PDB Short entry for 2JT2 HEADER HYDROLASE 18-JUL-07 2JT2 TITLE SOLUTION STRUCTURE OF THE AQUIFEX AEOLICUS LPXC- CHIR-090 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 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 GENE: LPXC, ENVA; 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: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET21A KEYWDS ANTIBIOTIC, LIPID A, HYDROXAMATE, CHIR-090, HYDROLASE, LIPID A KEYWDS 2 BIOSYNTHESIS, LIPID SYNTHESIS EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR A.W.BARB,L.JIANG,C.R.H.RAETZ,P.ZHOU REVDAT 4 20-OCT-21 2JT2 1 REMARK SEQADV REVDAT 3 14-MAR-18 2JT2 1 REMARK ATOM REVDAT 2 24-FEB-09 2JT2 1 VERSN REVDAT 1 04-DEC-07 2JT2 0 JRNL AUTH A.W.BARB,L.JIANG,C.R.RAETZ,P.ZHOU JRNL TITL STRUCTURE OF THE DEACETYLASE LPXC BOUND TO THE ANTIBIOTIC JRNL TITL 2 CHIR-090: TIME-DEPENDENT INHIBITION AND SPECIFICITY IN JRNL TITL 3 LIGAND BINDING JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 18433 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 18025458 JRNL DOI 10.1073/PNAS.0709412104 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USING X-PLOR REMARK 4 REMARK 4 2JT2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000100254. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 MM KCL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] AQUIFEX REMARK 210 AEOLICUS LPXC, 1 MM CHIR-090, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 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 : 25 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 THR A 270 REMARK 465 ARG A 271 REMARK 465 ASP A 272 REMARK 465 LEU A 273 REMARK 465 PRO A 274 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 OD1 ASN A 221 HE ARG A 225 1.42 REMARK 500 O HIS A 50 H VAL A 53 1.42 REMARK 500 H THR A 20 OE1 GLU A 95 1.54 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 51 -16.39 -43.59 REMARK 500 1 HIS A 58 11.02 48.94 REMARK 500 1 SER A 59 146.13 162.52 REMARK 500 1 THR A 71 73.49 50.00 REMARK 500 1 LEU A 99 -121.47 56.07 REMARK 500 1 ASN A 113 31.70 -143.86 REMARK 500 1 ASN A 118 68.84 -112.23 REMARK 500 1 ASP A 134 105.94 -175.44 REMARK 500 1 PHE A 158 -1.52 -49.18 REMARK 500 1 GLU A 172 -6.09 -53.89 REMARK 500 1 ASP A 209 24.45 -153.26 REMARK 500 1 ASN A 221 43.01 -151.38 REMARK 500 1 LEU A 237 -2.39 -50.78 REMARK 500 1 PRO A 241 150.67 -48.53 REMARK 500 1 LYS A 268 -162.99 54.23 REMARK 500 2 GLU A 51 -16.73 -43.25 REMARK 500 2 HIS A 58 7.90 51.98 REMARK 500 2 SER A 59 153.54 161.90 REMARK 500 2 THR A 71 