PDB Short entry for 1T7D HEADER HYDROLASE/ANTIBIOTIC 09-MAY-04 1T7D TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI TYPE I SIGNAL PEPTIDASE IN TITLE 2 COMPLEX WITH A LIPOPEPTIDE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIGNAL PEPTIDASE I; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 76-324; COMPND 5 SYNONYM: SPASE I, LEADER PEPTIDASE I; COMPND 6 EC: 3.4.21.89; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ARYLOMYCIN A2; COMPND 10 CHAIN: C, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: LEPB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3D; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: STREPTOMYCES TU; SOURCE 12 ORGANISM_TAXID: 1931 KEYWDS SIGNAL PEPTIDASE, SER/LYS DYAD, HYDROLASE, LIPOPEPTIDE, ANTIBIOTIC, KEYWDS 2 BIARYL BRIDGE, HYDROLASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.PAETZEL,J.J.GOODALL,M.KANIA,R.E.DALBEY,M.G.P.PAGE REVDAT 5 23-AUG-23 1T7D 1 SEQADV SEQRES LINK REVDAT 4 27-JUL-11 1T7D 1 DBREF REMARK REVDAT 3 13-JUL-11 1T7D 1 VERSN REVDAT 2 24-FEB-09 1T7D 1 VERSN REVDAT 1 13-JUL-04 1T7D 0 JRNL AUTH M.PAETZEL,J.J.GOODALL,M.KANIA,R.E.DALBEY,M.G.P.PAGE JRNL TITL CRYSTALLOGRAPHIC AND BIOPHYSICAL ANALYSIS OF A BACTERIAL JRNL TITL 2 SIGNAL PEPTIDASE IN COMPLEX WITH A LIPOPEPTIDE BASED JRNL TITL 3 INHIBITOR. JRNL REF J.BIOL.CHEM. V. 279 30781 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15136583 JRNL DOI 10.1074/JBC.M401686200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.PAETZEL,R.E.DALBEY,N.C.STRYNADKA REMARK 1 TITL CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APOENZYME: REMARK 1 TITL 2 IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD REMARK 1 TITL 3 MECHANISM REMARK 1 REF J.BIOL.CHEM. V. 277 9512 2002 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M110983200 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.PAETZEL,R.E.DALBEY,N.C.STRYNADKA REMARK 1 TITL CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE IN COMPLEX REMARK 1 TITL 2 WITH A BETA-LACTAM INHIBITOR. REMARK 1 REF NATURE V. 396 186 1998 REMARK 1 REFN ISSN 0028-0836 REMARK 1 DOI 10.1038/25403 REMARK 2 REMARK 2 RESOLUTION. 2.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2098721.280 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 21584 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) : 0.230 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2142 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2952 REMARK 3 BIN R VALUE (WORKING SET) : 0.3110 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 334 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3495 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 265 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.48000 REMARK 3 B22 (A**2) : 6.48000 REMARK 3 B33 (A**2) : -12.95000 REMARK 3 B12 (A**2) : 0.00000 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) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.38 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) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.49 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.960 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) : 1.710 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.040 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.060 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.150 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 49.11 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 : ION.PARAM REMARK 3 PARAMETER FILE 4 : DRGCNS.