HEADER MEMBRANE PROTEIN 21-NOV-01 1KFM 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 16-AUG-23 1KFM 1 REMARK REVDAT 4 27-OCT-21 1KFM 1 REMARK SEQADV REVDAT 3 13-JUL-11 1KFM 1 VERSN REVDAT 2 24-FEB-09 1KFM 1 VERSN REVDAT 1 28-JUN-02 1KFM 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.26 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) (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 2761 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) : 0.260 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.200 REMARK 3 FREE R VALUE TEST SET COUNT : 254 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.018 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 267 REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 25 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.074 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 363 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.61000 REMARK 3 B22 (A**2) : 1.61000 REMARK 3 B33 (A**2) : -3.21000 REMARK 3 B12 (A**2) : 4.24000 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) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.21 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) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.630 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) : 1.510 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.380 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.660 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.170 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.43 REMARK 3 BSOL : 62.15 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 1KFM 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_1000014904. 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 : 6.8 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 : 2761 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.09700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 12.30 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: PDB ENTRY 1EQ7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM CACODYLATE, AMMONIUM REMARK 280 ACETATE, PH 6.8, VAPOR DIFFUSION, HANGING DROP AT 293K, VAPOR REMARK 280 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 18.52850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 10.69743 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.30400 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 18.52850 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 10.69743 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.30400 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 18.52850 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 10.69743 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.30400 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 21.39487 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 54.60800 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 21.39487 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 54.60800 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 21.39487 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 54.60800 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: 5690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 55.58550 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -32.09230 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 55.58550 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 32.09230 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 SER A 1 REMARK 465 ALA A 52 REMARK 465 THR A 53 REMARK 465 LYS A 54 REMARK 465 TYR A 55 REMARK 465 ARG A 56 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 3 CG OD1 ND2 REMARK 470 ASP A 12 CG OD1 OD2 REMARK 470 GLN A 14 CG CD OE1 NE2 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 THE STRUCTURE OF THE SAME SEQUENCE REFINED AT A LOWER SOLUTION REMARK 900 RELATED ID: 1KFN RELATED DB: PDB REMARK 900 MUTANT OF 1EQ7 DBREF 1KFM A 1 56 UNP P69776 LPP_ECOLI 22 77 SEQADV 1KFM ALA A 30 UNP P69776 MET 51 ENGINEERED MUTATION SEQADV 1KFM 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 LEU SER ASN ASP SEQRES 3 A 56 VAL 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 *19(H2 O) HELIX 1 1 SER A 2 ASN A 50 1 49 CRYST1 37.057 37.057 81.912 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 0.026985 0.015580 0.000000 0.00000 SCALE2 0.000000 0.031160 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012208 0.00000