HEADER LIPID BINDING PROTEIN 05-JUN-21 7F0K TITLE CRYSTAL STRUCTURE OF KMP11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: KINETOPLASTID MEMBRANE PROTEIN KMP-11; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI GAMBIENSE (STRAIN SOURCE 3 MHOM/CI/86/DAL972); SOURCE 4 ORGANISM_TAXID: 679716; SOURCE 5 STRAIN: MHOM/CI/86/DAL972; SOURCE 6 GENE: TBGDAL_IX8640, TBGDAL_IX8650, TBGDAL_IX8660, TBGDAL_IX8670; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KMP11, KINETOPLASTID, MEMBRANE BINDING PROTEIN, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.MO REVDAT 1 11-AUG-21 7F0K 0 JRNL AUTH X.MO JRNL TITL STRUCTURAL INSIGHT INTO DYNAMIC CHARACTERISTIC OF THE JRNL TITL 2 POLYMERIZED FORMS OF KINETOPLASTID MEMBRANE PROTEIN-11 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 2581 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.257 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 128 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 0.0000 - 3.5000 0.97 2453 128 0.2574 0.2984 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) : 0.463 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.812 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.87 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 : 0.002 1424 REMARK 3 ANGLE : 0.334 1888 REMARK 3 CHIRALITY : 0.027 181 REMARK 3 PLANARITY : 0.004 249 REMARK 3 DIHEDRAL : 3.165 171 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN 'A' AND RESID 4 THROUGH 80) REMARK 3 SELECTION : CHAIN 'B' REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7F0K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022626. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-19 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 : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2583 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.63 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: SAD REMARK 200 SOFTWARE USED: PHENIX 1.14_3260 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, POLYETHYLENE GLYCOL REMARK 280 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 280K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.44950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.04750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.27200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.04750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.44950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.27200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL 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 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 ALA A 87 REMARK 465 GLN A 88 REMARK 465 PHE A 89 REMARK 465 PRO A 90 REMARK 465 GLY A 91 REMARK 465 LYS A 92 REMARK 465 MSE B 1 REMARK 465 ALA B 2 REMARK 465 THR B 3 REMARK 465 LEU B 81 REMARK 465 GLU B 82 REMARK 465 GLN B 83 REMARK 465 GLN B 84 REMARK 465 LYS B 85 REMARK 465 ASN B 86 REMARK 465 ALA B 87 REMARK 465 GLN B 88 REMARK 465 PHE B 89 REMARK 465 PRO B 90 REMARK 465 GLY B 91 REMARK 465 LYS B 92 DBREF 7F0K A 1 92 UNP C9ZZD9 C9ZZD9_TRYB9 1 92 DBREF 7F0K B 