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : DRGCNS.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1T7D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022404. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21589 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.470 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.000 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 1B12 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5% TRITON X-100, 15% PEG 4000, 20% REMARK 280 PROPANOL, 0.1 M SODIUM CITRATE, PH 6.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 129.23300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.80450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.80450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 193.84950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.80450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.80450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 64.61650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.80450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.80450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 193.84950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.80450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.80450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 64.61650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 129.23300 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 MONOMER 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 400 REMARK 400 COMPOUND REMARK 400 ARYLOMYCIN A2 IS A CYCLIC LIPOHEXAPEPTIDE, A MEMBER OF REMARK 400 THE ARYLOMYCIN FAMILY. ALL MEMBERS HAVE A FATTY ACID AT THE REMARK 400 N-TERM AND A CORE STRUCTURE OF TRIPEPTIDE MACROCYCLE REMARK 400 FORMED BY A C-C BIARYL LINKAGE BETWEEN RESIDUES 4 AND 6. REMARK 400 HERE, ARYLOMYCIN A2 IS REPRESENTED BY GROUPING TOGETHER THE REMARK 400 SEQUENCE (SEQRES) AND ONE LIGAND (HET) M12. REMARK 400 REMARK 400 THE ARYLOMYCIN A2 IS LIPOPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: ARYLOMYCIN A2 REMARK 400 CHAIN: C, D REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE M12 REMARK 400 DESCRIPTION: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE REMARK 400 SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC REMARK 400 TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] REMARK 400 BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ISO-C12 FATTY REMARK 400 ACID IS LINKED TO RESIDUE 1. 