HEADER HYDROLASE 26-SEP-06 2J65 TITLE STRUCTURE OF LPXC FROM AQUIFEX AEOLICUS IN COMPLEX WITH UDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE COMPND 3 DEACETYLASE; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: RESIDUES 1-271; COMPND 6 SYNONYM: UDP-3-O-ACYL-N-ACETYLGLUCOSAMINE DEACETYLASE, UDP-3-O-ACYL- COMPND 7 GLCNAC DEACETYLASE; COMPND 8 EC: 3.5.1.-; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET21A; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A-LPXC C181A D272-282 KEYWDS HYDROLASE, LIPID SYNTHESIS, LIPID A BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR L.BUETOW,A.DAWSON,W.N.HUNTER REVDAT 6 13-DEC-23 2J65 1 REMARK LINK REVDAT 5 08-MAY-19 2J65 1 REMARK REVDAT 4 06-MAR-19 2J65 1 REMARK REVDAT 3 16-MAR-11 2J65 1 VERSN REVDAT 2 24-FEB-09 2J65 1 VERSN REVDAT 1 08-NOV-06 2J65 0 JRNL AUTH L.BUETOW,A.DAWSON,W.N.HUNTER JRNL TITL THE NUCLEOTIDE-BINDING SITE OF AQUIFEX AEOLICUS LPXC. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 62 1082 2006 JRNL REFN ESSN 1744-3091 JRNL PMID 17077484 JRNL DOI 10.1107/S1744309106041893 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 34736 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 + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1836 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2498 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4314 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 107 REMARK 3 SOLVENT ATOMS : 488 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.86000 REMARK 3 B22 (A**2) : -0.86000 REMARK 3 B33 (A**2) : 1.28000 REMARK 3 B12 (A**2) : -0.43000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.216 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.662 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4530 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6101 ; 1.340 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 539 ; 5.973 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 213 ;35.024 ;24.460 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 829 ;14.182 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;21.107 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 668 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3344 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2055 ; 0.187 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3058 ; 0.300 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 423 ; 0.142 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 38 ; 0.178 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 26 ; 0.199 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2742 ; 0.653 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4284 ; 1.058 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2014 ; 1.671 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1813 ; 2.701 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. RESIDUES 269-271 ARE DISORDERED IN BOTH CHAINS. REMARK 4 REMARK 4 2J65 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1290030068. