HEADER MEMBRANE PROTEIN 21-NOV-01 1KFN TITLE CORE SIDE-CHAIN PACKING AND BACKBONE CONFORMATION IN LPP-56 COILED- TITLE 2 COIL MUTANTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR OUTER MEMBRANE LIPOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MUREIN-LIPOPROTEIN LPP, MUREIN-LIPOPROTEIN LPP; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS LIPOPROTEIN, PROTEIN FOLDING, HELIX CAPPING, ALANINE-ZIPPER, MEMBRANE KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,W.CAO,M.LU REVDAT 5 07-FEB-24 1KFN 1 REMARK REVDAT 4 27-OCT-21 1KFN 1 REMARK SEQADV REVDAT 3 13-JUL-11 1KFN 1 VERSN REVDAT 2 24-FEB-09 1KFN 1 VERSN REVDAT 1 28-JUN-02 1KFN 0 JRNL AUTH J.LIU,W.CAO,M.LU JRNL TITL CORE SIDE-CHAIN PACKING AND BACKBONE CONFORMATION IN LPP-56 JRNL TITL 2 COILED-COIL MUTANTS. JRNL REF J.MOL.BIOL. V. 318 877 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12054830 JRNL DOI 10.1016/S0022-2836(02)00138-9 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 4921 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.500 REMARK 3 FREE R VALUE TEST SET COUNT : 517 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.71 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 413 REMARK 3 BIN R VALUE (WORKING SET) : 0.3420 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 12.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 57 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.044 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 386 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.00000 REMARK 3 B22 (A**2) : -3.00000 REMARK 3 B33 (A**2) : 6.00000 REMARK 3 B12 (A**2) : -0.21000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.530 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.200 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.740 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.100 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.46 REMARK 3 BSOL : 65.65 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KFN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000014905. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MADNESS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4921 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.20300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, AMMONIUM REMARK 280 ACETATE, L-CYSTEIN, PH 4.0, VAPOR DIFFUSION, HANGING DROP AT REMARK 280 293K, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 18.14500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 10.47602 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.82433 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 18.14500 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 10.47602 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.82433 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 18.14500 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 10.47602 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.82433 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 20.95204 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 55.64867 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 20.95204 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 55.64867 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 20.95204 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 55.64867 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TRIMER GENERATED FROM THE REMARK 300 MONOMER BY THE THREE FOLD AXIS. 