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 MET A 74 REMARK 465 ILE A 75 REMARK 465 VAL A 76 REMARK 465 ARG A 77 REMARK 465 SER A 78 REMARK 465 PHE A 79 REMARK 465 ALA A 107 REMARK 465 TYR A 108 REMARK 465 GLY A 109 REMARK 465 ILE A 110 REMARK 465 LYS A 111 REMARK 465 ASP A 112 REMARK 465 PRO A 113 REMARK 465 ILE A 114 REMARK 465 TYR A 115 REMARK 465 GLN A 116 REMARK 465 LYS A 117 REMARK 465 THR A 118 REMARK 465 LEU A 119 REMARK 465 ILE A 120 REMARK 465 GLU A 121 REMARK 465 THR A 122 REMARK 465 GLY A 123 REMARK 465 SER A 171 REMARK 465 SER A 172 REMARK 465 GLY A 173 REMARK 465 GLN A 174 REMARK 465 ALA A 175 REMARK 465 CYS A 176 REMARK 465 GLU A 177 REMARK 465 ASN A 200 REMARK 465 GLY A 201 REMARK 465 GLY A 202 REMARK 465 LYS A 305 REMARK 465 GLN A 306 REMARK 465 GLU A 307 REMARK 465 GLY A 308 REMARK 465 GLU A 309 REMARK 465 TRP A 310 REMARK 465 PRO A 311 REMARK 465 THR A 312 REMARK 465 GLY A 313 REMARK 465 MET B 74 REMARK 465 ILE B 75 REMARK 465 VAL B 76 REMARK 465 ARG B 77 REMARK 465 SER B 78 REMARK 465 PHE B 79 REMARK 465 TYR B 108 REMARK 465 GLY B 109 REMARK 465 ILE B 110 REMARK 465 LYS B 111 REMARK 465 ASP B 112 REMARK 465 PRO B 113 REMARK 465 ILE B 114 REMARK 465 TYR B 115 REMARK 465 GLN B 116 REMARK 465 LYS B 117 REMARK 465 THR B 118 REMARK 465 LEU B 119 REMARK 465 ILE B 120 REMARK 465 ARG B 198 REMARK 465 ARG B 199 REMARK 465 ASN B 200 REMARK 465 GLY B 201 REMARK 465 GLY B 202 REMARK 465 GLU B 203 REMARK 465 ALA B 204 REMARK 465 THR B 205 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 ARG A 198 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 199 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 121 CG CD OE1 OE2 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 199 N - CA - C ANGL. DEV. = -23.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 PRO A 139 0.45 -64.23 REMARK 500 PRO A 168 179.14 -58.36 REMARK 500 PRO A 181 84.78 -64.82 REMARK 500 LYS A 213 3.93 -61.95 REMARK 500 ASN A 214 -91.57 -86.33 REMARK 500 GLU A 215 172.95 -52.06 REMARK 500 ASN A 219 104.03 81.14 REMARK 500 ASN A 277 40.67 -141.11 REMARK 500 ASP A 280 -156.52 -133.10 REMARK 500 SER A 302 118.28 -161.91 REMARK 500 PRO B 139 -2.52 -56.72 REMARK 500 CYS B 170 32.73 -83.58 REMARK 500 SER B 171 -84.09 -44.60 REMARK 500 SER B 172 16.81 -66.89 REMARK 500 ALA B 175 72.25 -67.99 REMARK 500 GLU B 177 161.55 -49.30 REMARK 500 ASN B 178 154.81 -46.36 REMARK 500 LYS B 213 -10.63 -48.25 REMARK 500 PRO B 254 107.95 -48.49 REMARK 500 ALA B 259 24.59 82.10 REMARK 500 ARG B 275 -35.71 -32.85 REMARK 500 ASN B 277 48.69 -145.69 REMARK 500 ASP B 280 -165.91 -116.91 REMARK 500 ARG B 315 48.44 -147.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 M12 C 0 REMARK 610 M12 D 0 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF ARYLOMYCIN A2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF ARYLOMYCIN A2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B12 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTUTE OF TYPE 1 SIGNAL PEPTIDASE COMPLEXED WITH BETA- REMARK 900 LACTAM INHIBITOR REMARK 900 RELATED ID: 1KN9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SIGNAL PEPTIDASE APO_ENZYME REMARK 900 RELATED ID: 3IIQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCURE OF BACTERIAL SIGNAL PEPTIDASE IN TERNARY COMPLEX REMARK 900 WITH ARYLOMYCIN A2 AND A BETA-SULTAM INHIBITOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN IS A SOLUBLE CATALYTICALLY ACTIVE FRAGMENT REMARK 999 OF THE ESCHERICHIA COLI TYPE I SIGNAL PEPTIDASE REMARK 999 (DELTA 2-75). IT LACKS THE RESIDUES CORRESPONDING TO REMARK 999 THE TWO TRANSMEMBRANE SEGMENTS (RESIDUES 4-28 AND 58-76) REMARK 999 AND A SMALL CYTOPLASMIC REGION (RESIDUES 29-58). DBREF 1T7D A 75 323 UNP P00803 LEP_ECOLI 76 324 DBREF 1T7D B 75 323 UNP P00803 LEP_ECOLI 76 324 DBREF 1T7D C 1 6 NOR NOR01115 NOR01115 1 6 DBREF 1T7D D 1 6 NOR NOR01115 NOR00115 1 6 SEQADV 1T7D MET A 74 UNP P00803 INITIATING METHIONINE SEQADV 1T7D MET B 74 UNP P00803 INITIATING METHIONINE SEQRES 1 A 250 MET ILE VAL ARG SER PHE ILE TYR GLU PRO PHE GLN ILE SEQRES 2 A 250 PRO SER GLY SER MET MET PRO THR LEU LEU ILE GLY ASP SEQRES 3 A 250 PHE ILE LEU VAL GLU LYS PHE ALA TYR GLY ILE LYS ASP SEQRES 4 A 250 PRO ILE TYR GLN LYS THR LEU ILE GLU THR GLY HIS PRO SEQRES 5 A 250 LYS ARG GLY ASP ILE VAL VAL PHE LYS TYR PRO GLU ASP SEQRES 6 A 250 PRO LYS LEU ASP TYR ILE LYS ARG ALA VAL GLY LEU PRO SEQRES 7 A 250 GLY ASP LYS VAL THR TYR ASP PRO VAL SER LYS GLU LEU SEQRES 8 A 250 THR ILE GLN PRO GLY CYS SER SER GLY GLN ALA CYS GLU SEQRES 9 A 250 ASN ALA LEU PRO VAL THR TYR SER ASN VAL GLU PRO SER SEQRES 10 A 250 ASP PHE VAL GLN THR PHE SER ARG ARG ASN GLY GLY GLU SEQRES 11 A 250 ALA THR SER GLY PHE PHE GLU VAL PRO LYS ASN GLU THR SEQRES 12 A 250 LYS GLU ASN GLY ILE ARG LEU SER GLU ARG LYS GLU THR SEQRES 13 A 250 LEU GLY ASP VAL THR HIS ARG ILE LEU THR VAL PRO ILE SEQRES 14 A 250 ALA GLN ASP GLN VAL GLY MET TYR TYR GLN GLN PRO GLY SEQRES 15 A 250 GLN GLN LEU ALA THR TRP ILE VAL PRO PRO GLY GLN TYR SEQRES 16 A 250 PHE MET MET GLY ASP ASN ARG ASP ASN SER ALA ASP SER SEQRES 17 A 250 ARG TYR TRP GLY PHE VAL PRO GLU ALA ASN LEU VAL GLY SEQRES 18 A 250 ARG ALA THR ALA ILE TRP MET SER PHE ASP LYS GLN GLU SEQRES 19 A 250 GLY GLU TRP PRO THR GLY LEU ARG LEU SER ARG ILE GLY SEQRES 20 A 250 GLY ILE HIS SEQRES 1 B 250 MET ILE VAL ARG SER PHE ILE TYR GLU PRO PHE GLN ILE SEQRES 2 B 250 PRO SER GLY SER MET MET PRO THR LEU LEU ILE GLY ASP SEQRES 3 B 250 PHE ILE LEU VAL GLU LYS PHE ALA TYR GLY ILE LYS ASP SEQRES 4 B 250 PRO ILE TYR GLN LYS THR LEU ILE GLU THR GLY HIS PRO SEQRES 5 B 250 LYS ARG GLY ASP ILE VAL VAL PHE LYS TYR PRO GLU ASP SEQRES 6 B 250 PRO LYS LEU ASP TYR ILE LYS ARG ALA VAL GLY LEU PRO SEQRES 7 B 250 GLY ASP LYS VAL THR TYR ASP PRO VAL SER LYS GLU LEU SEQRES 8 B 250 THR ILE GLN PRO GLY CYS SER SER GLY GLN ALA CYS GLU SEQRES 9 B 250 ASN ALA LEU PRO VAL THR TYR SER ASN VAL GLU PRO SER SEQRES 10 B 250 ASP PHE VAL GLN THR PHE SER ARG ARG ASN GLY GLY GLU SEQRES 11 B 250 ALA THR SER GLY PHE PHE GLU VAL PRO LYS ASN GLU THR SEQRES 12 B 250 LYS GLU ASN GLY ILE ARG LEU SER GLU ARG LYS GLU THR SEQRES 13 B 250 LEU GLY ASP VAL THR HIS ARG ILE LEU THR VAL PRO ILE SEQRES 14 B 250 ALA GLN ASP GLN VAL GLY MET TYR TYR GLN GLN PRO GLY SEQRES 15 B 250 GLN GLN LEU ALA THR TRP ILE VAL PRO PRO GLY GLN TYR SEQRES 16 B 250 PHE MET MET GLY ASP ASN ARG ASP ASN SER ALA ASP SER SEQRES 17 B 250 ARG TYR TRP GLY PHE VAL PRO GLU ALA ASN LEU VAL GLY SEQRES 18 B 250 ARG ALA THR ALA ILE