PDB Short entry for 1XXE HEADER HYDROLASE 04-NOV-04 1XXE TITLE RDC REFINED SOLUTION STRUCTURE OF THE AALPXC/TU-514 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE COMPND 3 DEACETYLASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: UDP-3-O-ACYL-GLCNAC DEACETYLASE; COMPND 6 EC: 3.5.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: COMPLEXED WITH TU-514 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 GENE: LPXC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)STAR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS LPXC; TU-514; LPS; LIPID A; LIPOPOLYSACCHARIDE UDP-3-O-ACYL-N- KEYWDS 2 ACETYLGLUCOSAMINE DEACETYLASE; METALLOAMIDASE; ZINC METALLOAMIDASE, KEYWDS 3 HYDROLASE EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR B.E.COGGINS,A.L.MCCLERREN,L.JIANG,X.LI,J.RUDOLPH,O.HINDSGAUL, AUTHOR 2 C.R.H.RAETZ,P.ZHOU REVDAT 4 02-MAR-22 1XXE 1 REMARK LINK REVDAT 3 24-FEB-09 1XXE 1 VERSN REVDAT 2 08-FEB-05 1XXE 1 JRNL REVDAT 1 23-NOV-04 1XXE 0 SPRSDE 23-NOV-04 1XXE 1NZT JRNL AUTH B.E.COGGINS,A.L.MCCLERREN,L.JIANG,X.LI,J.RUDOLPH, JRNL AUTH 2 O.HINDSGAUL,C.R.H.RAETZ,P.ZHOU JRNL TITL REFINED SOLUTION STRUCTURE OF THE LPXC-TU-514 COMPLEX AND JRNL TITL 2 PK(A) ANALYSIS OF AN ACTIVE SITE HISTIDINE: INSIGHTS INTO JRNL TITL 3 THE MECHANISM AND INHIBITOR DESIGN JRNL REF BIOCHEMISTRY V. 44 1114 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15667205 JRNL DOI 10.1021/BI047820Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, XPLOR-NIH 2.9.7 REMARK 3 AUTHORS : GUNTERT P., MUMENTHALER C., WUTHRICH K. (DYANA), REMARK 3 SCHWIETERS C.D., KUSZEWSKI J.J., TJANDRA N., REMARK 3 MARIUS CLORE G. (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XXE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030875. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 323 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 MM KCL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM U-15N/13C AALPXC/TU-514; REMARK 210 0.5 MM DEUTERATED, 15N/13C, VIL- REMARK 210 METHYL PROTONATED AALPXC WITH TU- REMARK 210 514; 13C-TU514/15N AALPXC; 0.5 REMARK 210 MM U-15N AALPXC/TU-514 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; RDC; HNCO- REMARK 210 BASED RDC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-25 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 ARG A 271 REMARK 465 ASP A 272 REMARK 465 LEU A 273 REMARK 465 PRO A 274 REMARK 465 HIS A 275 REMARK 465 LEU A 276 REMARK 465 PRO A 277 REMARK 465 SER A 278 REMARK 465 VAL A 279 REMARK 465 GLN A 280 REMARK 465 ALA A 281 REMARK 465 LEU A 282 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HIS A 50 H VAL A 53 1.44 REMARK 500 OD1 ASN A 221 HH21 ARG A 225 1.52 REMARK 500 OE2 GLU A 168 HZ1 LYS A 243 1.52 REMARK 500 H LEU A 147 OE2 GLU A 168 1.55 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 1 GLU A 33 152.20 -47.68 REMARK 500 1 ASN A 57 -154.26 -166.68 REMARK 500 1 LEU A 99 -126.13 57.59 REMARK 500 1 GLN A 117 -166.69 -108.29 REMARK 500 1 ASN A 118 70.70 -116.73 REMARK 500 1 ASP A 134 147.99 -174.17 REMARK 500 1 ASP A 209 16.16 -147.76 REMARK 500 1 GLU A 220 -16.24 -46.50 REMARK 500 2 ASN A 57 -153.89 -166.63 REMARK 500 2 HIS A 58 -11.40 -48.59 REMARK 500 2 THR A 71 70.35 52.41 REMARK 500 2 THR A 85 -74.63 -104.28 REMARK 500 2 LEU A 99 -113.49 58.35 REMARK 500 2 GLN A 117 -161.19 -102.66 REMARK 500 2 ASN A 157 -167.97 -70.43 REMARK 500 2 ASP A 209 10.39 -149.96 REMARK 500 2 GLU A 220 -16.67 -45.47 REMARK 500 3 LYS A 41 126.69 -176.06 REMARK 500 3 ASN A 57 -154.32 -166.00 REMARK 500 3 HIS A 58 -12.16 -48.32 REMARK 500 3 THR A 85 -76.68 -106.34 REMARK 500 3 LEU A 99 -105.68 55.32 REMARK 500 3 SER A 102 -166.78 -123.98 REMARK 500 3 GLU A 120 167.40 -47.88 REMARK 500 3 ASN A 157 -166.64 -70.15 REMARK 500 3 GLU A 220 -10.15 -49.34 REMARK 500 3 ASN A 221 35.95 -143.11 REMARK 500 4 LYS A 41 143.75 -170.70 REMARK 500 4 GLU A 51 -15.62 -45.26 REMARK 500 4 ASN A 57 -154.71 -166.47 REMARK 500 4 HIS A 58 -11.95 -48.03 REMARK 500 4 GLU A 83 60.72 63.41 REMARK 500 4 LEU A 99 -111.72 55.24 REMARK 500 4 SER A 102 -166.78 -109.93 REMARK 500 4 GLN A 117 -163.03 -103.86 REMARK 500 4 ASP A 134 137.93 -175.26 REMARK 500 4 ASN A 157 -169.40 -73.74 REMARK 500 4 ASP A 209 11.44 -152.56 REMARK 500 4 LEU A 269 -84.39 -57.36 REMARK 500 5 LYS A 41 139.46 -170.00 REMARK 500 5 GLU A 51 -16.33 -45.55 REMARK 500 5 ASN A 57 -154.30 -166.07 REMARK 500 5 HIS A 58 -12.10 -47.81 REMARK 500 5 LEU A 99 -110.87 57.06 REMARK 500 5 SER A 102 -168.84 -119.04 REMARK 500 5 ASN A 113 32.18 -144.37 REMARK 500 5 GLN A 117 -162.36 -105.41 REMARK 500 5 GLU A 135 19.74 56.61 REMARK 500 5 ASN A 157 -169.94 -76.35 REMARK 500 5 ASP A 209 10.12 -150.49 REMARK 500 REMARK 500 THIS ENTRY HAS 279 RAMACHANDRAN OUTLIERS. 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 319 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 74 NE2 REMARK 620 2 HIS A 226 NE2 76.1 REMARK 620 3 ASP A 230 OD2 81.1 85.5 REMARK 620 4 TUX A 320 OYH 104.8 116.1 158.3 REMARK 620 5 TUX A 320 OXH 81.0 155.0 100.8 60.5 REMARK 620 N 1 2 3 4 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 319 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TUX A 320 DBREF 1XXE A 1 282 UNP O67648 LPXC_AQUAE 1 282 SEQRES 1 A 282 MET GLY LEU GLU LYS THR VAL LYS GLU LYS LEU SER PHE SEQRES 2 A 282 GLU GLY VAL GLY ILE HIS THR GLY GLU TYR SER LYS LEU SEQRES 3 A 282 ILE ILE HIS PRO GLU LYS GLU GLY THR GLY ILE ARG PHE SEQRES 4 A 282 PHE LYS ASN GLY VAL TYR ILE PRO ALA ARG HIS GLU PHE SEQRES 5 A 282 VAL VAL HIS THR ASN HIS SER THR ASP LEU GLY PHE LYS SEQRES 6 A 282 GLY GLN ARG ILE LYS THR VAL GLU HIS ILE LEU SER VAL SEQRES 7 A 282 LEU HIS LEU LEU GLU ILE THR ASN VAL THR ILE GLU VAL SEQRES 8 A 282 ILE GLY ASN GLU ILE PRO ILE LEU ASP GLY SER