HEADER STRUCTURAL PROTEIN 17-MAY-23 8P3D TITLE FULL LENGTH STRUCTURE OF TCMIP WITH BOUND INHIBITOR NJS224. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYLPROLYL ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.2.1.8; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA CRUZI; SOURCE 3 ORGANISM_TAXID: 5693; SOURCE 4 GENE: TC00.1047053508897.110; 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,B.GORETZKI,U.A.HELLMICH REVDAT 1 12-JUN-24 8P3D 0 JRNL AUTH J.J.WHITTAKER,A.GUSKOV,B.GORETZKI,U.A.HELLMICH JRNL TITL STRUCTURAL DYNAMICS OF MACROPHAGE INFECTIVITY POTENTIATOR JRNL TITL 2 PROTEINS (MIPS) ARE DIFFERENTIALLY MODULATED BY INHIBITORS JRNL TITL 3 AND APPENDAGE DOMAINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.71 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 18058 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 860 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 46.7700 - 3.1100 0.98 2977 163 0.1721 0.2147 REMARK 3 2 3.1100 - 2.4700 0.98 2940 132 0.1925 0.1997 REMARK 3 3 2.4700 - 2.1500 0.87 2601 117 0.1753 0.2126 REMARK 3 4 2.1500 - 1.9600 0.99 2920 132 0.1822 0.2176 REMARK 3 5 1.9600 - 1.8200 0.99 2876 162 0.1965 0.2474 REMARK 3 6 1.8200 - 1.7100 0.98 2884 154 0.2240 0.2825 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.600 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 : 0.013 1354 REMARK 3 ANGLE : 1.006 1820 REMARK 3 CHIRALITY : 0.068 185 REMARK 3 PLANARITY : 0.014 243 REMARK 3 DIHEDRAL : 9.029 202 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 8P3D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130591. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-AUG-21 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 : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18060 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 46.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5 MM TRIS PH 7.5 150 MM NACL PEG2000 REMARK 280 12 %, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 17.34800 REMARK 290 SMTRY3 2 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: 530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 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 SER A 75 118.05 -160.26 REMARK 500 ALA A 116 -121.41 -129.22 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 NA A 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 67 O REMARK 620 2 GLU A 133 OE1 131.4 REMARK 620 3 HOH A 439 O 123.6 101.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 204 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 100 O REMARK 620 2 ASP A 105 OD2 102.3 REMARK 620 3 HOH A 400 O 137.3 115.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 118 O REMARK 620 2 PRO A 127 O 114.7 REMARK 620 N 1 DBREF 8P3D A 5 166 UNP Q4D932 Q4D932_TRYCC 34 195 SEQRES 1 A 162 ALA SER HIS GLU GLU ARG MET ASN ASN TYR ARG LYS ARG SEQRES 2 A 162 VAL GLY ARG LEU PHE MET GLU GLN LYS ALA ALA GLN PRO SEQRES 3 A 162 ASP ALA VAL LYS LEU PRO SER GLY LEU VAL PHE GLN ARG SEQRES 4 A 162 ILE ALA ARG GLY SER GLY LYS ARG ALA PRO ALA ILE ASP SEQRES 5 A 162 ASP LYS CYS GLU VAL HIS TYR THR GLY ARG LEU ARG ASP SEQRES 6 A 162 GLY THR VAL PHE ASP SER SER ARG GLU ARG GLY LYS PRO SEQRES 7 A 162 THR THR PHE ARG PRO ASN GLU VAL ILE LYS GLY TRP THR SEQRES 8 A 162 GLU ALA LEU GLN LEU MET ARG GLU GLY ASP ARG TRP ARG SEQRES 9 A 162 LEU PHE ILE PRO TYR ASP LEU ALA TYR GLY VAL THR GLY SEQRES 10 A 162 GLY GLY GLY MET ILE PRO PRO TYR SER PRO LEU GLU PHE SEQRES 11 A 162 ASP VAL GLU LEU ILE SER ILE LYS ASP GLY GLY LYS GLY SEQRES 12 A 162 ARG THR ALA GLU GLU VAL ASP GLU ILE LEU ARG LYS ALA SEQRES 13 A 162 GLU GLU ASP ARG GLU ASP HET WS5 A 201 68 HET NA A 202 1 HET NA A 203 1 HET NA A 204 1 HET NA A 205 1 HETNAM WS5 (2~{S})-1-[(4-FLUOROPHENYL)METHYLSULFONYL]-~{N}- HETNAM 2 WS5 [(2~{S})-4-METHYL-1-OXIDANYLIDENE-1-(PYRIDIN-3- HETNAM 3 WS5 YLMETHYLAMINO)PENTAN-2-YL]PIPERIDINE-2-CARBOXAMIDE HETNAM NA SODIUM ION FORMUL 2 WS5 C25 H33 F N4 O4 S FORMUL 3 NA 4(NA 1+) FORMUL 7 HOH *168(H2 O) HELIX 1 AA1 SER A 6 ALA A 28 1 23 HELIX 2 AA2 SER A 76 GLY A 80 1 5 HELIX 3 AA3 ARG A 86 VAL A 90 5 5 HELIX 4 AA4 ILE A 91 GLN A 99 1 9 HELIX 5 AA5 PRO A 112 ALA A 116 5 5 HELIX 6 AA6 ASP A 143 GLY A 145 5 3 HELIX 7 AA7 THR A 149 ASP A 163 1 15 SHEET 1 AA1 6 ALA A 32 LYS A 34 0 SHEET 2 AA1 6 VAL A 40 ALA A 45 -1 O PHE A 41 N VAL A 33 SHEET 3 AA1 6 ARG A 106 ILE A 111 -1 O PHE A 110 N VAL A 40 SHEET 4 AA1 6 LEU A 132 ILE A 141 -1 O PHE A 134 N LEU A 109 SHEET 5 AA1 6 CYS A 59 ARG A 66 -1 N ARG A 66 O GLU A 133 SHEET 6 AA1 6 VAL A 72 SER A 75 -1 O ASP A 74 N GLY A 65 SHEET 1 AA2 6 ALA A 32 LYS A 34 0 SHEET 2 AA2 6 VAL A 40 ALA A 45 -1 O PHE A 41 N VAL A 33 SHEET 3 AA2 6 ARG A 106 ILE A 111 -1 O PHE A 110 N VAL A 40 SHEET 4 AA2 6 LEU A 132 ILE A 141 -1 O PHE A 134 N LEU A 109 SHEET 5 AA2 6 CYS A 59 ARG A 66 -1 N ARG A 66 O GLU A 133 SHEET 6 AA2 6 THR A 83 PHE A 85 -1 O PHE A 85 N CYS A 59 LINK O LEU A 67 NA NA A 205 1555 1555 2.79 LINK O LEU A 100 NA NA A 204 1555 1555 2.90 LINK OD2 ASP A 105 NA NA A 204 1555 1555 2.71 LINK O GLY A 118 NA NA A 202 1555 1555 2.72 LINK O PRO A 127 NA NA A 202 1555 1555 2.76 LINK O SER A 130 NA NA A 203 1555 1555 2.78 LINK OE1 GLU A 133 NA NA A 205 1555 1555 2.65 LINK NA NA A 204 O HOH A 400 1555 1555 2.72 LINK NA NA A 205 O HOH A 439 1555 1555 2.42 CRYST1 46.858 34.696 53.081 90.00 93.53 90.00 P 1 21 1 2 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 0.021341 0.000000 0.001316 0.00000 SCALE2 0.000000 0.028822 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018875 0.00000