74.57 49.91 REMARK 500 2 LEU A 99 -121.98 55.78 REMARK 500 2 ASN A 113 36.34 -145.73 REMARK 500 2 ASN A 118 67.99 -106.91 REMARK 500 2 ASP A 134 102.17 -173.66 REMARK 500 2 THR A 146 -169.86 -120.46 REMARK 500 2 PHE A 158 3.11 -53.48 REMARK 500 2 ASP A 209 24.32 -153.90 REMARK 500 2 ASN A 221 51.17 -141.82 REMARK 500 2 LEU A 237 -3.01 -50.36 REMARK 500 2 ARG A 250 17.38 52.34 REMARK 500 2 GLN A 267 -35.52 -34.59 REMARK 500 3 GLU A 51 -16.64 -43.06 REMARK 500 3 HIS A 58 5.37 52.72 REMARK 500 3 SER A 59 155.92 165.14 REMARK 500 3 THR A 71 74.41 49.96 REMARK 500 3 LEU A 99 -118.54 56.86 REMARK 500 3 ASN A 118 68.97 -109.46 REMARK 500 3 ASP A 134 101.94 -170.28 REMARK 500 3 THR A 146 -169.22 -121.90 REMARK 500 3 PHE A 158 2.46 -55.85 REMARK 500 3 ASP A 209 24.23 -152.28 REMARK 500 3 ASN A 221 48.84 -147.68 REMARK 500 3 LEU A 237 -4.01 -49.87 REMARK 500 3 GLN A 267 30.83 -73.84 REMARK 500 3 LYS A 268 48.47 -177.76 REMARK 500 4 GLU A 51 -17.33 -43.53 REMARK 500 4 HIS A 58 13.12 46.54 REMARK 500 4 SER A 59 152.61 164.89 REMARK 500 4 THR A 71 75.32 48.97 REMARK 500 4 LEU A 99 -118.43 56.84 REMARK 500 4 ASN A 113 33.72 -144.58 REMARK 500 REMARK 500 THIS ENTRY HAS 365 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 336 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 74 NE2 REMARK 620 2 HIS A 226 NE2 101.4 REMARK 620 3 ASP A 230 OD1 102.1 103.0 REMARK 620 4 C90 A 501 O22 131.9 90.9 120.2 REMARK 620 5 C90 A 501 O24 98.4 160.2 71.9 76.2 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 336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C90 A 501 DBREF 2JT2 A 1 274 UNP O67648 LPXC_AQUAE 1 274 SEQADV 2JT2 ALA A 181 UNP O67648 CYS 181 ENGINEERED MUTATION SEQRES 1 A 274 MET GLY LEU GLU LYS THR VAL LYS GLU LYS LEU SER PHE SEQRES 2 A 274 GLU GLY VAL GLY ILE HIS THR GLY GLU TYR SER LYS LEU SEQRES 3 A 274 ILE ILE HIS PRO GLU LYS GLU GLY THR GLY ILE ARG PHE SEQRES 4 A 274 PHE LYS ASN GLY VAL TYR ILE PRO ALA ARG HIS GLU PHE SEQRES 5 A 274 VAL VAL HIS THR ASN HIS SER THR ASP LEU GLY PHE LYS SEQRES 6 A 274 GLY GLN ARG ILE LYS THR VAL GLU HIS ILE LEU SER VAL SEQRES 7 A 274 LEU HIS LEU LEU GLU ILE THR ASN VAL THR ILE GLU VAL SEQRES 8 A 274 ILE GLY ASN GLU ILE PRO ILE LEU ASP GLY SER GLY TRP SEQRES 9 A 274 GLU PHE TYR GLU ALA ILE ARG LYS ASN ILE LEU ASN GLN SEQRES 10 A 274 ASN ARG GLU ILE ASP TYR PHE VAL VAL GLU GLU PRO ILE SEQRES 11 A 274 ILE VAL GLU ASP GLU GLY ARG LEU ILE LYS ALA GLU PRO SEQRES 12 A 274 SER ASP THR LEU GLU VAL THR TYR GLU GLY GLU PHE LYS SEQRES 13 A 