TRP MET SER PHE ASP LYS GLN GLU SEQRES 19 B 250 GLY GLU TRP PRO THR GLY LEU ARG LEU SER ARG ILE GLY SEQRES 20 B 250 GLY ILE HIS SEQRES 1 C 6 DSE DAL GLY 5PG ALA TYR SEQRES 1 D 6 DSE DAL GLY 5PG ALA TYR HET DSE C 1 7 HET DAL C 2 5 HET 5PG C 4 12 HET DSE D 1 7 HET DAL D 2 5 HET 5PG D 4 12 HET M12 C 0 3 HET M12 D 0 3 HETNAM DSE N-METHYL-D-SERINE HETNAM DAL D-ALANINE HETNAM 5PG (2S)-(4-HYDROXYPHENYL)(METHYLAMINO)ETHANOIC ACID HETNAM M12 10-METHYLUNDECANOIC ACID HETSYN 5PG N-METHYL-4-HYDROXY-PHENYLGLYCINE FORMUL 3 DSE 2(C4 H9 N O3) FORMUL 3 DAL 2(C3 H7 N O2) FORMUL 3 5PG 2(C9 H11 N O3) FORMUL 5 M12 2(C12 H24 O2) FORMUL 7 HOH *265(H2 O) HELIX 1 1 GLN A 246 TYR A 250 5 5 HELIX 2 2 ASP A 280 GLY A 285 1 6 HELIX 3 3 ARG A 315 ILE A 319 5 5 HELIX 4 4 GLN B 246 TYR B 250 5 5 HELIX 5 5 ASP B 280 GLY B 285 1 6 HELIX 6 6 LEU B 316 ILE B 319 5 4 SHEET 1 AA 4 TYR A 81 GLN A 85 0 SHEET 2 AA 4 ASP A 99 LYS A 105 -1 O ILE A 101 N PHE A 84 SHEET 3 AA 4 LEU A 292 SER A 302 -1 O ARG A 295 N GLU A 104 SHEET 4 AA 4 GLY A 320 GLY A 321 -1 O GLY A 320 N ILE A 299 SHEET 1 AB 7 TYR A 81 GLN A 85 0 SHEET 2 AB 7 ASP A 99 LYS A 105 -1 O ILE A 101 N PHE A 84 SHEET 3 AB 7 LEU A 292 SER A 302 -1 O ARG A 295 N GLU A 104 SHEET 4 AB 7 ILE A 130 LYS A 134 -1 O ILE A 130 N ALA A 296 SHEET 5 AB 7 ASP A 142 GLY A 149 -1 O TYR A 143 N PHE A 133 SHEET 6 AB 7 GLN A 267 MET A 271 -1 O PHE A 269 N GLY A 149 SHEET 7 AB 7 VAL A 287 PRO A 288 -1 O VAL A 287 N TYR A 268 SHEET 1 AC 2 GLY A 320 GLY A 321 0 SHEET 2 AC 2 LEU A 292 SER A 302 -1 O ILE A 299 N GLY A 320 SHEET 1 AD 3 GLU A 163 GLN A 167 0 SHEET 2 AD 3 LYS A 154 ASP A 158 -1 O LYS A 154 N GLN A 167 SHEET 3 AD 3 THR A 260 ILE A 262 -1 O TRP A 261 N VAL A 155 SHEET 1 AE 2 VAL A 182 TYR A 184 0 SHEET 2 AE 2 ILE A 221 LEU A 230 -1 O THR A 229 N THR A 183 SHEET 1 AF 4 ALA A 204 GLU A 210 0 SHEET 2 AF 4 GLU A 188 ARG A 198 -1 O VAL A 193 N PHE A 209 SHEET 3 AF 4 ILE A 221 LEU A 230 -1 O ILE A 221 N GLN A 194 SHEET 4 AF 4 VAL A 233 THR A 239 1 O VAL A 233 N LEU A 230 SHEET 1 AG 4 ALA A 204 GLU A 210 0 SHEET 2 AG 4 GLU A 188 ARG A 198 -1 O VAL A 193 N PHE A 209 SHEET 3 AG 4 ILE A 221 LEU A 230 -1 O ILE A 221 N GLN A 194 SHEET 4 AG 4 VAL A 182 TYR A 184 -1 O THR A 183 N THR A 229 SHEET 1 AH 2 VAL A 233 THR A 239 0 SHEET 2 AH 2 ILE A 221 LEU A 230 1 O SER A 224 N THR A 239 SHEET 1 BA 4 TYR B 81 GLN B 85 0 SHEET 2 BA 4 ASP B 99 LYS B 105 -1 O ILE B 101 N PHE B 84 SHEET 3 BA 4 LEU B 292 ASP B 304 -1 O ARG B 295 N GLU B 104 SHEET 4 BA 4 GLY B 313 LEU B 314 -1 O GLY B 313 N ASP B 304 SHEET 1 BB 4 TYR B 81 GLN B 85 0 SHEET 2 BB 4 ASP B 99 LYS B 105 -1 O ILE B 101 N PHE B 84 SHEET 3 BB 4 LEU B 292 ASP B 304 -1 O ARG B 295 N GLU B 104 SHEET 4 BB 4 GLY B 320 GLY B 321 -1 O GLY B 320 N ILE B 299 SHEET 1 BC 6 VAL B 287 PRO B 288 0 SHEET 2 BC 6 GLN B 267 MET B 271 -1 O TYR B 268 N VAL B 287 SHEET 3 BC 6 ASP B 142 GLY B 149 -1 O ARG B 146 N MET B 271 SHEET 4 BC 6 ILE B 130 LYS B 134 -1 O VAL B 131 N LYS B 145 SHEET 5 BC 6 LEU B 292 ASP B 304 -1 N VAL B 293 O VAL B 132 SHEET 6 BC 6 GLY B 313 LEU B 314 -1 O GLY B 313 N ASP B 304 SHEET 1 BD 7 TYR B 81 GLN B 85 0 