HEADER TRANSFERASE/TRANSFERASE INHIBITOR 17-AUG-05 2AQ9 TITLE STRUCTURE OF E. COLI LPXA WITH A BOUND PEPTIDE THAT IS COMPETITIVE TITLE 2 WITH ACYL-ACP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O- COMPND 3 ACYLTRANSFERASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: UDP-N-ACETYLGLUCOSAMINE ACYLTRANSFERASE; COMPND 6 EC: 2.3.1.129; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PEPTIDE INHIBITOR; COMPND 10 CHAIN: X; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: LPXA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPET23C-LPXA(1-262) PT01; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS LPXA, PEPTIDE INHIBITOR, ACYL ACP, ACP, UDP-GLCNAC, LIPID A, KEYWDS 2 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.H.WILLIAMS,R.M.IMMORMINO,D.T.GEWIRTH,C.R.RAETZ REVDAT 6 23-AUG-23 2AQ9 1 REMARK REVDAT 5 13-JUL-11 2AQ9 1 VERSN REVDAT 4 30-JUN-09 2AQ9 1 HELIX SHEET REVDAT 3 24-FEB-09 2AQ9 1 VERSN REVDAT 2 01-AUG-06 2AQ9 1 JRNL REVDAT 1 27-JUN-06 2AQ9 0 JRNL AUTH A.H.WILLIAMS,R.M.IMMORMINO,D.T.GEWIRTH,C.R.RAETZ JRNL TITL STRUCTURE OF UDP-N-ACETYLGLUCOSAMINE ACYLTRANSFERASE WITH A JRNL TITL 2 BOUND ANTIBACTERIAL PENTADECAPEPTIDE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 10877 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16835299 JRNL DOI 10.1073/PNAS.0604465103 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 354940.880 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 26451 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) : 0.194 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2283 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2188 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 221 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2062 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 297 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 3.420 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) : 1.100 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.660 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.770 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.510 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 80.69 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : PO4.PARAM REMARK 3 PARAMETER FILE 5 : DMSO.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : PO4.TOP REMARK 3 TOPOLOGY FILE 5 : DMSO.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AQ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 42 REMARK 42 MOLPROBITY STRUCTURE VALIDATION REMARK 42 PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) REMARK 42 AUTHORS : I.W.DAVIS,J.M.WORD REMARK 42 URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ REMARK 42 AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REMARK 42 REFERENCE : NEW TOOLS AND DATA FOR IMPROVING REMARK 42 : STRUCTURES, USING ALL-ATOM CONTACTS REMARK 42 : METHODS IN ENZYMOLOGY. 2003;374:385-412. REMARK 42 MOLPROBITY OUTPUT SCORES: REMARK 42 ALL-ATOM CLASHSCORE : 6.42 (4.23 B<40) REMARK 42 LPXA (PROTEIN CHAIN) REMARK 42 BAD ROTAMERS : 0.5% 1/204 (TARGET 0-1%) REMARK 42 RAMACHANDRAN OUTLIERS : 0.0% 0/260 (TARGET 0.2%) REMARK 42 RAMACHANDRAN FAVORED : 97.7% 254/260 (TARGET 98.0%) REMARK 42 PEPTIDE 920 (PEPTIDE INHIBITOR OF LPXA) REMARK 42 BAD ROTAMERS : 0.0% 0/9 (TARGET 0-1%) REMARK 42 RAMACHANDRAN OUTLIERS : 0.0% 0/10 (TARGET 0.2%) REMARK 42 RAMACHANDRAN FAVORED :100.0% 10/10 (TARGET 98.0%) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000034185. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : COPPER KALPHA REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28264 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 25.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.75700 REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1LXA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DMSO, SODIUM POTASSIUM PHOSPHATE, PH REMARK 280 6.3-6.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+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 48.36700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.36700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.36700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.36700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.36700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.36700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 48.36700 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 48.36700 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 48.36700 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 48.36700 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 48.36700 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 48.36700 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 48.36700 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 48.36700 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 48.36700 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 48.36700 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 48.36700 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 48.36700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). THERE IS ONE COPY OF THE REMARK 300 LPXA MONOMER BOUND TO ONE INHIBITORY PEPTIDE PER REMARK 300 ASYMMETRIC UNIT. THE BIOLOGICALLY ACTIVE LPXA MOLECULE, REMARK 300 WHICH IS A HOMO-TRIMER, SITS ON A CRYSTALLOGRAPHIC REMARK 300 THREE-FOLD AXIS. SWITCHING THE INDEX OF THE LPXA-PEPTIDE REMARK 300 COMPLEX FROM THE CUBIC P2(1)3 TO THE ORTHORHOMBIC REMARK 300 P2(1)2(1)2(1), WHICH IS THE MAXIMAL NON-ISOMORPHIC REMARK 300 SUBGROUP LACKING THE THREE-FOLD AXIS, RESULTS IN A REMARK 300 TRIPLING OF MOLECULES IN THE ASYMMETRIC UNIT, AND THE REMARK 300 FORMATION OF THE BIOLOGICALLY ACTIVE 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 24900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X 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 0.000000 0.000000 -1.000000 96.73400 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 48.36700 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 145.10100 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 -48.36700 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 145.10100 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 96.73400 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 617 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 637 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 639 LIES ON A SPECIAL POSITION. 