274 ASN PHE LEU GLY ARG GLN LYS PHE THR PHE VAL GLU GLY SEQRES 14 A 274 ASN GLU GLU GLU ILE VAL LEU ALA ARG THR PHE ALA PHE SEQRES 15 A 274 ASP TRP GLU ILE GLU HIS ILE LYS LYS VAL GLY LEU GLY SEQRES 16 A 274 LYS GLY GLY SER LEU LYS ASN THR LEU VAL LEU GLY LYS SEQRES 17 A 274 ASP LYS VAL TYR ASN PRO GLU GLY LEU ARG TYR GLU ASN SEQRES 18 A 274 GLU PRO VAL ARG HIS LYS VAL PHE ASP LEU ILE GLY ASP SEQRES 19 A 274 LEU TYR LEU LEU GLY SER PRO VAL LYS GLY LYS PHE TYR SEQRES 20 A 274 SER PHE ARG GLY GLY HIS SER LEU ASN VAL LYS LEU VAL SEQRES 21 A 274 LYS GLU LEU ALA LYS LYS GLN LYS LEU THR ARG ASP LEU SEQRES 22 A 274 PRO HET ZN A 336 1 HET C90 A 501 58 HETNAM ZN ZINC ION HETNAM C90 N-{(1S,2R)-2-HYDROXY-1-[(HYDROXYAMINO)CARBONYL]PROPYL}- HETNAM 2 C90 4-{[4-(MORPHOLIN-4-YLMETHYL)PHENYL]ETHYNYL}BENZAMIDE FORMUL 2 ZN ZN 2+ FORMUL 3 C90 C24 H27 N3 O5 HELIX 1 1 ARG A 49 GLU A 51 5 3 HELIX 2 2 VAL A 72 GLU A 83 1 12 HELIX 3 3 GLY A 103 LYS A 112 1 10 HELIX 4 4 ASN A 170 ILE A 174 5 5 HELIX 5 5 ASP A 183 VAL A 192 1 10 HELIX 6 6 ASN A 221 LEU A 237 1 17 HELIX 7 7 GLY A 252 LYS A 268 1 17 SHEET 1 A 2 LEU A 3 VAL A 7 0 SHEET 2 A 2 ILE A 114 GLU A 120 -1 O ARG A 119 N GLU A 4 SHEET 1 B 5 LEU A 11 VAL A 16 0 SHEET 2 B 5 TYR A 23 PRO A 30 -1 O LEU A 26 N PHE A 13 SHEET 3 B 5 VAL A 87 ILE A 92 -1 O ILE A 92 N LYS A 25 SHEET 4 B 5 ILE A 37 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 HIS A 55 SHEET 3 C 3 GLN A 67 ILE A 69 -1 O ILE A 69 N LEU A 62 SHEET 1 D 4 PHE A 124 VAL A 125 0 SHEET 2 D 4 VAL A 242 PHE A 249 1 O LYS A 243 N PHE A 124 SHEET 3 D 4 ARG A 137 GLU A 142 -1 N LEU A 138 O PHE A 249 SHEET 4 D 4 ILE A 130 ASP A 134 -1 N ILE A 130 O ALA A 141 SHEET 1 E 4 PHE A 124 VAL A 125 0 SHEET 2 E 4 VAL A 242 PHE A 249 1 O LYS A 243 N PHE A 124 SHEET 3 E 4 LEU A 147 GLU A 154 1 N GLU A 152 O SER A 248 SHEET 4 E 4 ARG A 161 VAL A 167 -1 O GLN A 162 N GLY A 153 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 ALA A 181 LINK NE2 HIS A 74 ZN ZN A 336 1555 1555 2.06 LINK NE2 HIS A 226 ZN ZN A 336 1555 1555 2.08 LINK OD1 ASP A 230 ZN ZN A 336 1555 1555 2.17 LINK ZN ZN A 336 O22 C90 A 501 1555 1555 2.19 LINK ZN ZN A 336 O24 C90 A 501 1555 1555 2.01 SITE 1 AC1 4 HIS A 74 HIS A 226 ASP A 230 C90 A 501 SITE 1 AC2 17 HIS A 19 HIS A 58 GLU A 73 HIS A 74 SITE 2 AC2 17 THR A 179 PHE A 180 ALA A 181 LYS A 190 SITE 3 AC2 17 GLY A 198 SER A 199 THR A 203 VAL A 205 SITE 4 AC2 17 HIS A 226 LYS A 227 ASP A 230 HIS A 253 SITE 5 AC2 17 ZN A 336 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