HEADER STRUCTURAL PROTEIN 08-NOV-22 8BK6 TITLE A TRUNCATED STRUCTURE OF LPMIP WITH BOUND INHIBITOR JK095. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA; SOURCE 3 ORGANISM_TAXID: 446; SOURCE 4 GENE: MIP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MACROPHAGE, POTENTIATOR, SOLUBLE, PROTEIN., STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.J.WHITTAKER,A.GUSKOV,A.U.HELLMICH,B.GORETZKI REVDAT 2 13-SEP-23 8BK6 1 JRNL REVDAT 1 06-SEP-23 8BK6 0 JRNL AUTH C.WIEDEMANN,J.J.WHITTAKER,V.H.PEREZ CARRILLO,B.GORETZKI, JRNL AUTH 2 M.DAJKA,F.TEBBE,J.M.HARDER,P.R.KRAJCZY,B.JOSEPH,F.HAUSCH, JRNL AUTH 3 A.GUSKOV,U.A.HELLMICH JRNL TITL LEGIONELLA PNEUMOPHILA MACROPHAGE INFECTIVITY POTENTIATOR JRNL TITL 2 PROTEIN APPENDAGE DOMAINS MODULATE PROTEIN DYNAMICS AND JRNL TITL 3 INHIBITOR BINDING. JRNL REF INT.J.BIOL.MACROMOL. V. 252 26366 2023 JRNL REFN ISSN 0141-8130 JRNL PMID 37633566 JRNL DOI 10.1016/J.IJBIOMAC.2023.126366 REMARK 2 REMARK 2 RESOLUTION. 2.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.263 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13801 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.287 REMARK 3 R VALUE (WORKING SET) : 0.287 REMARK 3 FREE R VALUE : 0.348 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 5.5000 - 3.8700 1.00 2784 134 0.2534 0.2897 REMARK 3 2 3.8700 - 3.0700 1.00 2639 135 0.2919 0.4063 REMARK 3 3 3.0700 - 2.6800 1.00 2594 133 0.3014 0.3540 REMARK 3 4 2.6800 - 2.4400 1.00 2553 139 0.2979 0.3579 REMARK 3 5 2.4400 - 2.2630 1.00 2566 124 0.3166 0.4167 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.011 1760 REMARK 3 ANGLE : 1.797 2386 REMARK 3 CHIRALITY : 0.085 274 REMARK 3 PLANARITY : 0.015 296 REMARK 3 DIHEDRAL : 14.927 257 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 8BK6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126463. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-22 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 : ESRF REMARK 200 BEAMLINE : ID23-1 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13801 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.263 REMARK 200 RESOLUTION RANGE LOW (A) : 59.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 5.50 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: 1FD9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 %(V/V) 2-PROPANOL, 0.2 M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE, 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 51.64300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.77850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.77850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.46450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.77850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.77850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.82150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.77850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.77850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 77.46450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.77850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.77850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.82150 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 51.64300 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 146 CG CD CE NZ 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 ALA A 184 -103.18 -130.49 REMARK 500 ALA B 184 -117.70 -123.78 REMARK 500 SER B 189 144.89 73.