HEADER HYDROLASE 07-JAN-05 1YH8 TITLE CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASE COMPLEXED WITH TITLE 2 PALMITATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE COMPND 3 DEACETYLASE; COMPND 4 CHAIN: A, B; 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS X-RAY CRYSTALLOGRAPHY; A.AEOLICUS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.HERNICK,H.A.GENNADIOS,D.A.WHITTINGTON,K.M.RUSCHE,D.W.CHRISTIANSON, AUTHOR 2 C.A.FIERKE REVDAT 5 23-AUG-23 1YH8 1 REMARK REVDAT 4 20-OCT-21 1YH8 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1YH8 1 VERSN REVDAT 2 03-MAY-05 1YH8 1 JRNL REVDAT 1 15-FEB-05 1YH8 0 JRNL AUTH M.HERNICK,H.A.GENNADIOS,D.A.WHITTINGTON,K.M.RUSCHE, JRNL AUTH 2 D.W.CHRISTIANSON,C.A.FIERKE JRNL TITL UDP-3-O-((R)-3-HYDROXYMYRISTOYL)-N-ACETYLGLUCOSAMINE JRNL TITL 2 DEACETYLASE FUNCTIONS THROUGH A GENERAL ACID-BASE CATALYST JRNL TITL 3 PAIR MECHANISM JRNL REF J.BIOL.CHEM. V. 280 16969 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15705580 JRNL DOI 10.1074/JBC.M413560200 REMARK 2 REMARK 2 RESOLUTION. 2.70 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 19524 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) : 0.201 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1919 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.80 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 306 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4296 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 118 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.63000 REMARK 3 B22 (A**2) : -1.63000 REMARK 3 B33 (A**2) : 3.26000 REMARK 3 B12 (A**2) : 4.52000 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) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.31 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) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.760 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) : 1.078 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.799 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.798 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.860 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YH8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031508. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK, CRYSTALCLEAR REMARK 200 (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19665 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 5.830 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : 0.11500 REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.84 REMARK 200 R MERGE FOR SHELL (I) : 0.11500 REMARK 200 R SYM FOR SHELL (I) : 0.11500 REMARK 200 FOR SHELL : 4.700 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 