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : PT-COATED MIRRORS, MICROFOCUS REMARK 200 BEAMLINE REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36577 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 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 1P42 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): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS OF LPXC WERE GROWN BY HANGING REMARK 280 VAPOR DIFFUSION AT 20 DEG C USING 1 UL OF PROTEIN (184 UM) AND 1 REMARK 280 UL OF A RESERVOIR SOLUTION CONTAINING 8% PEG 6000, 100 MM TRIS, REMARK 280 PH 8.5, AND 300 MM NACL., PH 8.50, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 41.41433 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 82.82867 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 62.12150 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 103.53583 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 20.70717 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PQS 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 181 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 181 TO ALA 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 MET A 1 REMARK 465 LEU A 269 REMARK 465 THR A 270 REMARK 465 ARG A 271 REMARK 465 MET B 1 REMARK 465 LEU B 269 REMARK 465 THR B 270 REMARK 465 ARG B 271 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 HOH A 2134 O HOH A 2145 2.13 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 SER A 59 167.30 174.98 REMARK 500 LEU A 99 -127.23 56.55 REMARK 500 ASN A 118 44.55 -103.45 REMARK 500 ASP A 134 110.65 -162.64 REMARK 500 GLU A 135 70.18 32.81 REMARK 500 ASN A 157 -163.12 -107.53 REMARK 500 GLN A 267 87.96 68.53 REMARK 500 THR B 6 -168.35 -128.74 REMARK 500 SER B 59 167.41 179.39 REMARK 500 LEU B 99 -124.39 56.71 REMARK 500 ASN B 118 39.20 -96.86 REMARK 500 GLU B 135 81.25 14.85 REMARK 500 ASN B 157 -164.68 -113.09 REMARK 500 GLN B 267 38.29 86.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2009 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH B2020 DISTANCE = 6.26 ANGSTROMS 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 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 58 NE2 REMARK 620 2 HIS A 188 NE2 107.2 REMARK 620 3 CL A 305 CL 114.0 117.5 REMARK 620 4 HOH A2239 O 102.9 105.6 108.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 73 OE2 REMARK 620 2 HIS A 253 NE2 103.3 REMARK 620 3 MYR A 401 O1 103.9 101.9 REMARK 620 4 HOH A2238 O 111.1 139.6 90.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 74 NE2 REMARK 620 2 HIS A 226 NE2 98.0 REMARK 620 3 ASP A 230 OD1 102.5 105.8 REMARK 620 4 HOH A2238 O 106.2 116.6 123.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 120 OE1 REMARK 620 2 HIS B 29 NE2 118.5 REMARK 620 3 GLU B 90 OE2 99.7 104.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 58 NE2 REMARK 620 2 HIS B 188 NE2 111.7 REMARK 620 3 CL B 304 CL 105.9 115.2 REMARK 620 4 HOH B2240 O 105.0 108.5 110.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 73 OE2 REMARK 620 2 HIS B 253 NE2 93.0 REMARK 620 3 HOH B2238 O 119.5 142.5 REMARK 620 4 HOH B2239 O 112.6 101.7 83.