HEADER HYDROLASE 04-OCT-10 3P3E TITLE CRYSTAL STRUCTURE OF THE PSEUDOMONAS AERUGINOSA LPXC/LPC-009 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE COMPND 3 DEACETYLASE; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 1-299; COMPND 6 SYNONYM: UDP-3-O-ACYL-GLCNAC DEACETYLASE, PROTEIN ENVA; COMPND 7 EC: 3.5.1.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: ENVA, LPXC, PA4406; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PET21B KEYWDS LIPID A BIOSYNTHESIS, LIPID A SYNTHESIS, LPXC, BAAB SANDWICH, KEYWDS 2 HYDROLASE, DEACETYLATION, ANTIBIOTIC, ACYL UDP-GLCNAC, HYDROXAMATE, KEYWDS 3 LPC-009 EXPDTA X-RAY DIFFRACTION AUTHOR C.-J.LEE,P.ZHOU REVDAT 5 21-FEB-24 3P3E 1 REMARK SEQADV LINK REVDAT 4 24-JAN-18 3P3E 1 AUTHOR REVDAT 3 08-NOV-17 3P3E 1 REMARK REVDAT 2 16-MAR-11 3P3E 1 JRNL REVDAT 1 05-JAN-11 3P3E 0 JRNL AUTH C.J.LEE,X.LIANG,X.CHEN,D.ZENG,S.H.JOO,H.S.CHUNG,A.W.BARB, JRNL AUTH 2 S.M.SWANSON,R.A.NICHOLAS,Y.LI,E.J.TOONE,C.R.RAETZ,P.ZHOU JRNL TITL SPECIES-SPECIFIC AND INHIBITOR-DEPENDENT CONFORMATIONS OF JRNL TITL 2 LPXC: IMPLICATIONS FOR ANTIBIOTIC DESIGN. JRNL REF CHEM.BIOL. V. 18 38 2011 JRNL REFN ISSN 1074-5521 JRNL PMID 21167751 JRNL DOI 10.1016/J.CHEMBIOL.2010.11.011 REMARK 2 REMARK 2 RESOLUTION. 1.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 88305 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 4429 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 22.9915 - 2.7584 0.99 8732 469 0.1780 0.1850 REMARK 3 2 2.7584 - 2.1900 1.00 8528 448 0.1790 0.1959 REMARK 3 3 2.1900 - 1.9133 1.00 8417 455 0.1669 0.1794 REMARK 3 4 1.9133 - 1.7384 1.00 8346 479 0.1766 0.1881 REMARK 3 5 1.7384 - 1.6139 1.00 8363 456 0.1835 0.1902 REMARK 3 6 1.6139 - 1.5187 1.00 8375 414 0.1816 0.2019 REMARK 3 7 1.5187 - 1.4427 1.00 8327 432 0.1932 0.2081 REMARK 3 8 1.4427 - 1.3799 1.00 8305 447 0.2038 0.2261 REMARK 3 9 1.3799 - 1.3268 1.00 8340 422 0.2234 0.2377 REMARK 3 10 1.3268 - 1.2800 0.98 8143 407 0.2507 0.2571 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.53 REMARK 3 K_SOL : 0.47 REMARK 3 B_SOL : 53.09 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.26140 REMARK 3 B22 (A**2) : -0.08190 REMARK 3 B33 (A**2) : -0.17950 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 2593 REMARK 3 ANGLE : 0.857 3496 REMARK 3 CHIRALITY : 0.051 383 REMARK 3 PLANARITY : 0.004 473 REMARK 3 DIHEDRAL : 11.988 947 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID ALL REMARK 3 ORIGIN FOR THE GROUP (A): -16.4203 3.9916 -7.8744 REMARK 3 T TENSOR REMARK 3 T11: 0.0682 T22: 0.0806 REMARK 3 T33: 0.0819 T12: 0.0063 REMARK 3 T13: -0.0004 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.4192 L22: 0.5059 REMARK 3 L33: 0.6718 L12: -0.0545 REMARK 3 L13: 0.2016 L23: 0.2002 REMARK 3 S TENSOR REMARK 3 S11: 0.0121 S12: 0.0227 S13: -0.0067 REMARK 3 S21: -0.0041 S22: 0.0290 S23: 0.0095 REMARK 3 S31: 0.0303 S32: 0.0317 S33: -0.0360 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3P3E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000061905. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0001 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 88611 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.45600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE TRIHYDRATE PH REMARK 280 5.0, AND 2.7 M AMMONIUM NITRATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 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 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 26.31850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.15400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.80400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.15400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.31850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.80400 REMARK 290 SMTRY3 4 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ARG A 298 REMARK 465 PRO A 299 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 8 CE REMARK 480 GLU A 55 CD REMARK 480 ARG A 133 CG NE CZ 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 MET A 103 -126.06 56.19 REMARK 500 SER A 106 -168.34 -115.69 REMARK 500 ASP A 159 51.86 -145.58 REMARK 500 ASP A 218 -161.31 -101.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 78 NE2 REMARK 620 2 HIS A 237 NE2 95.0 REMARK 620 3 ASP A 241 OD1 94.1 100.5 REMARK 620 4 ASP A 241 OD2 151.3 88.5 57.3 REMARK 620 5 3P3 A 501 O04 99.0 163.0 88.1 83.9 REMARK 620 6 3P3 A 501 O01 121.3 87.7 143.0 87.2 76.8 REMARK 620 7 3P3 A 501 O01 114.0 89.8 149.2 94.4 75.7 7.4 REMARK 620 8 3P3 A 501 O04 98.7 159.9 93.1 86.5 5.0 72.6 71.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 162 ND1 REMARK 620 2 GLU A 219 OE1 103.2 REMARK 620 3 GLU A 219 OE2 85.9 63.5 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3P3 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 708 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 709 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 710 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 711 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 712 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 713 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 714 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 715 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 716 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 717 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 718 