1 92 UNP C9ZZD9 C9ZZD9_TRYB9 1 92 SEQRES 1 A 92 MSE ALA THR THR TYR GLU GLU PHE ALA ALA LYS LEU ASP SEQRES 2 A 92 ARG LEU ASP ALA GLU PHE ALA LYS LYS MSE GLU GLU GLN SEQRES 3 A 92 ASN LYS ARG PHE PHE ALA ASP LYS PRO ASP GLU ALA THR SEQRES 4 A 92 LEU SER PRO GLU MSE LYS GLU HIS TYR GLU LYS PHE GLU SEQRES 5 A 92 LYS MSE ILE GLN GLU HIS THR ASP LYS PHE ASN LYS LYS SEQRES 6 A 92 MSE ARG GLU HIS SER GLU HIS PHE LYS ALA LYS PHE ALA SEQRES 7 A 92 GLU LEU LEU GLU GLN GLN LYS ASN ALA GLN PHE PRO GLY SEQRES 8 A 92 LYS SEQRES 1 B 92 MSE ALA THR THR TYR GLU GLU PHE ALA ALA LYS LEU ASP SEQRES 2 B 92 ARG LEU ASP ALA GLU PHE ALA LYS LYS MSE GLU GLU GLN SEQRES 3 B 92 ASN LYS ARG PHE PHE ALA ASP LYS PRO ASP GLU ALA THR SEQRES 4 B 92 LEU SER PRO GLU MSE LYS GLU HIS TYR GLU LYS PHE GLU SEQRES 5 B 92 LYS MSE ILE GLN GLU HIS THR ASP LYS PHE ASN LYS LYS SEQRES 6 B 92 MSE ARG GLU HIS SER GLU HIS PHE LYS ALA LYS PHE ALA SEQRES 7 B 92 GLU LEU LEU GLU GLN GLN LYS ASN ALA GLN PHE PRO GLY SEQRES 8 B 92 LYS MODRES 7F0K MSE A 1 MET MODIFIED RESIDUE MODRES 7F0K MSE A 23 MET MODIFIED RESIDUE MODRES 7F0K MSE A 44 MET MODIFIED RESIDUE MODRES 7F0K MSE A 54 MET MODIFIED RESIDUE MODRES 7F0K MSE A 66 MET MODIFIED RESIDUE MODRES 7F0K MSE B 23 MET MODIFIED RESIDUE MODRES 7F0K MSE B 44 MET MODIFIED RESIDUE MODRES 7F0K MSE B 54 MET MODIFIED RESIDUE MODRES 7F0K MSE B 66 MET MODIFIED RESIDUE HET MSE A 1 8 HET MSE A 23 8 HET MSE A 44 8 HET MSE A 54 8 HET MSE A 66 8 HET MSE B 23 8 HET MSE B 44 8 HET MSE B 54 8 HET MSE B 66 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 9(C5 H11 N O2 SE) HELIX 1 AA1 MSE A 1 ALA A 32 1 32 HELIX 2 AA2 SER A 41 ASN A 86 1 46 HELIX 3 AA3 TYR B 5 PHE B 31 1 27 HELIX 4 AA4 ALA B 32 LYS B 34 5 3 HELIX 5 AA5 SER B 41 LEU B 80 1 40 LINK C MSE A 1 N ALA A 2 1555 1555 1.34 LINK C LYS A 22 N MSE A 23 1555 1555 1.33 LINK C MSE A 23 N GLU A 24 1555 1555 1.34 LINK C GLU A 43 N MSE A 44 1555 1555 1.33 LINK C MSE A 44 N LYS A 45 1555 1555 1.34 LINK C LYS A 53 N MSE A 54 1555 1555 1.33 LINK C MSE A 54 N ILE A 55 1555 1555 1.34 LINK C LYS A 65 N MSE A 66 1555 1555 1.33 LINK C MSE A 66 N ARG A 67 1555 1555 1.34 LINK C LYS B 22 N MSE B 23 1555 1555 1.33 LINK C MSE B 23 N GLU B 24 1555 1555 1.33 LINK C GLU B 43 N MSE B 44 1555 1555 1.33 LINK C MSE B 44 N LYS B 45 1555 1555 1.33 LINK C LYS B 53 N MSE B 54 1555 1555 1.33 LINK C MSE B 54 N ILE B 55 1555 1555 1.34 LINK C LYS B 65 N MSE B 66 1555 1555 1.33 LINK C MSE B 66 N ARG B 67 1555 1555 1.33 CRYST1 34.899 38.544 142.095 90.00 90.00 90.00 P 21 21 21 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 0.028654 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007038 0.00000 HETATM 1 N MSE A 1 18.978 8.669 58.633 1.00 20.31 N HETATM 2 CA MSE A 1 17.612 8.857 58.157 1.00 34.21 C HETATM 3 C MSE A 1 17.604 9.694 56.884 1.00 34.01 C HETATM 4 O MSE A 1 17.025 9.298 55.872 1.00 29.61 O HETATM 5 CB MSE A 1 16.751 9.519 59.238 1.00 60.09 C HETATM 6 CG MSE A 1 15.242 9.318 59.076 1.00 76.09 C HETATM 7 SE MSE A 1 14.395 10.567 57.832 1.00 83.22 SE HETATM 8 CE MSE A 1 12.542 10.406 58.419 1.00 23.42 C