PDB Short entry for 1JCD HEADER MEMBRANE PROTEIN 08-JUN-01 1JCD TITLE CRYSTAL STRUCTURE OF A NOVEL ALANINE-ZIPPER TRIMER AT 1.3 A TITLE 2 RESOLUTION, I6A,L9A,V13A,L16A,V20A,L23A,V27A,M30A,V34A,L48A,M51A TITLE 3 MUTATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR OUTER MEMBRANE LIPOPROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: MUREIN-LIPOPROTEIN; 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, COILED COIL, HELIX CAPPING, ALANINE- KEYWDS 2 ZIPPER, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,M.LU REVDAT 5 16-AUG-23 1JCD 1 REMARK REVDAT 4 27-OCT-21 1JCD 1 SEQADV REVDAT 3 04-OCT-17 1JCD 1 REMARK REVDAT 2 24-FEB-09 1JCD 1 VERSN REVDAT 1 17-JUN-03 1JCD 0 JRNL AUTH J.LIU,M.LU JRNL TITL AN ALANINE-ZIPPER STRUCTURE DETERMINED BY LONG RANGE JRNL TITL 2 INTERMOLECULAR INTERACTIONS JRNL REF J.BIOL.CHEM. V. 277 48708 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 12368282 JRNL DOI 10.1074/JBC.M208773200 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.150 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2352 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 23835 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1052 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 186 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1238.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 11157 REMARK 3 NUMBER OF RESTRAINTS : 13054 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.026 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.017 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.054 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.055 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.008 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.054 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.070 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 4 REMARK 4 1JCD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013618. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-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 : 23835 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 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 (%) : 93.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.10600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.80 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 1JCC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 17.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, SODIUM CITRATE, PH REMARK 280 4.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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. 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 REMARK 350 TOTAL BURIED SURFACE AREA: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 SER A 1 REMARK 465 SER A 2 REMARK 465 SER C 1 REMARK 465 SER C 2 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 LYS B 5 CE NZ REMARK 470 GLN B 46 CD OE1 NE2 REMARK 470 LYS C 19 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 31 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EQ7 RELATED DB: PDB REMARK 900 1EQ7 IS THE WILD TYPE PROTEIN STRUCTURE REMARK 900 RELATED ID: 1JCB RELATED DB: PDB REMARK 900 1JCB HAS THE FOLLOWING MUTATIONS: M30A,V34A REMARK 900 RELATED ID: 1JCC RELATED DB: PDB REMARK 900 1JCC HAS THE