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 719 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 720 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 721 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 722 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 723 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 724 REMARK 800 REMARK 800 SITE_IDENTIFIER: DC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 725 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VES RELATED DB: PDB REMARK 900 RELATED ID: 3P3C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE AQUIFEX AEOLICUS LPXC/LPC-009 COMPLEX REMARK 900 RELATED ID: 3P3G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI LPXC/LPC-009 COMPLEX DBREF 3P3E A 1 299 UNP P47205 LPXC_PSEAE 1 299 SEQADV 3P3E SER A 40 UNP P47205 CYS 40 ENGINEERED MUTATION SEQRES 1 A 299 MET ILE LYS GLN ARG THR LEU LYS ASN ILE ILE ARG ALA SEQRES 2 A 299 THR GLY VAL GLY LEU HIS SER GLY GLU LYS VAL TYR LEU SEQRES 3 A 299 THR LEU LYS PRO ALA PRO VAL ASP THR GLY ILE VAL PHE SEQRES 4 A 299 SER ARG THR ASP LEU ASP PRO VAL VAL GLU ILE PRO ALA SEQRES 5 A 299 ARG ALA GLU ASN VAL GLY GLU THR THR MET SER THR THR SEQRES 6 A 299 LEU VAL LYS GLY ASP VAL LYS VAL ASP THR VAL GLU HIS SEQRES 7 A 299 LEU LEU SER ALA MET ALA GLY LEU GLY ILE ASP ASN ALA SEQRES 8 A 299 TYR VAL GLU LEU SER ALA SER GLU VAL PRO ILE MET ASP SEQRES 9 A 299 GLY SER ALA GLY PRO PHE VAL PHE LEU ILE GLN SER ALA SEQRES 10 A 299 GLY LEU GLN GLU GLN GLU ALA ALA LYS LYS PHE ILE ARG SEQRES 11 A 299 ILE LYS ARG GLU VAL SER VAL GLU GLU GLY ASP LYS ARG SEQRES 12 A 299 ALA VAL PHE VAL PRO PHE ASP GLY PHE LYS VAL SER PHE SEQRES 13 A 299 GLU ILE ASP PHE ASP HIS PRO VAL PHE ARG GLY ARG THR SEQRES 14 A 299 GLN GLN ALA SER VAL ASP PHE SER SER THR SER PHE VAL SEQRES 15 A 299 LYS GLU VAL SER ARG ALA ARG THR PHE GLY PHE MET ARG SEQRES 16 A 299 ASP ILE GLU TYR LEU ARG SER GLN ASN LEU ALA LEU GLY SEQRES 17 A 299 GLY SER VAL GLU ASN ALA ILE VAL VAL ASP GLU ASN ARG SEQRES 18 A 299 VAL LEU ASN GLU ASP GLY LEU ARG TYR GLU ASP GLU PHE SEQRES 19 A 299 VAL LYS HIS LYS ILE LEU ASP ALA ILE GLY ASP LEU TYR SEQRES 20 A 299 LEU LEU GLY ASN SER LEU ILE GLY GLU PHE ARG GLY PHE SEQRES 21 A 299 LYS SER GLY HIS ALA LEU ASN ASN GLN LEU LEU ARG THR SEQRES 22 A 299 LEU ILE ALA ASP LYS ASP ALA TRP GLU VAL VAL THR PHE SEQRES 23 A 299 GLU ASP ALA ARG THR ALA PRO ILE SER TYR MET ARG PRO HET ZN A 400 1 HET ZN A 401 1 HET 3P3 A 501 54 HET NA A 601 1 HET NO3 A 701 4 HET NO3 A 702 4 HET NO3 A 703 4 HET NO3 A 704 4 HET NO3 A 705 4 HET NO3 A 706 4 HET NO3 A 707 4 HET NO3 A 708 4 HET NO3 A 709 4 HET NO3 A 710 4 HET NO3 A 711 4 HET NO3 A 712 4 HET NO3 A 713 4 HET NO3 A 714 4 HET NO3 A 715 