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 74 NE2 REMARK 620 2 HIS B 226 NE2 101.1 REMARK 620 3 ASP B 230 OD1 105.2 102.8 REMARK 620 4 HOH B2238 O 108.9 103.9 131.0 REMARK 620 N 1 2 3 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MYR A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MYR B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MYR B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P42 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASE(ZINC- REMARK 900 INHIBITED FORM) REMARK 900 RELATED ID: 1XXE RELATED DB: PDB REMARK 900 RDC REFINED SOLUTION STRUCTURE OF THE AALPXC /TU-514 COMPLEX REMARK 900 RELATED ID: 1YH8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASECOMPLEXED REMARK 900 WITH PALMITATE REMARK 900 RELATED ID: 1YHC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASECOMPLEXED REMARK 900 WITH CACODYLATE REMARK 900 RELATED ID: 2GO3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC COMPLEXED WITHIMIDAZOLE. REMARK 900 RELATED ID: 2GO4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC COMPLEXED WITHTU-514 DBREF 2J65 A 1 271 UNP O67648 LPXC_AQUAE 1 271 DBREF 2J65 B 1 271 UNP O67648 LPXC_AQUAE 1 271 SEQADV 2J65 ALA A 181 UNP O67648 CYS 181 ENGINEERED MUTATION SEQADV 2J65 ALA B 181 UNP O67648 CYS 181 ENGINEERED MUTATION SEQRES 1 A 271 MET GLY LEU GLU LYS THR VAL LYS GLU LYS LEU SER PHE SEQRES 2 A 271 GLU GLY VAL GLY ILE HIS THR GLY GLU TYR SER LYS LEU SEQRES 3 A 271 ILE ILE HIS PRO GLU LYS GLU GLY THR GLY ILE ARG PHE SEQRES 4 A 271 PHE LYS ASN GLY VAL TYR ILE PRO ALA ARG HIS GLU PHE SEQRES 5 A 271 VAL VAL HIS THR ASN HIS SER THR ASP LEU GLY PHE LYS SEQRES 6 A 271 GLY GLN ARG ILE LYS THR VAL GLU HIS ILE LEU SER VAL SEQRES 7 A 271 LEU HIS LEU LEU GLU ILE THR ASN VAL THR ILE GLU VAL SEQRES 8 A 271 ILE GLY ASN GLU ILE PRO ILE LEU ASP GLY SER GLY TRP SEQRES 9 A 271 GLU PHE TYR GLU ALA ILE ARG LYS ASN ILE LEU ASN GLN SEQRES 10 A 271 ASN ARG GLU ILE ASP TYR PHE VAL VAL GLU GLU PRO ILE SEQRES 11 A 271 ILE VAL GLU ASP GLU GLY ARG LEU ILE LYS ALA GLU PRO SEQRES 12 A 271 SER ASP THR LEU GLU VAL THR TYR GLU GLY GLU PHE LYS SEQRES 13 A 271 ASN PHE LEU GLY ARG GLN LYS PHE THR PHE VAL GLU GLY SEQRES 14 A 271 ASN GLU GLU GLU ILE VAL LEU ALA ARG THR PHE ALA PHE SEQRES 15 A 271 ASP TRP GLU ILE GLU HIS ILE LYS LYS VAL GLY LEU GLY SEQRES 16 A 271 LYS GLY GLY SER LEU LYS ASN THR LEU VAL LEU GLY LYS SEQRES 17 A 271 ASP LYS VAL TYR ASN PRO GLU GLY LEU ARG TYR GLU ASN SEQRES 18 A 271 GLU PRO VAL ARG HIS LYS VAL PHE ASP LEU ILE GLY ASP SEQRES 19 A 271 LEU TYR LEU LEU GLY SER PRO VAL LYS GLY LYS PHE TYR SEQRES 20 A 271 SER PHE ARG GLY GLY HIS SER LEU ASN VAL LYS LEU VAL SEQRES 21 A 271 LYS GLU LEU ALA LYS LYS GLN LYS LEU THR ARG SEQRES 1 B 271 MET GLY LEU GLU LYS THR VAL LYS GLU LYS LEU SER PHE SEQRES 2 B 271 GLU GLY VAL GLY ILE HIS THR GLY GLU TYR SER LYS LEU SEQRES 3 B 271 ILE ILE HIS PRO GLU LYS GLU GLY THR GLY ILE ARG PHE SEQRES 4 B 271 PHE LYS ASN GLY VAL TYR ILE PRO ALA ARG HIS GLU PHE SEQRES 5 B 271 VAL VAL HIS THR ASN HIS SER THR ASP LEU GLY PHE LYS SEQRES 6 B 271 GLY GLN ARG ILE LYS THR VAL GLU HIS ILE LEU SER VAL SEQRES 7 B 271 LEU HIS LEU LEU GLU ILE THR ASN VAL THR ILE GLU VAL SEQRES 8 B 271 ILE GLY ASN GLU ILE PRO ILE LEU ASP GLY SER GLY TRP SEQRES 9 B 271 GLU PHE TYR GLU ALA ILE ARG LYS ASN ILE LEU ASN GLN SEQRES 10 B 271 ASN ARG GLU ILE ASP TYR PHE VAL VAL GLU GLU PRO ILE