1P42 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, NACL, ZNSO4, HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.39333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 82.78667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 62.09000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 103.48333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 20.69667 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 LYS A 280 REMARK 465 LEU A 281 REMARK 465 THR A 282 REMARK 465 ARG A 283 REMARK 465 LYS B 280 REMARK 465 LEU B 281 REMARK 465 THR B 282 REMARK 465 ARG B 283 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 42 51.37 37.13 REMARK 500 SER A 59 160.61 176.51 REMARK 500 THR A 76 72.82 58.94 REMARK 500 LEU A 104 -129.85 57.94 REMARK 500 SER A 107 -166.05 -119.00 REMARK 500 GLN A 123 -169.96 -112.03 REMARK 500 ASN A 124 75.29 -107.31 REMARK 500 ARG A 125 138.39 176.98 REMARK 500 ASP A 140 119.37 175.22 REMARK 500 ASN A 163 -158.58 -97.84 REMARK 500 ASP A 221 28.44 -171.29 REMARK 500 ASN B 42 52.49 36.67 REMARK 500 HIS B 58 -0.01 70.73 REMARK 500 SER B 59 161.70 176.80 REMARK 500 THR B 76 73.27 58.05 REMARK 500 LEU B 104 -127.78 58.37 REMARK 500 SER B 107 -164.75 -118.92 REMARK 500 ASN B 124 73.58 -106.64 REMARK 500 ARG B 125 138.16 177.86 REMARK 500 ASP B 140 119.58 176.73 REMARK 500 ASN B 163 -158.43 -97.05 REMARK 500 ASP B 221 28.25 -171.27 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 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 29 NE2 REMARK 620 2 GLU A 95 OE1 103.4 REMARK 620 3 GLU A 95 OE2 69.2 49.9 REMARK 620 4 GLY B 2 N 105.8 113.3 88.6 REMARK 620 5 GLU B 126 OE2 103.6 137.5 171.9 89.9 REMARK 620 6 GLU B 126 OE1 145.3 74.9 123.7 106.5 64.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 58 NE2 REMARK 620 2 HIS A 200 NE2 103.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 79 NE2 REMARK 620 2 HIS A 238 NE2 100.1 REMARK 620 3 ASP A 242 OD1 99.2 110.2 REMARK 620 4 ASP A 242 OD2 151.6 87.3 52.8 REMARK 620 5 PAM A 801 O1 108.1 141.1 91.4 80.5 REMARK 620 6 PAM A 801 O2 101.6 91.8 146.4 105.6 57.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 507 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 58 NE2 REMARK 620 2 HIS B 200 NE2 100.9 REMARK 620 3 CL B 603 CL 81.3 86.0 REMARK 620 4 HOH B 863 O 118.3 125.6 133.