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 -0.500000 -0.866025 0.000000 36.29000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 18.14500 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 31.42806 REMARK 350 BIOMT3 3 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 LYS A 54 REMARK 465 TYR A 55 REMARK 465 ARG A 56 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EQ7 RELATED DB: PDB REMARK 900 THE WILD TYPE PROTEIN STRUCTURE REMARK 900 RELATED ID: 1JCB RELATED DB: PDB REMARK 900 MUTANT OF 1EQ7 REMARK 900 RELATED ID: 1KFM RELATED DB: PDB REMARK 900 MUTANT OF 1EQ7 DBREF 1KFN A 1 56 UNP P69776 LPP_ECOLI 22 77 SEQADV 1KFN ALA A 23 UNP P69776 LEU 44 ENGINEERED MUTATION SEQADV 1KFN ALA A 27 UNP P69776 VAL 48 ENGINEERED MUTATION SEQADV 1KFN ALA A 30 UNP P69776 MET 51 ENGINEERED MUTATION SEQADV 1KFN ALA A 34 UNP P69776 VAL 55 ENGINEERED MUTATION SEQRES 1 A 56 SER SER ASN ALA LYS ILE ASP GLN LEU SER SER ASP VAL SEQRES 2 A 56 GLN THR LEU ASN ALA LYS VAL ASP GLN ALA SER ASN ASP SEQRES 3 A 56 ALA ASN ALA ALA ARG SER ASP ALA GLN ALA ALA LYS ASP SEQRES 4 A 56 ASP ALA ALA ARG ALA ASN GLN ARG LEU ASP ASN MET ALA SEQRES 5 A 56 THR LYS TYR ARG FORMUL 2 HOH *41(H2 O) HELIX 1 1 SER A 1 ASN A 50 1 50 CRYST1 36.290 36.290 83.473 90.00 90.00 120.00 H 3 9 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 0.027556 0.015909 0.000000 0.00000 SCALE2 0.000000 0.031819 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011980 0.00000 TER 387 THR A 53 HETATM 388 O HOH A 101 21.628 15.510 -9.480 1.00 26.13 O HETATM 389 O HOH A 102 24.178 10.339 16.149 1.00 23.68 O HETATM 390 O HOH A 103 14.638 2.753 21.182 1.00 23.14 O HETATM 391 O HOH A 104 15.675 21.451 -39.207 1.00 24.85 O HETATM 392 O HOH A 105 27.144 7.812 -1.374 1.00 32.06 O HETATM 393 O HOH A 106 25.325 3.916 8.474 1.00 29.89 O HETATM 394 O HOH A 107 23.651 17.376 -9.944 1.00 45.19 O HETATM 395 O HOH A 108 22.811 19.096 -22.590 1.00 33.42 O HETATM 396 O HOH A 109 24.495 2.367 24.629 1.00 35.72 O HETATM 397 O HOH A 110 28.045 12.485 -17.990 1.00 37.01 O HETATM 398 O HOH A 111 21.529 -0.135 21.466 1.00 46.94 O HETATM 399 O HOH A 112 22.348 20.419 -31.873 1.00 34.74 O HETATM 400 O HOH A 113 24.979 4.951 17.788 1.00 37.80 O HETATM 401 O HOH A 114 24.148 0.597 22.952 1.00 42.52 O HETATM 402 O HOH A 115 25.337 17.648 -15.285 1.00 40.11 O HETATM 403 O HOH A 116 22.532 -0.248 11.488 1.00 34.38 O HETATM 404 O HOH A 117 21.181 15.112 -6.216 1.00 35.69 O HETATM 405 O HOH A 118 23.320 13.578 6.072 1.00 36.63 O HETATM 406 O HOH A 119 16.536 5.828 38.929 1.00 38.29 O HETATM 407 O HOH A 120 27.126 16.773 -22.378 1.00 41.16 O HETATM 408 O HOH A 121 29.269 11.789 -15.898 1.00 36.28 O HETATM 409 O HOH A 122 30.735 7.190 -11.421 1.00 36.18 O HETATM 410 O HOH A 123 28.806 8.236 -9.343 1.00 48.35 O HETATM 411 O HOH A 124 19.967 15.366 -40.707 1.00 36.14 O HETATM 412 O HOH A 125 22.946 6.293 30.609 1.00 41.02 O HETATM 413 O HOH A 126 22.176 7.996 32.490 1.00 43.11 O HETATM 414 O HOH A 127 26.342 16.449 -28.622 1.00 30.88 O HETATM 415 O HOH A 128 17.088 20.035 -31.205 1.00 40.43 O HETATM 416 O HOH A 129 29.211 16.398 -24.461 1.00 43.98 O HETATM 417 O HOH A 130 13.567 0.319 33.345 1.00 47.45 O HETATM 418 O HOH A 131 27.923 14.863 -29.980 1.00 35.80 O HETATM 419 O HOH A 132 12.971 4.312 20.185 1.00 40.46 O HETATM 420 O HOH A 133 19.571 7.514 36.872 1.00 48.27 O HETATM 421 O HOH A 134 28.445 11.369 -20.574 1.00 49.20 O HETATM 422 O HOH A 135 18.862 4.247 37.965 1.00 35.57 O HETATM 423 O HOH A 136 26.391 19.178 -28.716 1.00 40.95 O HETATM 424 O HOH A 137 19.492 21.567 -30.161 1.00 37.00 O HETATM 425 O HOH A 138 20.967 0.781 30.389 1.00 38.22 O HETATM 426 O HOH A 139 26.623 5.894 -9.522 1.00 49.27 O HETATM 427 O HOH A 140 25.707 10.800 -25.170 1.00 35.66 O HETATM 428 O HOH A 141 15.826 3.848 41.561 1.00 41.52 O MASTER 264 0 0 1 0 0 0 6 427 1 0 5 END