SEQRES 11 B 271 ILE VAL GLU ASP GLU GLY ARG LEU ILE LYS ALA GLU PRO SEQRES 12 B 271 SER ASP THR LEU GLU VAL THR TYR GLU GLY GLU PHE LYS SEQRES 13 B 271 ASN PHE LEU GLY ARG GLN LYS PHE THR PHE VAL GLU GLY SEQRES 14 B 271 ASN GLU GLU GLU ILE VAL LEU ALA ARG THR PHE ALA PHE SEQRES 15 B 271 ASP TRP GLU ILE GLU HIS ILE LYS LYS VAL GLY LEU GLY SEQRES 16 B 271 LYS GLY GLY SER LEU LYS ASN THR LEU VAL LEU GLY LYS SEQRES 17 B 271 ASP LYS VAL TYR ASN PRO GLU GLY LEU ARG TYR GLU ASN SEQRES 18 B 271 GLU PRO VAL ARG HIS LYS VAL PHE ASP LEU ILE GLY ASP SEQRES 19 B 271 LEU TYR LEU LEU GLY SER PRO VAL LYS GLY LYS PHE TYR SEQRES 20 B 271 SER PHE ARG GLY GLY HIS SER LEU ASN VAL LYS LEU VAL SEQRES 21 B 271 LYS GLU LEU ALA LYS LYS GLN LYS LEU THR ARG HET ZN A 301 1 HET ZN A 302 1 HET ZN A 303 1 HET ZN A 304 1 HET CL A 305 1 HET MYR A 401 16 HET UDP A 402 25 HET ZN B 301 1 HET ZN B 302 1 HET ZN B 303 1 HET CL B 304 1 HET MYR B 401 16 HET UDP B 402 25 HET MYR B 403 16 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM MYR MYRISTIC ACID HETNAM UDP URIDINE-5'-DIPHOSPHATE FORMUL 3 ZN 7(ZN 2+) FORMUL 7 CL 2(CL 1-) FORMUL 8 MYR 3(C14 H28 O2) FORMUL 9 UDP 2(C9 H14 N2 O12 P2) FORMUL 17 HOH *488(H2 O) HELIX 1 1 ARG A 49 GLU A 51 5 3 HELIX 2 2 VAL A 72 LEU A 82 1 11 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 GLU A 185 VAL A 192 1 8 HELIX 6 6 ASN A 221 TYR A 236 1 16 HELIX 7 7 LEU A 237 GLY A 239 5 3 HELIX 8 8 GLY A 252 GLN A 267 1 16 HELIX 9 9 ARG B 49 GLU B 51 5 3 HELIX 10 10 VAL B 72 GLU B 83 1 12 HELIX 11 11 GLY B 103 LYS B 112 1 10 HELIX 12 12 ASN B 170 ILE B 174 5 5 HELIX 13 13 GLU B 185 VAL B 192 1 8 HELIX 14 14 ASN B 221 TYR B 236 1 16 HELIX 15 15 LEU B 237 GLY B 239 5 3 HELIX 16 16 GLY B 252 GLN B 267 1 16 SHEET 1 AA 2 LEU A 3 VAL A 7 0 SHEET 2 AA 2 ILE A 114 GLU A 120 -1 O LEU A 115 N THR A 6 SHEET 1 AB 5 LEU A 11 VAL A 16 0 SHEET 2 AB 5 TYR A 23 PRO A 30 -1 O SER A 24 N GLY A 15 SHEET 3 AB 5 VAL A 87 ILE A 92 -1 O THR A 88 N HIS A 29 SHEET 4 AB 5 ILE A 37 LYS A 41 1 O ARG A 38 N ILE A 89 SHEET 5 AB 5 VAL A 44 PRO A 47 -1 O VAL A 44 N LYS A 41 SHEET 1 AC 3 VAL A 53 HIS A 55 0 SHEET 2 AC 3 ASP A 61 PHE A 64 -1 O ASP A 61 N VAL A 54 SHEET 3 AC 3 GLN A 67 ILE A 69 -1 O GLN A 67 N PHE A 64 SHEET 1 AD 4 PHE A 124 VAL A 125 0 SHEET 2 AD 4 VAL A 242 PHE A 249 1 N LYS A 243 O PHE A 124 SHEET 3 AD 4 ARG A 137 GLU A 142 -1 O LEU A 138 N PHE A 249 SHEET 4 AD 4 ILE A 130 ASP A 134 -1 O ILE A 130 N ALA A 141 SHEET 1 AE 4 PHE A 124 VAL A 125 0 SHEET 2 AE 4 VAL A 242 PHE A 249 1 N LYS A 243 O PHE A 124 SHEET 3 AE 4 LEU A 147 GLU A 154 1 O GLU A 148 N PHE A 246 SHEET 4 AE 4 ARG A 161 VAL A 167 -1 O GLN A 162 N GLY A 153 SHEET 1 AF 2 PHE A 180 PHE A 182 0 SHEET 2 AF 2 LEU A 204 LEU A 206 1 O LEU A 204 N ALA A 181 SHEET 1 BA 2 LEU B 3 VAL B 7 0 SHEET 2 BA 2 ILE B 114 GLU B 120 -1 O LEU B 115 N THR B 6 SHEET 1 BB 5 LEU B 11 VAL B 16 0 SHEET 2 BB 5 TYR B 23 PRO B 30 -1 O SER B 24 N GLY B 15 SHEET 3 BB 5 VAL B 87 ILE B 92 -1 O THR B 88 N HIS B 29 SHEET 4 BB 5 ILE B 37 LYS B 41 1 O ARG B 38 N ILE B 89 SHEET 5 BB 5 VAL B 44 PRO B 47 -1 O VAL B 44 N LYS B 41 SHEET 1 BC 3 VAL B 53 HIS B 55 0 SHEET 2 BC 3 ASP B 61 PHE B 64 -1 O ASP B 61 N