HEADER TOXIN 09-JUN-20 6ZC1 TITLE CRYSTAL STRUCTURE OF RAHU PROTEIN FROM PSEUDOMONAS AERUGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAHU PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 GENE: PA0122; 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_VECTOR: PET21C KEYWDS AEGEROLYSIN, PSEUDOMONAS AERUGINOSA, RAHU PROTEIN, PROTEIN-MEMBRANE KEYWDS 2 INTERACTION, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR M.PODOBNIK,G.ANDERLUH,T.LENARCIC REVDAT 2 24-JAN-24 6ZC1 1 REMARK REVDAT 1 07-APR-21 6ZC1 0 JRNL AUTH E.KOCAR,T.LENARCIC,V.HODNIK,A.PANEVSKA,Y.HUANG,G.BAJC, JRNL AUTH 2 R.KOSTANJSEK,A.P.NAREN,P.MACEK,G.ANDERLUH,K.SEPCIC, JRNL AUTH 3 M.PODOBNIK,M.BUTALA JRNL TITL CRYSTAL STRUCTURE OF RAHU, AN AEGEROLYSIN PROTEIN FROM THE JRNL TITL 2 HUMAN PATHOGEN PSEUDOMONAS AERUGINOSA, AND ITS INTERACTION JRNL TITL 3 WITH MEMBRANE CERAMIDE PHOSPHORYLETHANOLAMINE. JRNL REF SCI REP V. 11 6572 2021 JRNL REFN ESSN 2045-2322 JRNL PMID 33753805 JRNL DOI 10.1038/S41598-021-85956-2 REMARK 2 REMARK 2 RESOLUTION. 1.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1 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) : 1.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 39461 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 30.8700 - 3.0599 0.99 2922 156 0.1373 0.1260 REMARK 3 2 3.0599 - 2.4290 1.00 2853 152 0.1630 0.1748 REMARK 3 3 2.4290 - 2.1221 0.99 2838 152 0.1589 0.1800 REMARK 3 4 2.1221 - 1.9281 0.99 2794 149 0.1522 0.1747 REMARK 3 5 1.9281 - 1.7899 0.99 2831 152 0.1592 0.1727 REMARK 3 6 1.7899 - 1.6844 0.98 2800 149 0.1522 0.1645 REMARK 3 7 1.6844 - 1.6000 0.98 2777 148 0.1468 0.1692 REMARK 3 8 1.6000 - 1.5304 0.98 2793 149 0.1588 0.1592 REMARK 3 9 1.5304 - 1.4715 0.97 2740 147 0.1600 0.1778 REMARK 3 10 1.4715 - 1.4207 0.96 2729 145 0.1738 0.1861 REMARK 3 11 1.4207 - 1.3763 0.93 2663 142 0.1740 0.1920 REMARK 3 12 1.3763 - 1.3369 0.89 2492 134 0.2051 0.2275 REMARK 3 13 1.3369 - 1.3017 0.83 2373 126 0.2755 0.2994 REMARK 3 14 1.3017 - 1.2700 0.66 1856 99 0.3525 0.2957 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.97 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 1088 REMARK 3 ANGLE : 0.733 1489 REMARK 3 CHIRALITY : 0.077 161 REMARK 3 PLANARITY : 0.004 193 REMARK 3 DIHEDRAL : 8.044 583 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): 25.1309 36.6105 25.7700 REMARK 3 T TENSOR REMARK 3 T11: 0.0844 T22: 0.0910 REMARK 3 T33: 0.0836 T12: -0.0031 REMARK 3 T13: 0.0029 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 0.9703 L22: 0.8044 REMARK 3 L33: 0.7180 L12: 0.1768 REMARK 3 L13: 0.1739 L23: 0.1370 REMARK 3 S TENSOR REMARK 3 S11: 0.0377 S12: -0.0111 S13: -0.0930 REMARK 3 S21: 0.0670 S22: -0.0146 S23: 0.0373 REMARK 3 S31: 0.0415 S32: -0.0171 S33: 0.0020 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 6ZC1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109010. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JAN-15 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 : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : A VERTICAL COLLIMATING MIRROR, A REMARK 200 DOUBLE-CRYSTAL SI(111) REMARK 200 MONOCHROMATOR, A BENDABLE REMARK 200 FOCUSSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JAN 26, 2018 REMARK 200 DATA SCALING SOFTWARE : XSCALE JAN 26, 2018 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.270 REMARK 200 RESOLUTION RANGE LOW (A) : 30.