE II SECRETION SYSTEM, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.FULARA,S.N.SAVVIDES REVDAT 2 21-NOV-18 5N7S 1 OBSLTE REVDAT 1 14-MAR-18 5N7S 0 JRNL AUTH A.FULARA,S.N.SAVVIDES JRNL TITL CRYSTAL STRUCTURE OF THE PERIPLASMIC DOMAIN OF XCPY, OP JRNL TITL 2 CRYSTAL FORM. JRNL REF TO BE PUBLISHED JRNL REFN 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 533 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 - 3.1741 0.98 2647 140 0.2057 0.2543 REMARK 3 2 3.1741 - 2.5195 0.99 2540 132 0.2389 0.2694 REMARK 3 3 2.5195 - 2.2011 0.99 2500 131 0.2490 0.3119 REMARK 3 4 2.2011 - 1.9998 0.99 2471 130 0.3150 0.3696 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.53 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 : 0.005 1205 REMARK 3 ANGLE : 1.102 1641 REMARK 3 CHIRALITY : 0.058 198 REMARK 3 PLANARITY : 0.006 222 REMARK 3 DIHEDRAL : 2.935 953 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 6.0270 -0.3538 -12.2706 REMARK 3 T TENSOR REMARK 3 T11: 0.2559 T22: 0.2445 REMARK 3 T33: 0.2493 T12: -0.0178 REMARK 3 T13: -0.0064 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 0.4719 L22: 0.6617 REMARK 3 L33: 1.7794 L12: -0.2815 REMARK 3 L13: -0.0092 L23: 1.4233 REMARK 3 S TENSOR REMARK 3 S11: -0.0237 S12: 0.0522 S13: -0.0517 REMARK 3 S21: 0.0102 S22: -0.0315 S23: 0.0322 REMARK 3 S31: 0.0790 S32: -0.0814 S33: -0.0000 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 5N7S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003622. 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10733 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.11 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.510 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, PHASER REMARK 200 STARTING MODEL: 5N7L REMARK 200 REMARK 200 REMARK: THIN PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 2.10 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 B 306 -49.53 161.45 REMARK 500 LEU B 306 -53.10 -132.50 REMARK 500 LEU A 306 -60.20 -144.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 453 DISTANCE = 6.53 ANGSTROMS DBREF 5N7S B 304 381 UNP P25060 GSPL_PSEAE 304 381 DBREF 5N7S A 304 381 UNP P25060 GSPL_PSEAE 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 *109(H2 O) HELIX 1 AA1 LEU B 306 GLY B 318 1 13 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 VAL B 336 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 LEU A 378 N LEU A 338 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 VAL B 336 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 LEU A 378 N LEU A 338 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