4 HET NO3 A 716 4 HET NO3 A 717 4 HET NO3 A 718 4 HET NO3 A 719 4 HET NO3 A 720 4 HET NO3 A 721 4 HET NO3 A 722 4 HET NO3 A 723 4 HET NO3 A 724 4 HET NO3 A 725 4 HETNAM ZN ZINC ION HETNAM 3P3 N-[(1S,2R)-2-HYDROXY-1-(HYDROXYCARBAMOYL)PROPYL]-4-(4- HETNAM 2 3P3 PHENYLBUTA-1,3-DIYN-1-YL)BENZAMIDE HETNAM NA SODIUM ION HETNAM NO3 NITRATE ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 3P3 C21 H18 N2 O4 FORMUL 5 NA NA 1+ FORMUL 6 NO3 25(N O3 1-) FORMUL 31 HOH *413(H2 O) HELIX 1 1 ARG A 53 VAL A 57 5 5 HELIX 2 2 VAL A 76 LEU A 86 1 11 HELIX 3 3 ALA A 107 GLY A 118 1 12 HELIX 4 4 HIS A 162 ARG A 166 5 5 HELIX 5 5 SER A 180 VAL A 185 1 6 HELIX 6 6 MET A 194 GLN A 203 1 10 HELIX 7 7 ASP A 232 TYR A 247 1 16 HELIX 8 8 LEU A 248 GLY A 250 5 3 HELIX 9 9 GLY A 263 ASP A 277 1 15 HELIX 10 10 ASP A 288 ALA A 292 5 5 SHEET 1 A 2 LYS A 3 LEU A 7 0 SHEET 2 A 2 LEU A 119 ALA A 125 -1 O GLN A 120 N THR A 6 SHEET 1 B 5 ILE A 11 VAL A 16 0 SHEET 2 B 5 LYS A 23 LYS A 29 -1 O LEU A 28 N ILE A 11 SHEET 3 B 5 ALA A 91 LEU A 95 -1 O TYR A 92 N LYS A 29 SHEET 4 B 5 ILE A 37 ARG A 41 1 N SER A 40 O VAL A 93 SHEET 5 B 5 VAL A 48 PRO A 51 -1 O ILE A 50 N PHE A 39 SHEET 1 C 2 LEU A 66 LYS A 68 0 SHEET 2 C 2 VAL A 71 VAL A 73 -1 O VAL A 73 N LEU A 66 SHEET 1 D 5 VAL A 135 GLU A 139 0 SHEET 2 D 5 LYS A 142 VAL A 147 -1 O PHE A 146 N VAL A 135 SHEET 3 D 5 SER A 252 PHE A 260 -1 O PHE A 260 N ARG A 143 SHEET 4 D 5 PHE A 152 GLU A 157 1 N SER A 155 O PHE A 257 SHEET 5 D 5 GLN A 171 ASP A 175 -1 O VAL A 174 N VAL A 154 SHEET 1 E 5 VAL A 135 GLU A 139 0 SHEET 2 E 5 LYS A 142 VAL A 147 -1 O PHE A 146 N VAL A 135 SHEET 3 E 5 SER A 252 PHE A 260 -1 O PHE A 260 N ARG A 143 SHEET 4 E 5 PHE A 128 ILE A 131 1 N ILE A 129 O SER A 252 SHEET 5 E 5 TRP A 281 VAL A 284 -1 O GLU A 282 N ARG A 130 SHEET 1 F 2 PHE A 191 PHE A 193 0 SHEET 2 F 2 ILE A 215 VAL A 217 1 O ILE A 215 N GLY A 192 LINK NE2 HIS A 78 ZN ZN A 400 1555 1555 2.08 LINK ND1 HIS A 162 ZN ZN A 401 1555 1555 2.04 LINK OE1 GLU A 219 ZN ZN A 401 1555 1555 2.05 LINK OE2 GLU A 219 ZN ZN A 401 1555 1555 2.07 LINK NE2 HIS A 237 ZN ZN A 400 1555 1555 2.07 LINK OD1 ASP A 241 ZN ZN A 400 1555 1555 2.04 LINK OD2 ASP A 241 ZN ZN A 400 1555 1555 2.37 LINK ZN ZN A 400 O04A3P3 A 501 1555 1555 2.06 LINK ZN ZN A 400 O01A3P3 A 501 1555 1555 2.10 LINK ZN ZN A 400 O01B3P3 A 501 1555 1555 2.11 LINK ZN ZN A 400 O04B3P3 A 501 1555 1555 2.35 CISPEP 1 ASP A 45 PRO A 46 0 1.96 SITE 1 AC1 4 HIS A 78 HIS A 237 ASP A 241 3P3 A 501 SITE 1 AC2 4 HIS A 162 GLU A 219 ASP A 277 ASP A 279 SITE 1 AC3 19 MET A 62 GLU A 77 HIS A 78 PHE A 112 SITE 2 AC3 19 GLN A 115 THR A 190 PHE A 191 ILE A 197 SITE 3 AC3 19 ARG A 201 GLY A 209 SER A 210 VAL A 211 SITE 4 AC3 19 