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 188 0.25 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8BK6 A 100 212 UNP Q933L8 Q933L8_LEGPN 120 232 DBREF 8BK6 B 100 212 UNP Q933L8 Q933L8_LEGPN 120 232 SEQRES 1 A 113 GLY VAL VAL VAL LEU PRO SER GLY LEU GLN TYR LYS VAL SEQRES 2 A 113 ILE ASN SER GLY ASN GLY VAL LYS PRO GLY LYS SER ASP SEQRES 3 A 113 THR VAL THR VAL GLU TYR THR GLY ARG LEU ILE ASP GLY SEQRES 4 A 113 THR VAL PHE ASP SER THR GLU LYS THR GLY LYS PRO ALA SEQRES 5 A 113 THR PHE GLN VAL SER GLN VAL ILE PRO GLY TRP THR GLU SEQRES 6 A 113 ALA LEU GLN LEU MET PRO ALA GLY SER THR TRP GLU ILE SEQRES 7 A 113 TYR VAL PRO SER GLY LEU ALA TYR GLY PRO ARG SER VAL SEQRES 8 A 113 GLY GLY PRO ILE GLY PRO ASN GLU THR LEU ILE PHE LYS SEQRES 9 A 113 ILE HIS LEU ILE SER VAL LYS LYS SER SEQRES 1 B 113 GLY VAL VAL VAL LEU PRO SER GLY LEU GLN TYR LYS VAL SEQRES 2 B 113 ILE ASN SER GLY ASN GLY VAL LYS PRO GLY LYS SER ASP SEQRES 3 B 113 THR VAL THR VAL GLU TYR THR GLY ARG LEU ILE ASP GLY SEQRES 4 B 113 THR VAL PHE ASP SER THR GLU LYS THR GLY LYS PRO ALA SEQRES 5 B 113 THR PHE GLN VAL SER GLN VAL ILE PRO GLY TRP THR GLU SEQRES 6 B 113 ALA LEU GLN LEU MET PRO ALA GLY SER THR TRP GLU ILE SEQRES 7 B 113 TYR VAL PRO SER GLY LEU ALA TYR GLY PRO ARG SER VAL SEQRES 8 B 113 GLY GLY PRO ILE GLY PRO ASN GLU THR LEU ILE PHE LYS SEQRES 9 B 113 ILE HIS LEU ILE SER VAL LYS LYS SER HET PEG A 301 7 HET PEG A 302 7 HET MES A 303 12 HET PEG B 301 7 HET PEG B 302 7 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 3 PEG 4(C4 H10 O3) FORMUL 5 MES C6 H13 N O4 S FORMUL 8 HOH *13(H2 O) HELIX 1 AA1 THR A 144 GLY A 148 1 5 HELIX 2 AA2 SER A 156 VAL A 158 5 3 HELIX 3 AA3 ILE A 159 GLN A 167 1 9 HELIX 4 AA4 PRO A 180 ALA A 184 5 5 HELIX 5 AA5 SER B 156 VAL B 158 5 3 HELIX 6 AA6 ILE B 159 MET B 169 1 11 HELIX 7 AA7 PRO B 180 ALA B 184 5 5 HELIX 8 AA8 TYR B 185 SER B 189 5 5 SHEET 1 AA1 6 VAL A 102 VAL A 103 0 SHEET 2 AA1 6 GLN A 109 ASN A 114 -1 O TYR A 110 N VAL A 102 SHEET 3 AA1 6 THR A 174 VAL A 179 -1 O TYR A 178 N GLN A 109 SHEET 4 AA1 6 LEU A 200 LYS A 210 -1 O ILE A 204 N TRP A 175 SHEET 5 AA1 6 THR A 126 ARG A 134 -1 N GLU A 130 O HIS A 205 SHEET 6 AA1 6 VAL A 140 SER A 143 -1 O PHE A 141 N GLY A 133 SHEET 1 AA2 6 VAL A 102 VAL A 103 0 SHEET 2 AA2 6 GLN A 109 ASN A 114 -1 O TYR A 110 N VAL A 102 SHEET 3 AA2 6 THR A 174 VAL A 179 -1 O TYR A 178 N GLN A 109 SHEET 4 AA2 6 LEU A 200 LYS A 210 -1 O ILE A 204 N TRP A 175 SHEET 5 AA2 6 THR A 126 ARG A 134 -1 N GLU A 130 O HIS A 205 SHEET 6 AA2 6 ALA A 151 GLN A 154 -1 O ALA A 151 N VAL A 129 SHEET 1 AA3 6 VAL B 102 VAL B 103 0 SHEET 2 AA3 6 GLN B 109 ASN B 114 -1 O TYR B 110 N VAL B 102 SHEET 3 AA3 6 THR B 174 VAL B 179 -1 O THR B 174 N ASN B 114 SHEET 4 AA3 6 LEU B 200 LYS B 210 -1 O LEU B 200 N VAL B 179 SHEET 5 AA3 6 THR B 126 LEU B 135 -1 N THR B 126 O LYS B 210 SHEET 6 AA3 6 VAL B 140 SER B 143 -1 O ASP B 142 N GLY B 133 SHEET 1 AA4 6 VAL B 102 VAL B 103 0 SHEET 2 AA4 6 GLN B 109 ASN B 114 -1 O TYR B 110 N VAL B 102 SHEET 3 AA4 6 THR B 174 VAL B 179 -1 O THR B 174 N ASN B 114 SHEET 4 AA4 6 LEU B 200 LYS B 210 -1 O LEU B 200 N VAL B 179 SHEET 5 AA4 6 THR B 126 LEU B 135 -1 N THR B 126 O LYS B 210 SHEET 6 AA4 6 ALA B 151 GLN B 154 -1 O PHE B 153 N VAL B 127 CRYST1 73.557 73.557 103.286 90.00 90.00 90.00 P 43 21 2 16 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 0.013595 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013595 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009682 0.00000