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 79 NE2 REMARK 620 2 HIS B 238 NE2 100.7 REMARK 620 3 ASP B 242 OD1 95.4 110.5 REMARK 620 4 ASP B 242 OD2 147.0 90.3 51.8 REMARK 620 5 PAM B 802 O2 97.4 97.3 146.6 112.0 REMARK 620 6 PAM B 802 O1 101.4 151.2 85.6 81.1 61.6 REMARK 620 N 1 2 3 4 5 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PAM A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PAM B 802 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P42 RELATED DB: PDB REMARK 900 THE ZINC-INHIBITED ENZYME REMARK 900 RELATED ID: 1XXE RELATED DB: PDB REMARK 900 THE NMR STRUCTURE OF THE ENZYME COMPLEXED WITH TU-514 REMARK 900 RELATED ID: 1YHC RELATED DB: PDB DBREF 1YH8 A 2 283 UNP O67648 LPXC_AQUAE 2 271 DBREF 1YH8 B 2 283 UNP O67648 LPXC_AQUAE 2 271 SEQADV 1YH8 ALA A 114 UNP O67648 CYS 181 ENGINEERED MUTATION SEQADV 1YH8 ALA B 114 UNP O67648 CYS 181 ENGINEERED MUTATION SEQRES 1 A 270 GLY LEU GLU LYS THR VAL LYS GLU LYS LEU SER PHE GLU SEQRES 2 A 270 GLY VAL GLY ILE HIS THR GLY GLU TYR SER LYS LEU ILE SEQRES 3 A 270 ILE HIS PRO GLU LYS GLU GLY THR GLY ILE ARG PHE PHE SEQRES 4 A 270 LYS ASN GLY VAL TYR ILE PRO ALA ARG HIS GLU PHE VAL SEQRES 5 A 270 VAL HIS THR ASN HIS SER THR ASP LEU GLY PHE LYS GLY SEQRES 6 A 270 GLN ARG ILE LYS THR VAL GLU HIS ILE LEU SER VAL LEU SEQRES 7 A 270 HIS LEU LEU GLU ILE THR ASN VAL THR ILE GLU VAL ILE SEQRES 8 A 270 GLY ASN GLU ILE PRO ILE LEU ASP GLY SER GLY TRP GLU SEQRES 9 A 270 PHE TYR GLU ALA ILE ARG LYS ASN ILE LEU ASN GLN ASN SEQRES 10 A 270 ARG GLU ILE ASP TYR PHE VAL VAL GLU GLU PRO ILE ILE SEQRES 11 A 270 VAL GLU ASP GLU GLY ARG LEU ILE LYS ALA GLU PRO SER SEQRES 12 A 270 ASP THR LEU GLU VAL THR TYR GLU GLY GLU PHE LYS ASN SEQRES 13 A 270 PHE LEU GLY ARG GLN LYS PHE THR PHE VAL GLU GLY ASN SEQRES 14 A 270 GLU GLU GLU ILE VAL LEU ALA ARG THR PHE ALA PHE ASP SEQRES 15 A 270 TRP GLU ILE GLU HIS ILE LYS LYS VAL GLY LEU GLY LYS SEQRES 16 A 270 GLY GLY SER LEU LYS ASN THR LEU VAL LEU GLY LYS ASP SEQRES 17 A 270 LYS VAL TYR ASN PRO GLU GLY LEU ARG TYR GLU ASN GLU SEQRES 18 A 270 PRO VAL ARG HIS LYS VAL PHE ASP LEU ILE GLY ASP LEU SEQRES 19 A 270 TYR LEU LEU GLY SER PRO VAL LYS GLY LYS PHE TYR SER SEQRES 20 A 270 PHE ARG GLY GLY HIS SER LEU ASN VAL LYS LEU VAL LYS SEQRES 21 A 270 GLU LEU ALA LYS LYS GLN LYS LEU THR ARG SEQRES 1 B 270 GLY LEU GLU LYS THR VAL LYS GLU LYS LEU SER PHE GLU SEQRES 2 B 270 GLY VAL GLY ILE HIS THR GLY GLU TYR SER LYS LEU ILE SEQRES 3 B 270 ILE HIS PRO GLU LYS GLU GLY THR GLY ILE ARG PHE PHE SEQRES 4 B 270 LYS ASN GLY VAL TYR ILE PRO ALA ARG HIS GLU PHE VAL SEQRES 5 B 270 VAL HIS THR ASN HIS SER THR ASP LEU GLY PHE LYS GLY SEQRES 6 B 270 GLN ARG ILE LYS THR VAL GLU HIS ILE LEU SER VAL LEU SEQRES 7 B 270 HIS LEU LEU GLU ILE THR ASN VAL THR ILE GLU VAL ILE SEQRES 8 B 270 GLY ASN GLU ILE PRO ILE LEU ASP GLY SER GLY TRP GLU SEQRES 9 B 270 PHE TYR GLU ALA ILE ARG LYS ASN ILE LEU ASN GLN ASN SEQRES 10 B 270 ARG GLU ILE ASP TYR PHE VAL VAL GLU GLU PRO ILE ILE SEQRES 11 B 270 VAL GLU ASP GLU GLY ARG LEU ILE