HIS A 237 ASP A 241 HIS A 264 ZN A 400 SITE 5 AC3 19 NO3 A 709 HOH A1274 HOH A1406 SITE 1 AC4 3 MET A 194 ARG A 195 ASP A 218 SITE 1 AC5 6 ILE A 10 ARG A 12 ARG A 143 ARG A 258 SITE 2 AC5 6 PHE A 260 HOH A1304 SITE 1 AC6 9 ILE A 158 ARG A 168 THR A 169 GLN A 170 SITE 2 AC6 9 ASP A 232 GLU A 233 PHE A 234 VAL A 235 SITE 3 AC6 9 HOH A1072 SITE 1 AC7 8 ARG A 189 SER A 202 GLN A 203 ASN A 204 SITE 2 AC7 8 ARG A 229 HOH A1017 HOH A1166 HOH A1261 SITE 1 AC8 8 TYR A 25 SER A 96 PRO A 148 PHE A 149 SITE 2 AC8 8 ASP A 150 HOH A1015 HOH A1037 HOH A1116 SITE 1 AC9 3 SER A 180 HOH A1076 HOH A1390 SITE 1 BC1 6 ILE A 158 ASP A 159 PHE A 160 LYS A 261 SITE 2 BC1 6 HOH A1203 HOH A1303 SITE 1 BC2 9 THR A 14 TYR A 25 ARG A 133 GLU A 134 SITE 2 BC2 9 PRO A 148 HOH A1014 HOH A1093 HOH A1140 SITE 3 BC2 9 HOH A1238 SITE 1 BC3 5 TYR A 230 GLU A 231 ASP A 232 LYS A 236 SITE 2 BC3 5 NO3 A 714 SITE 1 BC4 7 MET A 62 LYS A 238 GLY A 263 HIS A 264 SITE 2 BC4 7 3P3 A 501 NO3 A 716 HOH A1035 SITE 1 BC5 8 VAL A 137 GLU A 138 GLN A 269 HOH A1050 SITE 2 BC5 8 HOH A1106 HOH A1218 HOH A1348 HOH A1379 SITE 1 BC6 5 THR A 14 GLY A 15 VAL A 16 LYS A 23 SITE 2 BC6 5 HOH A1356 SITE 1 BC7 6 SER A 173 VAL A 174 THR A 179 LYS A 236 SITE 2 BC7 6 HOH A1107 HOH A1411 SITE 1 BC8 10 LYS A 8 ASN A 9 ALA A 117 GLY A 118 SITE 2 BC8 10 LEU A 223 GLU A 225 HOH A1019 HOH A1152 SITE 3 BC8 10 HOH A1281 HOH A1375 SITE 1 BC9 5 GLU A 184 TYR A 230 NO3 A 708 HOH A1052 SITE 2 BC9 5 HOH A1378 SITE 1 CC1 4 PRO A 30 HOH A1158 HOH A1180 HOH A1271 SITE 1 CC2 10 THR A 60 THR A 61 MET A 62 SER A 63 SITE 2 CC2 10 GLY A 263 HIS A 264 ALA A 265 NO3 A 709 SITE 3 CC2 10 NO3 A 717 HOH A1318 SITE 1 CC3 8 GLU A 139 LYS A 142 GLY A 263 ALA A 265 SITE 2 CC3 8 LEU A 266 NO3 A 716 HOH A1144 HOH A1360 SITE 1 CC4 5 HIS A 19 LEU A 200 LEU A 205 ALA A 206 SITE 2 CC4 5 HOH A1308 SITE 1 CC5 4 ILE A 2 TYR A 296 MET A 297 HOH A1089 SITE 1 CC6 6 ARG A 166 GLN A 269 ARG A 272 HOH A1122 SITE 2 CC6 6 HOH A1188 HOH A1221 SITE 1 CC7 6 ARG A 41 ASP A 70 VAL A 71 LYS A 72 SITE 2 CC7 6 HOH A1299 HOH A1332 SITE 1 CC8 5 LYS A 23 LYS A 132 ARG A 133 HOH A1197 SITE 2 CC8 5 HOH A1222 SITE 1 CC9 5 SER A 136 VAL A 137 ARG A 143 ARG A 221 SITE 2 CC9 5 HOH A1050 SITE 1 DC1 10 PHE A 152 PHE A 176 SER A 177 PRO A 293 SITE 2 DC1 10 ILE A 294 SER A 295 HOH A1045 HOH A1090 SITE 3 DC1 10 HOH A1161 HOH A1309 SITE 1 DC2 8 MET A 103 ASP A 104 PRO A 109 GLU A 198 SITE 2 DC2 8 HOH A1131 HOH A1157 HOH A1301 HOH A1386 CRYST1 52.637 73.608 88.308 90.00 90.00 90.00 P 21 21 21 4 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 0.018998 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013585 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011324 0.00000