HEADER MEMBRANE PROTEIN 24-OCT-23 8QXP TITLE CRYSTAL STRUCTURE OF THE OUTER MEMBRANE PORIN OMPW FROM KLEBSIELLA TITLE 2 PNEUMONIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OMPW PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OUTER MEMBRANE PROTEIN OMPW; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: SEQUENCE OF MATURE PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: OMPW, BN49_2384, KPZU09_20550; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OUTER MEMBRANE PORIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.SEDDON,K.BEIS REVDAT 1 24-JAN-24 8QXP 0 JRNL AUTH C.SEDDON,G.FRANKEL,K.BEIS JRNL TITL STRUCTURE OF THE OUTER MEMBRANE PORIN OMPW FROM THE JRNL TITL 2 PERVASIVE PATHOGEN KLEBSIELLA PNEUMONIAE. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 80 22 2024 JRNL REFN ESSN 2053-230X JRNL PMID 38206593 JRNL DOI 10.1107/S2053230X23010579 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 5633 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.269 REMARK 3 R VALUE (WORKING SET) : 0.267 REMARK 3 FREE R VALUE : 0.312 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.190 REMARK 3 FREE R VALUE TEST SET COUNT : 236 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 52.9700 - 4.0300 1.00 2757 120 0.2643 0.2945 REMARK 3 2 3.3100 - 3.2000 1.00 0 0 0.2640 0.3636 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 98.04 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 : 0.003 1432 REMARK 3 ANGLE : 0.622 1950 REMARK 3 CHIRALITY : 0.045 211 REMARK 3 PLANARITY : 0.006 250 REMARK 3 DIHEDRAL : 14.720 191 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 8QXP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1292134152. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5639 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 52.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 64.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.32 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.35 M LITHIUM SULPHATE, 0.1 M SODIUM REMARK 280 ACETATE PH 4.0, 11% PEG 600, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 43.96400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 69.31800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.96400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 69.31800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.96400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 69.31800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.96400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 69.31800 REMARK 290 SMTRY3 8 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: 360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 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 53 REMARK 465 SER A 54 REMARK 465 ASP A 55 REMARK 465 ASN A 56 REMARK 465 VAL A 57 REMARK 465 LEU A 58 REMARK 465 GLY A 59 REMARK 465 SER A 60 REMARK 465 LEU A 61 REMARK 465 GLY A 62 REMARK 465 SER A 63 REMARK 465 PHE A 64 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 51 -14.49 -143.95 REMARK 500 THR A 81 -162.56 -102.88 REMARK 500 THR A 105 98.25 -59.86 REMARK 500 PRO A 113 64.09 -119.84 REMARK 500 ASP A 158 76.05 49.69 REMARK 500 ASN A 178 -145.00 -147.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 8QXP A 35 224 UNP W9B759 W9B759_KLEPN 35 224 SEQRES 1 A 190 GLU ALA GLY GLU PHE PHE ILE ARG ALA GLY THR ALA THR SEQRES 2 A 190 VAL ARG PRO THR GLU GLY SER ASP ASN VAL LEU GLY SER SEQRES 3 A 190 LEU GLY SER PHE ASN VAL SER ASN ASN THR GLN LEU GLY SEQRES 4 A 190 LEU THR PHE THR TYR MET ALA THR ASP ASN ILE GLY VAL SEQRES 5 A 190 GLU LEU LEU ALA ALA THR PRO PHE ARG HIS LYS VAL GLY SEQRES 6 A 190 THR GLY PRO THR GLY THR ILE ALA THR VAL HIS GLN LEU SEQRES 7 A 190 PRO PRO THR LEU MET ALA GLN TRP TYR PHE GLY ASP ALA SEQRES 8 A 190 GLN SER LYS VAL ARG PRO TYR VAL GLY ALA GLY ILE ASN SEQRES 9 A 190 TYR THR THR PHE PHE ASN GLU ASP PHE ASN ASP THR GLY SEQRES 10 A 190 LYS ALA ALA GLY LEU SER ASP LEU SER LEU LYS ASP SER SEQRES 11 A 190 TRP GLY ALA ALA GLY GLN VAL GLY LEU ASP TYR LEU ILE SEQRES 12 A 190 ASN ARG ASP TRP LEU LEU ASN MET SER VAL TRP TYR MET SEQRES 13 A 190 ASP ILE ASP THR ASP VAL LYS PHE LYS ALA GLY GLY VAL SEQRES 14 A 190 ASP GLN LYS VAL SER THR ARG LEU ASP PRO TRP VAL PHE SEQRES 15 A 190 MET PHE SER ALA GLY TYR ARG PHE HET SO4 A 301 5 HET SO4 A 302 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) HELIX 1 AA1 ASN A 148 ALA A 153 1 6 SHEET 1 AA111 PHE A 94 THR A 100 0 SHEET 2 AA111 GLY A 104 LEU A 112 -1 O VAL A 109 N HIS A 96 SHEET 3 AA111 VAL A 129 PHE A 147 -1 O PHE A 143 N HIS A 110 SHEET 4 AA111 SER A 164 LEU A 176 -1 O GLY A 166 N ASN A 138 SHEET 5 AA111 TRP A 181 MET A 190 -1 O TYR A 189 N GLY A 169 SHEET 6 AA111 TRP A 214 ARG A 223 -1 O VAL A 215 N TRP A 188 SHEET 7 AA111 PHE A 39 ARG A 49 -1 N ARG A 49 O TRP A 214 SHEET 8 AA111 ASN A 69 MET A 79 -1 O GLN A 71 N ALA A 46 SHEET 9 AA111 ILE A 84 ALA A 91 -1 O ALA A 90 N LEU A 74 SHEET 10 AA111 THR A 115 TYR A 121 -1 O THR A 115 N LEU A 89 SHEET 11 AA111 VAL A 129 PHE A 147 -1 O ALA A 135 N ALA A 118 SHEET 1 AA2 3 LEU A 156 LEU A 161 0 SHEET 2 AA2 3 ASP A 193 ALA A 200 -1 O LYS A 199 N SER A 157 SHEET 3 AA2 3 VAL A 203 ARG A 210 -1 O GLN A 205 N PHE A 198 CRYST1 87.928 138.636 52.968 90.00 90.00 90.00 C 2 2 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 0.011373 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007213 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018879 0.00000