LYS ALA GLU PRO SER SEQRES 12 B 270 ASP THR LEU GLU VAL THR TYR GLU GLY GLU PHE LYS ASN SEQRES 13 B 270 PHE LEU GLY ARG GLN LYS PHE THR PHE VAL GLU GLY ASN SEQRES 14 B 270 GLU GLU GLU ILE VAL LEU ALA ARG THR PHE ALA PHE ASP SEQRES 15 B 270 TRP GLU ILE GLU HIS ILE LYS LYS VAL GLY LEU GLY LYS SEQRES 16 B 270 GLY GLY SER LEU LYS ASN THR LEU VAL LEU GLY LYS ASP SEQRES 17 B 270 LYS VAL TYR ASN PRO GLU GLY LEU ARG TYR GLU ASN GLU SEQRES 18 B 270 PRO VAL ARG HIS LYS VAL PHE ASP LEU ILE GLY ASP LEU SEQRES 19 B 270 TYR LEU LEU GLY SER PRO VAL LYS GLY LYS PHE TYR SER SEQRES 20 B 270 PHE ARG GLY GLY HIS SER LEU ASN VAL LYS LEU VAL LYS SEQRES 21 B 270 GLU LEU ALA LYS LYS GLN LYS LEU THR ARG HET ZN A 501 1 HET ZN A 503 1 HET ZN A 504 1 HET CL A 601 1 HET PAM A 801 18 HET ZN B 505 1 HET ZN B 507 1 HET CL B 602 1 HET CL B 603 1 HET PAM B 802 18 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM PAM PALMITOLEIC ACID FORMUL 3 ZN 5(ZN 2+) FORMUL 6 CL 3(CL 1-) FORMUL 7 PAM 2(C16 H30 O2) FORMUL 13 HOH *118(H2 O) HELIX 1 1 ARG A 49 GLU A 51 5 3 HELIX 2 2 VAL A 77 GLU A 88 1 12 HELIX 3 3 GLY A 108 LYS A 117 1 10 HELIX 4 4 ASN A 182 ILE A 186 5 5 HELIX 5 5 ASP A 195 VAL A 204 1 10 HELIX 6 6 ASN A 233 TYR A 248 1 16 HELIX 7 7 LEU A 249 GLY A 251 5 3 HELIX 8 8 GLY A 264 GLN A 279 1 16 HELIX 9 9 ARG B 49 GLU B 51 5 3 HELIX 10 10 VAL B 77 GLU B 88 1 12 HELIX 11 11 GLY B 108 LYS B 117 1 10 HELIX 12 12 ASN B 182 ILE B 186 5 5 HELIX 13 13 ASP B 195 VAL B 204 1 10 HELIX 14 14 ASN B 233 TYR B 248 1 16 HELIX 15 15 LEU B 249 GLY B 251 5 3 HELIX 16 16 GLY B 264 GLN B 279 1 16 SHEET 1 A 2 LEU A 3 VAL A 7 0 SHEET 2 A 2 ILE A 120 GLU A 126 -1 O GLN A 123 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 92 ILE A 97 -1 O ILE A 97 N LYS A 25 SHEET 4 B 5 ILE A 37 LYS A 41 1 N PHE A 40 O VAL A 96 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 HIS A 55 0 SHEET 2 C 3 ASP A 61 PHE A 69 -1 O ASP A 61 N VAL A 54 SHEET 3 C 3 GLN A 72 ILE A 74 -1 O ILE A 74 N LEU A 62 SHEET 1 D 2 PHE A 130 VAL A 131 0 SHEET 2 D 2 VAL A 254 LYS A 255 1 O LYS A 255 N PHE A 130 SHEET 1 E 5 ILE A 136 ASP A 140 0 SHEET 2 E 5 ARG A 143 GLU A 148 -1 O ALA A 147 N ILE A 136 SHEET 3 E 5 LYS A 257 PHE A 261 -1 O PHE A 261 N LEU A 144 SHEET 4 E 5 GLU A 154 GLU A 160 1 N GLU A 154 O PHE A 258 SHEET 5 E 5 ARG A 170 VAL A 179 -1 O PHE A 175 N VAL A 155 SHEET 1 F 2 THR A 191 PHE A 194 0 SHEET 2 F 2 THR A 215 LEU A 218 1 O LEU A 216 N THR A 191 SHEET 1 G 2 LEU B 3 VAL B 7 0 SHEET 2 G 2 ILE B 120 GLU B 126 -1 O GLN B 123 N GLU B 4 SHEET 1 H 5 LEU B 11 VAL B 16 0 SHEET 2 H 5 TYR B 23 PRO B 30 -1 O LEU B 26 N PHE B 13 SHEET 3 H 5 VAL B 92 ILE B 97 -1 O ILE B 97 N LYS B 25 SHEET 4 H 5 ILE B 37 LYS