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 X 1 REMARK 465 SER X 2 REMARK 465 GLY X 3 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 MET A 1 CG SD CE REMARK 470 ARG A 224 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 241 CG CD OE1 OE2 REMARK 470 MET X 5 CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN A 190 C HIS A 191 N -0.164 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 190 O - C - N ANGL. DEV. = -9.9 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 ASN A 23 19.32 58.03 REMARK 500 ILE A 119 126.57 -39.58 REMARK 500 ILE A 119 128.30 -39.58 REMARK 500 PHE A 150 -0.31 66.58 REMARK 500 PHE A 162 -0.80 70.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 420 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 421 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 X 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LXA RELATED DB: PDB REMARK 900 UDP N-ACETYLGLUCOSAMINE ACYLTRANSFERASE (STRUCTURE OF APO LPXA) DBREF 2AQ9 A 1 262 UNP P0A722 LPXA_ECOLI 1 262 DBREF 2AQ9 X 1 15 PDB 2AQ9 2AQ9 1 15 SEQRES 1 A 262 MET ILE ASP LYS SER ALA PHE VAL HIS PRO THR ALA ILE SEQRES 2 A 262 VAL GLU GLU GLY ALA SER ILE GLY ALA ASN ALA HIS ILE SEQRES 3 A 262 GLY PRO PHE CYS ILE VAL GLY PRO HIS VAL GLU ILE GLY SEQRES 4 A 262 GLU GLY THR VAL LEU LYS SER HIS VAL VAL VAL ASN GLY SEQRES 5 A 262 HIS THR LYS ILE GLY ARG ASP ASN GLU ILE TYR GLN PHE SEQRES 6 A 262 ALA SER ILE GLY GLU VAL ASN GLN ASP LEU LYS TYR ALA SEQRES 7 A 262 GLY GLU PRO THR ARG VAL GLU ILE GLY ASP ARG ASN ARG SEQRES 8 A 262 ILE ARG GLU SER VAL THR ILE HIS ARG GLY THR VAL GLN SEQRES 9 A 262 GLY GLY GLY LEU THR LYS VAL GLY SER ASP ASN LEU LEU SEQRES 10 A 262 MET ILE ASN ALA HIS ILE ALA HIS ASP CYS THR VAL GLY SEQRES 11 A 262 ASN ARG CYS ILE LEU ALA ASN ASN ALA THR LEU ALA GLY SEQRES 12 A 262 HIS VAL SER VAL ASP ASP PHE ALA ILE ILE GLY GLY MET SEQRES 13 A 262 THR ALA VAL HIS GLN PHE CYS ILE ILE GLY ALA HIS VAL SEQRES 14 A 262 MET VAL GLY GLY CYS SER GLY VAL ALA GLN ASP VAL PRO SEQRES 15 A 262 PRO TYR VAL ILE ALA GLN GLY ASN HIS ALA THR PRO PHE SEQRES 16 A 262 GLY VAL ASN ILE GLU GLY LEU LYS ARG ARG GLY PHE SER SEQRES 17 A 262 ARG GLU ALA ILE THR ALA ILE ARG ASN ALA TYR LYS LEU SEQRES 18 A 262 ILE TYR ARG SER GLY LYS THR LEU ASP GLU VAL LYS PRO SEQRES 19 A 262 GLU ILE ALA GLU LEU ALA GLU THR TYR PRO GLU VAL LYS SEQRES 20 A 262 ALA PHE THR ASP PHE PHE ALA ARG SER THR ARG GLY LEU SEQRES 21 A 262 ILE ARG SEQRES 1 X 15 SER SER GLY TRP MET LEU ASP PRO ILE ALA GLY LYS TRP SEQRES 2 X 15 SER ARG HET PO4 A 301 5 HET PO4 A 302 5 HET PO4 A 303 5 HET PO4 A 304 5 HET DMS A 401 4 HET DMS A 402 4 HET DMS A 403 4 HET DMS A 404 4 HET DMS A 405 4 HET DMS A 406 4 HET DMS A 407 4 HET DMS A 408 4 HET DMS A 409 4 HET DMS A 410 4 HET DMS A 411 4 HET DMS A 412 4 HET DMS A 413 4 HET DMS A 414 4 HET DMS A 415 4 HET DMS A 416 4 HET DMS A 417 4 HET DMS A 418 4 HET DMS A 419 4 HET DMS A 420 4 HET DMS A 421 4 HET DMS A 422 4 HET PO4 X 305 5 HETNAM PO4 PHOSPHATE ION HETNAM DMS DIMETHYL SULFOXIDE FORMUL 3 PO4 5(O4 P 3-) FORMUL 7 DMS 22(C2 H6 O S) FORMUL 30 HOH *297(H2 O) HELIX 1 HA ASN A 198 ARG A 205 1 8 HELIX 2 HB ARG A 209 TYR A 223 1 15 HELIX 3 HC LEU A 229 THR A 242 1 14 HELIX 4 HD VAL A 246 SER A 256 1 11 SHEET 1 BS1 9 MET A 1 ASP A 3 0 SHEET 2 BS1 9 ALA A 18 GLY A 21 1 N ILE A 20 O MET A 1 SHEET 3 BS1 9 VAL A 36 GLY A 39 1 N ILE A 38 O SER A 19 SHEET 4 BS1 9 THR A 54 GLY A 57 1 N ILE A 56 O GLU A 37 SHEET 5 BS1 9 ARG A 83 GLY A 87 1 N ILE A 86 O LYS A 55 SHEET 6 BS1 9 GLY A 107 GLY A 112 1 N VAL A 111 O GLU A 85 