FOLLOWING MUTATIONS: V13A,L16A,V20A,L23A,V27A,M30A,V34A DBREF 1JCD A 1 52 UNP P69776 LPP_ECOLI 22 73 DBREF 1JCD B 1 52 UNP P69776 LPP_ECOLI 22 73 DBREF 1JCD C 1 52 UNP P69776 LPP_ECOLI 22 73 SEQADV 1JCD ALA A 6 UNP P69776 ILE 27 ENGINEERED MUTATION SEQADV 1JCD ALA A 9 UNP P69776 LEU 30 ENGINEERED MUTATION SEQADV 1JCD ALA A 13 UNP P69776 VAL 34 ENGINEERED MUTATION SEQADV 1JCD ALA A 16 UNP P69776 LEU 37 ENGINEERED MUTATION SEQADV 1JCD ALA A 20 UNP P69776 VAL 41 ENGINEERED MUTATION SEQADV 1JCD ALA A 23 UNP P69776 LEU 44 ENGINEERED MUTATION SEQADV 1JCD ALA A 27 UNP P69776 VAL 48 ENGINEERED MUTATION SEQADV 1JCD ALA A 30 UNP P69776 MET 51 ENGINEERED MUTATION SEQADV 1JCD ALA A 34 UNP P69776 VAL 55 ENGINEERED MUTATION SEQADV 1JCD ALA A 48 UNP P69776 LEU 69 ENGINEERED MUTATION SEQADV 1JCD ALA A 51 UNP P69776 MET 72 ENGINEERED MUTATION SEQADV 1JCD ALA B 6 UNP P69776 ILE 27 ENGINEERED MUTATION SEQADV 1JCD ALA B 9 UNP P69776 LEU 30 ENGINEERED MUTATION SEQADV 1JCD ALA B 13 UNP P69776 VAL 34 ENGINEERED MUTATION SEQADV 1JCD ALA B 16 UNP P69776 LEU 37 ENGINEERED MUTATION SEQADV 1JCD ALA B 20 UNP P69776 VAL 41 ENGINEERED MUTATION SEQADV 1JCD ALA B 23 UNP P69776 LEU 44 ENGINEERED MUTATION SEQADV 1JCD ALA B 27 UNP P69776 VAL 48 ENGINEERED MUTATION SEQADV 1JCD ALA B 30 UNP P69776 MET 51 ENGINEERED MUTATION SEQADV 1JCD ALA B 34 UNP P69776 VAL 55 ENGINEERED MUTATION SEQADV 1JCD ALA B 48 UNP P69776 LEU 69 ENGINEERED MUTATION SEQADV 1JCD ALA B 51 UNP P69776 MET 72 ENGINEERED MUTATION SEQADV 1JCD ALA C 6 UNP P69776 ILE 27 ENGINEERED MUTATION SEQADV 1JCD ALA C 9 UNP P69776 LEU 30 ENGINEERED MUTATION SEQADV 1JCD ALA C 13 UNP P69776 VAL 34 ENGINEERED MUTATION SEQADV 1JCD ALA C 16 UNP P69776 LEU 37 ENGINEERED MUTATION SEQADV 1JCD ALA C 20 UNP P69776 VAL 41 ENGINEERED MUTATION SEQADV 1JCD ALA C 23 UNP P69776 LEU 44 ENGINEERED MUTATION SEQADV 1JCD ALA C 27 UNP P69776 VAL 48 ENGINEERED MUTATION SEQADV 1JCD ALA C 30 UNP P69776 MET 51 ENGINEERED MUTATION SEQADV 1JCD ALA C 34 UNP P69776 VAL 55 ENGINEERED MUTATION SEQADV 1JCD ALA C 48 UNP P69776 LEU 69 ENGINEERED MUTATION SEQADV 1JCD ALA C 51 UNP P69776 MET 72 ENGINEERED MUTATION SEQRES 1 A 52 SER SER ASN ALA LYS ALA ASP GLN ALA SER SER ASP ALA SEQRES 2 A 52 GLN THR ALA ASN ALA LYS ALA ASP GLN ALA SER ASN ASP SEQRES 3 A 52 ALA ASN ALA ALA ARG SER ASP ALA GLN ALA ALA LYS ASP SEQRES 4 A 52 ASP ALA ALA ARG ALA ASN GLN ARG ALA ASP ASN ALA ALA SEQRES 1 B 52 SER SER ASN ALA LYS ALA ASP GLN ALA SER SER ASP ALA SEQRES 2 B 52 GLN THR ALA ASN ALA LYS ALA ASP GLN ALA SER ASN ASP SEQRES 3 B 52 ALA ASN ALA ALA ARG SER ASP ALA GLN ALA ALA LYS ASP SEQRES 4 B 52 ASP ALA ALA ARG ALA ASN GLN ARG ALA ASP ASN ALA ALA SEQRES 1 C 52 SER SER ASN ALA LYS ALA ASP GLN ALA SER SER ASP ALA SEQRES 2 C 52 GLN THR ALA ASN ALA LYS ALA ASP GLN ALA SER ASN ASP SEQRES 3 C 52 ALA ASN ALA ALA ARG SER ASP ALA GLN ALA ALA LYS ASP SEQRES 4 C 52 ASP ALA ALA ARG ALA ASN GLN ARG ALA ASP ASN ALA ALA FORMUL 4 HOH *186(H2 O) HELIX 1 1 ASN A 3 ALA A 51 1 49 HELIX 2 2 ASN B 3 ALA B 52 1 50 HELIX 3 3 ASN C 3 ALA C 52 1 50 CRYST1 21.842 26.935 45.805 88.05 84.95 87.56 P 1 3 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 0.045783 -0.001951 -0.003988 0.00000 SCALE2 0.000000 0.037160 -0.001131 0.00000 SCALE3 0.000000 0.000000 0.021927 0.00000