B 41 1 N PHE B 40 O VAL B 96 SHEET 5 H 5 VAL B 44 PRO B 47 -1 O VAL B 44 N LYS B 41 SHEET 1 I 3 VAL B 53 HIS B 55 0 SHEET 2 I 3 ASP B 61 PHE B 69 -1 O ASP B 61 N HIS B 55 SHEET 3 I 3 GLN B 72 ILE B 74 -1 O ILE B 74 N LEU B 62 SHEET 1 J 2 PHE B 130 VAL B 131 0 SHEET 2 J 2 VAL B 254 LYS B 255 1 O LYS B 255 N PHE B 130 SHEET 1 K 5 ILE B 136 ASP B 140 0 SHEET 2 K 5 ARG B 143 GLU B 148 -1 O ALA B 147 N ILE B 136 SHEET 3 K 5 LYS B 257 PHE B 261 -1 O PHE B 261 N LEU B 144 SHEET 4 K 5 GLU B 154 GLU B 160 1 N GLU B 154 O PHE B 258 SHEET 5 K 5 ARG B 170 VAL B 179 -1 O PHE B 175 N VAL B 155 SHEET 1 L 2 PHE B 192 PHE B 194 0 SHEET 2 L 2 LEU B 216 LEU B 218 1 O LEU B 218 N ALA B 193 LINK NE2 HIS A 29 ZN ZN A 504 1555 1555 2.15 LINK NE2 HIS A 58 ZN ZN A 503 1555 1555 2.24 LINK NE2 HIS A 79 ZN ZN A 501 1555 1555 2.02 LINK OE1 GLU A 95 ZN ZN A 504 1555 1555 2.49 LINK OE2 GLU A 95 ZN ZN A 504 1555 1555 2.68 LINK NE2 HIS A 200 ZN ZN A 503 1555 1555 2.06 LINK NE2 HIS A 238 ZN ZN A 501 1555 1555 2.03 LINK OD1 ASP A 242 ZN ZN A 501 1555 1555 2.09 LINK OD2 ASP A 242 ZN ZN A 501 1555 1555 2.69 LINK ZN ZN A 501 O1 PAM A 801 1555 1555 2.41 LINK ZN ZN A 501 O2 PAM A 801 1555 1555 2.30 LINK ZN ZN A 504 N GLY B 2 1555 3574 2.39 LINK ZN ZN A 504 OE2 GLU B 126 1555 3574 2.09 LINK ZN ZN A 504 OE1 GLU B 126 1555 3574 2.03 LINK NE2 HIS B 58 ZN ZN B 507 1555 1555 2.26 LINK NE2 HIS B 79 ZN ZN B 505 1555 1555 2.10 LINK NE2 HIS B 200 ZN ZN B 507 1555 1555 2.13 LINK NE2 HIS B 238 ZN ZN B 505 1555 1555 1.96 LINK OD1 ASP B 242 ZN ZN B 505 1555 1555 2.18 LINK OD2 ASP B 242 ZN ZN B 505 1555 1555 2.70 LINK ZN ZN B 505 O2 PAM B 802 1555 1555 2.01 LINK ZN ZN B 505 O1 PAM B 802 1555 1555 2.35 LINK ZN ZN B 507 CL CL B 603 1555 1555 1.98 LINK ZN ZN B 507 O HOH B 863 1555 1555 1.79 SITE 1 AC1 4 HIS A 79 HIS A 238 ASP A 242 PAM A 801 SITE 1 AC2 2 HIS A 58 HIS A 200 SITE 1 AC3 5 ILE A 27 HIS A 29 GLU A 95 GLY B 2 SITE 2 AC3 5 GLU B 126 SITE 1 AC4 4 HIS B 79 HIS B 238 ASP B 242 PAM B 802 SITE 1 AC5 4 HIS B 58 HIS B 200 CL B 603 HOH B 863 SITE 1 AC6 3 HIS A 79 ILE A 103 SER A 107 SITE 1 AC7 4 GLY B 15 VAL B 16 ILE B 103 LEU B 104 SITE 1 AC8 3 HIS B 58 HIS B 200 ZN B 507 SITE 1 AC9 10 ILE A 18 HIS A 58 GLU A 78 HIS A 79 SITE 2 AC9 10 THR A 191 GLY A 210 HIS A 238 ASP A 242 SITE 3 AC9 10 HIS A 265 ZN A 501 SITE 1 BC1 11 LEU A 212 ILE B 18 HIS B 58 GLU B 78 SITE 2 BC1 11 HIS B 79 THR B 191 SER B 211 HIS B 238 SITE 3 BC1 11 ASP B 242 HIS B 265 ZN B 505 CRYST1 101.610 101.610 124.180 90.00 90.00 120.00 P 61 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 0.009842 0.005682 0.000000 0.00000 SCALE2 0.000000 0.011364 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008053 0.00000