GLY TRP SEQRES 9 A 282 GLU PHE TYR GLU ALA ILE ARG LYS ASN ILE LEU ASN GLN SEQRES 10 A 282 ASN ARG GLU ILE ASP TYR PHE VAL VAL GLU GLU PRO ILE SEQRES 11 A 282 ILE VAL GLU ASP GLU GLY ARG LEU ILE LYS ALA GLU PRO SEQRES 12 A 282 SER ASP THR LEU GLU VAL THR TYR GLU GLY GLU PHE LYS SEQRES 13 A 282 ASN PHE LEU GLY ARG GLN LYS PHE THR PHE VAL GLU GLY SEQRES 14 A 282 ASN GLU GLU GLU ILE VAL LEU ALA ARG THR PHE CYS PHE SEQRES 15 A 282 ASP TRP GLU ILE GLU HIS ILE LYS LYS VAL GLY LEU GLY SEQRES 16 A 282 LYS GLY GLY SER LEU LYS ASN THR LEU VAL LEU GLY LYS SEQRES 17 A 282 ASP LYS VAL TYR ASN PRO GLU GLY LEU ARG TYR GLU ASN SEQRES 18 A 282 GLU PRO VAL ARG HIS LYS VAL PHE ASP LEU ILE GLY ASP SEQRES 19 A 282 LEU TYR LEU LEU GLY SER PRO VAL LYS GLY LYS PHE TYR SEQRES 20 A 282 SER PHE ARG GLY GLY HIS SER LEU ASN VAL LYS LEU VAL SEQRES 21 A 282 LYS GLU LEU ALA LYS LYS GLN LYS LEU THR ARG ASP LEU SEQRES 22 A 282 PRO HIS LEU PRO SER VAL GLN ALA LEU HET ZN A 319 1 HET TUX A 320 71 HETNAM ZN ZINC ION HETNAM TUX 1,5-ANHYDRO-2-C-(CARBOXYMETHYL-N-HYDROXYAMIDE)-2-DEOXY- HETNAM 2 TUX 3-O-MYRISTOYL-D-GLUCITOL HETSYN TUX TU-514 FORMUL 2 ZN ZN 2+ FORMUL 3 TUX C22 H41 N O7 HELIX 1 1 GLU A 73 LEU A 82 1 10 HELIX 2 2 GLY A 103 LYS A 112 1 10 HELIX 3 3 GLU A 171 ILE A 174 5 4 HELIX 4 4 ASP A 183 LYS A 191 1 9 HELIX 5 5 GLU A 222 LEU A 235 1 14 HELIX 6 6 HIS A 253 LYS A 266 1 14 SHEET 1 A 2 LYS A 5 VAL A 7 0 SHEET 2 A 2 ILE A 114 ASN A 116 -1 O LEU A 115 N THR A 6 SHEET 1 B 5 LEU A 11 VAL A 16 0 SHEET 2 B 5 TYR A 23 PRO A 30 -1 O ILE A 28 N LEU A 11 SHEET 3 B 5 ASN A 86 ILE A 92 -1 O GLU A 90 N ILE A 27 SHEET 4 B 5 GLY A 36 LYS A 41 1 N ARG A 38 O ILE A 89 SHEET 5 B 5 VAL A 44 PRO A 47 -1 O ILE A 46 N PHE A 39 SHEET 1 C 3 VAL A 53 THR A 56 0 SHEET 2 C 3 THR A 60 PHE A 64 -1 O ASP A 61 N VAL A 54 SHEET 3 C 3 GLN A 67 ILE A 69 -1 O ILE A 69 N LEU A 62 SHEET 1 D 2 PHE A 124 VAL A 125 0 SHEET 2 D 2 VAL A 242 LYS A 243 1 O LYS A 243 N PHE A 124 SHEET 1 E 5 ILE A 130 ASP A 134 0 SHEET 2 E 5 ARG A 137 GLU A 142 -1 O ARG A 137 N ASP A 134 SHEET 3 E 5 LYS A 245 PHE A 249 -1 O LYS A 245 N GLU A 142 SHEET 4 E 5 GLU A 148 GLU A 154 1 N GLU A 148 O PHE A 246 SHEET 5 E 5 ARG A 161 VAL A 167 -1 O PHE A 166 N VAL A 149 SHEET 1 F 2 PHE A 180 PHE A 182 0 SHEET 2 F 2 LEU A 204 LEU A 206 1 O LEU A 206 N CYS A 181 LINK NE2 HIS A 74 ZN ZN A 319 1555 1555 2.51 LINK NE2 HIS A 226 ZN ZN A 319 1555 1555 2.51 LINK OD2 ASP A 230 ZN ZN A 319 1555 1555 2.45 LINK ZN ZN A 319 OYH TUX A 320 1555 1555 2.63 LINK ZN ZN A 319 OXH TUX A 320 1555 1555 2.67 SITE 1 AC1 5 HIS A 74 THR A 179 HIS A 226 ASP A 230 SITE 2 AC1 5 TUX A 320 SITE 1 AC2 15 HIS A 58 SER A 59 GLU A 73 HIS A 74 SITE 2 AC2 15 THR A 179 PHE A 180 CYS A 181 GLU A 185 SITE 3 AC2 15 ILE A 186 ILE A 189 GLY A 195 GLY A 198 SITE 4 AC2 15 TYR A 212 LYS A 227 ZN A 319 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000