HEADER STRUCTURAL PROTEIN 04-NOV-22 8BJD TITLE FULL LENGTH STRUCTURE OF LPMIP WITH BOUND INHIBITOR JK095 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.2.1.8; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA; SOURCE 3 ORGANISM_TAXID: 446; SOURCE 4 GENE: C3927_03235; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL23 (DE3) KEYWDS MACROPHAGE, POTENTIATOR, SOLUBLE, PROTEIN., STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.J.WHITTAKER,A.GUSKOV,B.GORETZKI,U.A.HELLMICH REVDAT 2 13-SEP-23 8BJD 1 JRNL REVDAT 1 06-SEP-23 8BJD 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. 2.40 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 55.5 REMARK 3 NUMBER OF REFLECTIONS : 19488 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.294 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 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 8BJD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126458. 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 : 6.5 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 : 19644 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 61.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.08000 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 (%): 62.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 %(W/V) PEG 6000, 500 MM ZINC REMARK 280 ACETATE DIHYDRATE, 100 MM MES, PH 6.5., VAPOR DIFFUSION, SITTING REMARK 280 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 51.79850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.37600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.37600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.69775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.37600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.37600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.89925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.37600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.37600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 77.69775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.37600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.37600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.89925 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 51.79850 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: 4660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -137.0 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 51.79850 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 ASN A 28 36.00 -94.36 REMARK 500 ALA A 184 -91.85 -115.79 REMARK 500 SER A 189 32.06 -147.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 164 OE1 REMARK 620 2 GLU A 164 OE2 58.7 REMARK 620 3 HIS A 205 NE2 24.0 63.3 REMARK 620 N 1 2 DBREF1 8BJD A 6 213 UNP A0A2S6FAG4_LEGPN DBREF2 8BJD A A0A2S6FAG4 28 235 SEQRES 1 A 208 SER LEU ALA THR ASP LYS ASP LYS LEU SER TYR SER ILE SEQRES 2 A 208 GLY ALA ASP LEU GLY LYS ASN PHE LYS ASN GLN GLY ILE SEQRES 3 A 208 ASP VAL ASN PRO GLU ALA MET ALA LYS GLY MET GLN ASP SEQRES 4 A 208 ALA MET SER GLY ALA GLN LEU ALA LEU THR GLU GLN GLN SEQRES 5 A 208 MET LYS ASP VAL LEU ASN LYS PHE GLN LYS ASP LEU MET SEQRES 6 A 208 ALA LYS ARG THR ALA GLU PHE ASN LYS LYS ALA ASP GLU SEQRES 7 A 208 ASN LYS VAL LYS GLY GLU ALA PHE LEU THR GLU ASN LYS SEQRES 8 A 208 ASN LYS PRO GLY VAL VAL VAL LEU PRO SER GLY LEU GLN SEQRES 9 A 208 TYR LYS VAL ILE ASN SER GLY ASN GLY VAL LYS PRO GLY SEQRES 10 A 208 LYS SER ASP THR VAL THR VAL GLU TYR THR GLY ARG LEU SEQRES 11 A 208 ILE ASP GLY THR VAL PHE ASP SER THR GLU LYS THR GLY SEQRES 12 A 208 LYS PRO ALA THR PHE GLN VAL SER GLN VAL ILE PRO GLY SEQRES 13 A 208 TRP THR GLU ALA LEU GLN LEU MET PRO ALA GLY SER THR SEQRES 14 A 208 TRP GLU ILE TYR VAL PRO SER GLY LEU ALA TYR GLY PRO SEQRES 15 A 208 ARG SER VAL GLY GLY PRO ILE GLY PRO ASN GLU THR LEU SEQRES 16 A 208 ILE PHE LYS ILE HIS LEU ILE SER VAL LYS LYS SER SER HET 9QN A 301 31 HET MES A 302 12 HET ZN A 303 1 HET ZN A 304 1 HET GOL A 305 6 HETNAM 9QN (1~{S},5~{S},6~{R})-10-[3,5-BIS(CHLORANYL) HETNAM 2 9QN PHENYL]SULFONYL-5-(HYDROXYMETHYL)-3-(PYRIDIN-2- HETNAM 3 9QN YLMETHYL)-3,10-DIAZABICYCLO[4.3.1]DECAN-2-ONE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 9QN C21 H23 CL2 N3 O4 S FORMUL 3 MES C6 H13 N O4 S FORMUL 4 ZN 2(ZN 2+) FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *15(H2 O) HELIX 1 AA1 THR A 9 ASN A 28 1 20 HELIX 2 AA2 ASN A 34 GLY A 48 1 15 HELIX 3 AA3 THR A 54 LYS A 96 1 43 HELIX 4 AA4 THR A 144 GLY A 148 1 5 HELIX 5 AA5 SER A 156 VAL A 158 5 3 HELIX 6 AA6 ILE A 159 GLN A 167 1 9 HELIX 7 AA7 PRO A 180 ALA A 184 5 5 SHEET 1 AA1 6 VAL A 101 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 LEU A 200 N VAL A 179 SHEET 5 AA1 6 THR A 126 LEU A 135 -1 N THR A 128 O ILE A 207 SHEET 6 AA1 6 VAL A 140 SER A 143 -1 O ASP A 142 N GLY A 133 SHEET 1 AA2 6 VAL A 101 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 LEU A 200 N VAL A 179 SHEET 5 AA2 6 THR A 126 LEU A 135 -1 N THR A 128 O ILE A 207 SHEET 6 AA2 6 ALA A 151 GLN A 154 -1 O PHE A 153 N VAL A 127 LINK OD1 ASP A 142 ZN ZN A 303 1555 1555 2.31 LINK OE1 GLU A 164 ZN ZN A 304 1555 1555 2.49 LINK OE2 GLU A 164 ZN ZN A 304 1555 1555 1.78 LINK NE2 HIS A 205 ZN ZN A 304 1555 3554 2.26 CRYST1 76.752 76.752 103.597 90.00 90.00 90.00 P 43 21 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 0.013029 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009653 0.00000