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 6.479 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.99 REMARK 200 R MERGE FOR SHELL (I) : 0.58900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.470 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.16 REMARK 200 STARTING MODEL: 4OEB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DI-SODIUM TARTRATE, PEG 3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, 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 44.06850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.96950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.06850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.96950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 408 LIES ON A SPECIAL POSITION. 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 LEU A 139 REMARK 465 TYR A 140 REMARK 465 PHE A 141 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 423 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A 424 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH A 425 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A 426 DISTANCE = 9.24 ANGSTROMS DBREF 6ZC1 A 1 136 UNP Q9I710 Q9I710_PSEAE 1 136 SEQADV 6ZC1 GLU A 137 UNP Q9I710 EXPRESSION TAG SEQADV 6ZC1 ASN A 138 UNP Q9I710 EXPRESSION TAG SEQADV 6ZC1 LEU A 139 UNP Q9I710 EXPRESSION TAG SEQADV 6ZC1 TYR A 140 UNP Q9I710 EXPRESSION TAG SEQADV 6ZC1 PHE A 141 UNP Q9I710 EXPRESSION TAG SEQRES 1 A 141 MET ALA TYR ALA GLU TRP ILE ALA VAL LYS VAL VAL VAL SEQRES 2 A 141 SER LYS SER ILE GLY THR VAL GLY ILE ARG ASN ALA THR SEQRES 3 A 141 LEU GLN TRP GLY LYS PHE TYR ARG TYR THR ASN LYS ASP SEQRES 4 A 141 ASP GLU ILE SER THR GLU GLU VAL SER SER MET ASN VAL SEQRES 5 A 141 GLN ALA GLY SER PRO GLN TRP ILE ALA SER CYS GLY ARG SEQRES 6 A 141 GLU ASN ALA SER SER GLY THR GLN GLY SER PHE ASP CYS SEQRES 7 A 141 TYR ASP GLY ASN THR LYS MET GLY THR PHE SER TRP ASP SEQRES 8 A 141 ASP PRO TRP LYS SER GLY ALA THR ASN THR TRP SER PHE SEQRES 9 A 141 THR PRO ALA SER ALA ASP TYR ALA GLY ILE THR SER GLY SEQRES 10 A 141 GLY ASN ALA THR GLY THR ASP ILE GLY GLU VAL THR LEU SEQRES 11 A 141 THR LEU GLY ARG PHE SER GLU ASN LEU TYR PHE FORMUL 2 HOH *226(H2 O) HELIX 1 AA1 SER A 43 SER A 48 1 6 SHEET 1 AA1 6 GLU A 41 ILE A 42 0 SHEET 2 AA1 6 LYS A 31 TYR A 33 -1 N PHE A 32 O ILE A 42 SHEET 3 AA1 6 GLN A 58 CYS A 63 -1 O CYS A 63 N LYS A 31 SHEET 4 AA1 6 TRP A 6 VAL A 13 -1 N VAL A 9 O ILE A 60 SHEET 5 AA1 6 GLY A 126 ARG A 134 1 O LEU A 130 N LYS A 10 SHEET 6 AA1 6 TYR A 111 GLY A 117 -1 N SER A 116 O THR A 129 SHEET 1 AA2 5 ASN A 51 GLN A 53 0 SHEET 2 AA2 5 THR A 19 TRP A 29 -1 N VAL A 20 O VAL A 52 SHEET 3 AA2 5 THR A 72 ASP A 80 -1 O ASP A 77 N ARG A 23 SHEET 4 AA2 5 THR A 83 ASP A 92 -1 O MET A 85 N CYS A 78 SHEET 5 AA2 5 THR A 101 PRO A 106 -1 O THR A 101 N ASP A 91 CISPEP 1 TYR A 35 THR A 36 0 12.20 CRYST1 88.137 47.939 40.649 90.00 110.28 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 0.011346 0.000000 0.004191 0.00000 SCALE2 0.000000 0.020860 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026226 0.00000