VAL B 54 SHEET 3 BC 3 GLN B 67 ILE B 69 -1 O GLN B 67 N PHE B 64 SHEET 1 BD 2 PHE B 124 VAL B 125 0 SHEET 2 BD 2 VAL B 242 LYS B 243 1 N LYS B 243 O PHE B 124 SHEET 1 BE 5 ILE B 130 ASP B 134 0 SHEET 2 BE 5 ARG B 137 GLU B 142 -1 O ARG B 137 N ASP B 134 SHEET 3 BE 5 LYS B 245 PHE B 249 -1 O LYS B 245 N GLU B 142 SHEET 4 BE 5 GLU B 148 GLU B 154 1 O GLU B 148 N PHE B 246 SHEET 5 BE 5 ARG B 161 VAL B 167 -1 O GLN B 162 N GLY B 153 SHEET 1 BF 2 PHE B 180 PHE B 182 0 SHEET 2 BF 2 LEU B 204 LEU B 206 1 O LEU B 204 N ALA B 181 LINK NE2 HIS A 58 ZN ZN A 303 1555 1555 2.18 LINK OE2 GLU A 73 ZN ZN A 302 1555 1555 2.25 LINK NE2 HIS A 74 ZN ZN A 301 1555 1555 2.11 LINK OE1 GLU A 120 ZN ZN A 304 1555 1555 1.95 LINK NE2 HIS A 188 ZN ZN A 303 1555 1555 2.13 LINK NE2 HIS A 226 ZN ZN A 301 1555 1555 2.04 LINK OD1 ASP A 230 ZN ZN A 301 1555 1555 2.05 LINK NE2 HIS A 253 ZN ZN A 302 1555 1555 2.05 LINK ZN ZN A 301 O HOH A2238 1555 1555 1.98 LINK ZN ZN A 302 O1 MYR A 401 1555 1555 2.25 LINK ZN ZN A 302 O HOH A2238 1555 1555 2.10 LINK ZN ZN A 303 CL CL A 305 1555 1555 2.23 LINK ZN ZN A 303 O HOH A2239 1555 1555 2.00 LINK ZN ZN A 304 NE2 HIS B 29 1555 3664 2.18 LINK ZN ZN A 304 OE2 GLU B 90 1555 3664 1.88 LINK NE2 HIS B 58 ZN ZN B 303 1555 1555 2.08 LINK OE2 GLU B 73 ZN ZN B 302 1555 1555 2.17 LINK NE2 HIS B 74 ZN ZN B 301 1555 1555 2.03 LINK NE2 HIS B 188 ZN ZN B 303 1555 1555 2.09 LINK NE2 HIS B 226 ZN ZN B 301 1555 1555 2.03 LINK OD1 ASP B 230 ZN ZN B 301 1555 1555 2.02 LINK NE2 HIS B 253 ZN ZN B 302 1555 1555 2.09 LINK ZN ZN B 301 O HOH B2238 1555 1555 2.23 LINK ZN ZN B 302 O HOH B2238 1555 1555 2.50 LINK ZN ZN B 302 O HOH B2239 1555 1555 2.26 LINK ZN ZN B 303 CL CL B 304 1555 1555 2.28 LINK ZN ZN B 303 O HOH B2240 1555 1555 1.96 SITE 1 AC1 6 HIS A 74 THR A 179 HIS A 226 ASP A 230 SITE 2 AC1 6 ZN A 302 HOH A2238 SITE 1 AC2 5 GLU A 73 HIS A 253 ZN A 301 MYR A 401 SITE 2 AC2 5 HOH A2238 SITE 1 AC3 4 HIS A 58 HIS A 188 CL A 305 HOH A2239 SITE 1 AC4 4 GLY A 2 GLU A 120 HIS B 29 GLU B 90 SITE 1 AC5 4 ASN A 57 HIS A 58 PHE A 158 ZN A 303 SITE 1 AC6 5 HIS B 74 HIS B 226 ASP B 230 ZN B 302 SITE 2 AC6 5 HOH B2238 SITE 1 AC7 5 GLU B 73 HIS B 253 ZN B 301 HOH B2238 SITE 2 AC7 5 HOH B2239 SITE 1 AC8 4 HIS B 58 HIS B 188 CL B 304 HOH B2240 SITE 1 AC9 6 ASN B 57 HIS B 58 PHE B 158 HIS B 188 SITE 2 AC9 6 ZN B 303 HOH B2207 SITE 1 BC1 8 HIS A 58 SER A 59 GLU A 73 GLY A 198 SITE 2 BC1 8 HIS A 253 ZN A 302 HOH A2238 HOH A2241 SITE 1 BC2 10 ARG A 137 TYR A 151 GLY A 153 GLU A 154 SITE 2 BC2 10 PHE A 155 LYS A 156 GLU A 185 LYS A 227 SITE 3 BC2 10 ARG A 250 GLY A 251 SITE 1 BC3 5 ILE A 186 TYR A 212 ILE B 186 GLY B 195 SITE 2 BC3 5 HOH B2241 SITE 1 BC4 12 ARG B 137 TYR B 151 GLY B 153 GLU B 154 SITE 2 BC4 12 PHE B 155 LYS B 156 GLU B 185 LYS B 227 SITE 3 BC4 12 ARG B 250 HOH B2242 HOH B2243 HOH B2244 SITE 1 BC5 10 SER A 199 HOH A2177 THR B 179 ILE B 186 SITE 2 BC5 10 GLY B 198 SER B 199 LEU B 200 HOH B2245 SITE 3 BC5 10 HOH B2246 HOH B2247 CRYST1 101.755 101.755 124.243 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 0.009828 0.005674 0.000000 0.00000 SCALE2 0.000000 0.011348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008049 0.00000