SHEET 7 BS1 9 CYS A 127 GLY A 130 1 N VAL A 129 O LYS A 110 SHEET 8 BS1 9 VAL A 145 ASP A 148 1 N VAL A 147 O THR A 128 SHEET 9 BS1 9 CYS A 163 GLY A 166 1 N ILE A 165 O SER A 146 SHEET 1 BS211 PHE A 7 HIS A 9 0 SHEET 2 BS211 ALA A 24 GLY A 27 1 N ILE A 26 O PHE A 7 SHEET 3 BS211 THR A 42 LYS A 45 1 N LEU A 44 O HIS A 25 SHEET 4 BS211 ASN A 60 TYR A 63 1 N ILE A 62 O VAL A 43 SHEET 5 BS211 ASN A 90 ARG A 93 1 N ILE A 92 O GLU A 61 SHEET 6 BS211 ASN A 115 MET A 118 1 N LEU A 117 O ARG A 91 SHEET 7 BS211 CYS A 133 ALA A 136 1 N LEU A 135 O LEU A 116 SHEET 8 BS211 ALA A 151 GLY A 154 1 N ILE A 153 O ILE A 134 SHEET 9 BS211 VAL A 169 GLY A 172 1 N VAL A 171 O ILE A 152 SHEET 10 BS211 VAL A 185 GLN A 188 1 N ALA A 187 O MET A 170 SHEET 11 BS211 THR A 193 GLY A 196 -1 N PHE A 195 O ILE A 186 SHEET 1 BS3 9 ILE A 13 GLU A 15 0 SHEET 2 BS3 9 CYS A 30 GLY A 33 1 N VAL A 32 O ILE A 13 SHEET 3 BS3 9 VAL A 48 ASN A 51 1 N VAL A 50 O ILE A 31 SHEET 4 BS3 9 ALA A 66 GLU A 70 1 N ILE A 68 O VAL A 49 SHEET 5 BS3 9 VAL A 96 HIS A 99 1 O VAL A 96 N SER A 67 SHEET 6 BS3 9 ALA A 121 ALA A 124 1 O ALA A 121 N THR A 97 SHEET 7 BS3 9 ALA A 139 ALA A 142 1 O ALA A 139 N HIS A 122 SHEET 8 BS3 9 THR A 157 HIS A 160 1 O THR A 157 N THR A 140 SHEET 9 BS3 9 SER A 175 VAL A 177 1 O SER A 175 N ALA A 158 SHEET 1 BS4 2 MET X 5 ASP X 7 0 SHEET 2 BS4 2 LYS X 12 SER X 14 -1 O LYS X 12 N ASP X 7 CISPEP 1 ASN A 190 HIS A 191 0 -17.11 SITE 1 AC1 9 ARG A 100 ARG A 216 LYS A 220 PO4 A 302 SITE 2 AC1 9 HOH A 453 HOH A 540 HOH A 542 HOH A 613 SITE 3 AC1 9 HOH A 689 SITE 1 AC2 10 PRO A 34 ASN A 51 GLY A 52 PO4 A 301 SITE 2 AC2 10 HOH A 431 HOH A 488 HOH A 517 HOH A 518 SITE 3 AC2 10 HOH A 605 HOH A 660 SITE 1 AC3 8 LYS A 76 GLN A 104 LYS A 203 HOH A 536 SITE 2 AC3 8 HOH A 572 HOH A 598 TRP X 4 ARG X 15 SITE 1 AC4 4 LEU A 75 ASP A 114 ARG A 132 CYS A 133 SITE 1 AC5 3 ILE A 13 VAL A 14 GLU A 16 SITE 1 AC6 3 ILE A 56 ILE A 86 DMS A 405 SITE 1 AC7 5 GLY A 17 PRO A 34 HIS A 35 VAL A 36 SITE 2 AC7 5 GLU A 37 SITE 1 AC8 7 ASN A 23 HIS A 25 GLY A 41 ASN A 217 SITE 2 AC8 7 LEU A 239 TYR A 243 DMS A 408 SITE 1 AC9 2 ASP A 88 DMS A 402 SITE 1 BC1 2 ASP A 148 ARG A 255 SITE 1 BC2 2 HIS A 25 HOH A 549 SITE 1 BC3 7 GLY A 41 ASP A 59 ASN A 60 GLU A 210 SITE 2 BC3 7 THR A 213 TYR A 243 DMS A 404 SITE 1 BC4 5 HIS A 144 SER A 146 PHE A 162 THR A 257 SITE 2 BC4 5 DMS A 412 SITE 1 BC5 2 PHE A 7 VAL A 8 SITE 1 BC6 2 ASP A 148 ASP A 149 SITE 1 BC7 7 ASP A 126 THR A 128 VAL A 145 SER A 146 SITE 2 BC7 7 DMS A 409 HOH A 450 HOH A 703 SITE 1 BC8 4 LYS A 4 ALA A 6 GLU A 238 HOH A 530 SITE 1 BC9 3 MET A 1 ASP A 3 ILE A 20 SITE 1 CC1 2 ASP A 3 LYS A 4 SITE 1 CC2 4 GLU A 15 PRO A 28 HOH A 491 HOH A 549 SITE 1 CC3 4 ASN A 131 ARG A 132 PHE A 150 HOH A 625 SITE 1 CC4 2 PRO A 194 TYR A 219 SITE 1 CC5 3 ARG A 205 GLU A 245 HOH A 445 SITE 1 CC6 4 HIS A 25 VAL A 43 LYS A 45 HOH A 695 SITE 1 CC7 5 GLN A 73 ARG A 91 ARG A 93 LEU A 116 SITE 2 CC7 5 HOH A 524 SITE 1 CC8 3 ALA A 78 PHE A 207 ARG A 209 SITE 1 CC9 8 GLN A 73 ASP A 74 LEU A 75 LYS A 76 SITE 2 CC9 8 GLN A 161 LEU X 6 PRO X 8 HOH X 28 CRYST1 96.734 96.734 96.734 90.00 90.00 90.00 P 21 3 12 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 0.010338 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010338 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010338 0.00000