SHEET 2 BD 7 ASP B 99 LYS B 105 -1 O ILE B 101 N PHE B 84 SHEET 3 BD 7 LEU B 292 ASP B 304 -1 O ARG B 295 N GLU B 104 SHEET 4 BD 7 ILE B 130 LYS B 134 -1 O ILE B 130 N ALA B 296 SHEET 5 BD 7 ASP B 142 GLY B 149 -1 O TYR B 143 N PHE B 133 SHEET 6 BD 7 GLN B 267 MET B 271 -1 O PHE B 269 N VAL B 148 SHEET 7 BD 7 VAL B 287 PRO B 288 -1 O VAL B 287 N TYR B 268 SHEET 1 BE 6 VAL B 287 PRO B 288 0 SHEET 2 BE 6 GLN B 267 MET B 271 -1 O TYR B 268 N VAL B 287 SHEET 3 BE 6 ASP B 142 GLY B 149 -1 O ARG B 146 N MET B 271 SHEET 4 BE 6 ILE B 130 LYS B 134 -1 O VAL B 131 N LYS B 145 SHEET 5 BE 6 LEU B 292 ASP B 304 -1 N VAL B 293 O VAL B 132 SHEET 6 BE 6 GLY B 320 GLY B 321 -1 O GLY B 320 N ILE B 299 SHEET 1 BF 2 GLY B 313 LEU B 314 0 SHEET 2 BF 2 LEU B 292 ASP B 304 -1 N ASP B 304 O GLY B 313 SHEET 1 BG 7 VAL B 287 PRO B 288 0 SHEET 2 BG 7 GLN B 267 MET B 271 -1 O TYR B 268 N VAL B 287 SHEET 3 BG 7 ASP B 142 GLY B 149 -1 O ARG B 146 N MET B 271 SHEET 4 BG 7 ILE B 130 LYS B 134 -1 O VAL B 131 N LYS B 145 SHEET 5 BG 7 LEU B 292 ASP B 304 -1 N VAL B 293 O VAL B 132 SHEET 6 BG 7 ASP B 99 LYS B 105 -1 O PHE B 100 N TRP B 300 SHEET 7 BG 7 TYR B 81 GLN B 85 -1 O GLU B 82 N VAL B 103 SHEET 1 BH 3 GLU B 163 GLN B 167 0 SHEET 2 BH 3 LYS B 154 ASP B 158 -1 O LYS B 154 N GLN B 167 SHEET 3 BH 3 THR B 260 ILE B 262 -1 O TRP B 261 N VAL B 155 SHEET 1 BI 2 VAL B 182 TYR B 184 0 SHEET 2 BI 2 GLY B 220 LEU B 230 1 N THR B 229 O THR B 183 SHEET 1 BJ 4 PHE B 208 GLU B 210 0 SHEET 2 BJ 4 GLU B 188 THR B 195 -1 O VAL B 193 N PHE B 209 SHEET 3 BJ 4 GLY B 220 LEU B 230 -1 O ILE B 221 N GLN B 194 SHEET 4 BJ 4 VAL B 233 THR B 239 -1 O VAL B 233 N LEU B 230 SHEET 1 BK 4 PHE B 208 GLU B 210 0 SHEET 2 BK 4 GLU B 188 THR B 195 -1 O VAL B 193 N PHE B 209 SHEET 3 BK 4 GLY B 220 LEU B 230 -1 O ILE B 221 N GLN B 194 SHEET 4 BK 4 VAL B 182 TYR B 184 1 O THR B 183 N THR B 229 SHEET 1 BL 2 VAL B 233 THR B 239 0 SHEET 2 BL 2 GLY B 220 LEU B 230 -1 O SER B 224 N THR B 239 SSBOND 1 CYS B 170 CYS B 176 1555 1555 2.03 LINK C1 M12 C 0 N DSE C 1 1555 1555 1.33 LINK C DSE C 1 N DAL C 2 1555 1555 1.33 LINK C DAL C 2 N GLY C 3 1555 1555 1.33 LINK C GLY C 3 N 5PG C 4 1555 1555 1.33 LINK C 5PG C 4 N ALA C 5 1555 1555 1.33 LINK CD1 5PG C 4 CE1 TYR C 6 1555 1555 1.39 LINK C1 M12 D 0 N DSE D 1 1555 1555 1.33 LINK C DSE D 1 N DAL D 2 1555 1555 1.33 LINK C DAL D 2 N GLY D 3 1555 1555 1.33 LINK C GLY D 3 N 5PG D 4 1555 1555 1.33 LINK C 5PG D 4 N ALA D 5 1555 1555 1.33 LINK CD1 5PG D 4 CE1 TYR D 6 1555 1555 1.39 CISPEP 1 MET A 92 PRO A 93 0 0.49 CISPEP 2 MET B 92 PRO B 93 0 0.05 SITE 1 AC1 11 GLU A 82 PRO A 83 GLN A 85 PRO A 87 SITE 2 AC1 11 SER A 90 ASP A 142 TYR A 143 ILE A 144 SITE 3 AC1 11 LYS A 145 HOH A2005 HOH A2006 SITE 1 AC2 12 PRO B 83 PHE B 84 GLN B 85 PRO B 87 SITE 2 AC2 12 SER B 88 SER B 90 ASP B 142 TYR B 143 SITE 3 AC2 12 ILE B 144 LYS B 145 HOH D2002 HOH D2003 CRYST1 69.609 69.609 258.466 90.00 90.00 90.00 P 43 21 2 16 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 0.014366 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014366 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003869 0.00000