HEADER HYDROLASE 07-AUG-18 6EBU TITLE CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LPXE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS (STRAIN VF5); SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 GENE: AQ_1706; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LPXE, LIPID A 1-PHOSPHATASE, UPPP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.WU,S.WANG,P.ZHOU REVDAT 6 13-MAR-24 6EBU 1 HETSYN REVDAT 5 29-JUL-20 6EBU 1 COMPND REMARK HETNAM SITE REVDAT 4 29-APR-20 6EBU 1 AUTHOR REVDAT 3 01-JAN-20 6EBU 1 REMARK REVDAT 2 03-JUL-19 6EBU 1 JRNL REVDAT 1 26-JUN-19 6EBU 0 JRNL AUTH J.ZHAO,J.AN,D.HWANG,Q.WU,S.WANG,R.A.GILLESPIE,E.G.YANG, JRNL AUTH 2 Z.GUAN,P.ZHOU,H.S.CHUNG JRNL TITL THE LIPID A 1-PHOSPHATASE, LPXE, FUNCTIONALLY CONNECTS JRNL TITL 2 MULTIPLE LAYERS OF BACTERIAL ENVELOPE BIOGENESIS. JRNL REF MBIO V. 10 2019 JRNL REFN ESSN 2150-7511 JRNL PMID 31213552 JRNL DOI 10.1128/MBIO.00886-19 REMARK 2 REMARK 2 RESOLUTION. 2.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 10718 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 547 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 56.6645 - 3.7653 1.00 2642 145 0.2174 0.2168 REMARK 3 2 3.7653 - 2.9886 1.00 2533 137 0.1859 0.2352 REMARK 3 3 2.9886 - 2.6109 1.00 2548 137 0.2032 0.2484 REMARK 3 4 2.6109 - 2.3721 0.97 2448 128 0.2328 0.2676 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.002 1410 REMARK 3 ANGLE : 0.478 1893 REMARK 3 CHIRALITY : 0.036 219 REMARK 3 PLANARITY : 0.005 225 REMARK 3 DIHEDRAL : 5.499 1102 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6EBU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000236031. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10720 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.372 REMARK 200 RESOLUTION RANGE LOW (A) : 46.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5 MM TRIS, 75 MM NACL, 1 MM TRIS(2 REMARK 280 -CARBOXYETHYL)PHOSPHINE (TCEP), 0.4% BETA-OG, 45 MM HEPES, 22.5 REMARK 280 MM LI2SO4, 4.5% GLYCEROL, 17.1% PEG600, 0.095 MM CYMAL-7., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.22000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.22000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 40.01500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.09800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.01500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.09800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.22000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.01500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.09800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.22000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.01500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.09800 REMARK 290 SMTRY3 8 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 GLY A -5 REMARK 465 PRO A -4 REMARK 465 ALA A -3 REMARK 465 VAL A -2 REMARK 465 PRO A -1 REMARK 465 ARG A 0 REMARK 465 SER A 166 REMARK 465 LYS A 167 REMARK 465 GLY A 168 REMARK 465 GLY A 169 REMARK 465 VAL A 170 REMARK 465 TYR A 171 REMARK 465 GLU A 172 REMARK 465 ARG A 173 REMARK 465 ASN A 174 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CB CG SD CE REMARK 470 GLU A 11 CG CD OE1 OE2 REMARK 470 LEU A 15 CG CD1 CD2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 PHE A 75 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 97 NE CZ NH1 NH2 REMARK 470 LYS A 164 CG CD CE NZ REMARK 470 TYR A 165 CG CD1 CD2 CE1 CE2 CZ OH 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 ASP A 5 74.22 -100.18 REMARK 500 ARG A 51 59.11 -149.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 BOG A 202 REMARK 610 BOG A 203 REMARK 610 BOG A 204 REMARK 610 BOG A 205 REMARK 610 BOG A 206 DBREF 6EBU A 1 174 UNP O67603 O67603_AQUAE 1 174 SEQADV 6EBU GLY A -5 UNP O67603 EXPRESSION TAG SEQADV 6EBU PRO A -4 UNP O67603 EXPRESSION TAG SEQADV 6EBU ALA A -3 UNP O67603 EXPRESSION TAG SEQADV 6EBU VAL A -2 UNP O67603 EXPRESSION TAG SEQADV 6EBU PRO A -1 UNP O67603 EXPRESSION TAG SEQADV 6EBU ARG A 0 UNP O67603 EXPRESSION TAG SEQADV 6EBU MET A 63 UNP O67603 ILE 63 ENGINEERED MUTATION SEQRES 1 A 180 GLY PRO ALA VAL PRO ARG MET VAL ILE GLU ASP PHE ALA SEQRES 2 A 180 LEU ASN LEU GLU LEU PHE ARG LEU ILE ASN ASN ALA ARG SEQRES 3 A 180 HIS PRO LEU LEU ASP VAL PHE PHE THR HIS PHE ALA TYR SEQRES 4 A 180 LEU GLY SER GLY TYR VAL LEU PHE PRO LEU LEU ILE PHE SEQRES 5 A 180 LEU PHE ILE PHE ARG LYS GLU LYS VAL LYS PRO LEU ILE SEQRES 6 A 180 LEU ALA ILE MET LEU GLU THR VAL LEU VAL ILE SER LEU SEQRES 7 A 180 LYS THR PHE PHE ASN GLN PRO ARG PRO ALA ILE LEU LEU SEQRES 8 A 180 GLU ASP VAL ASN LEU LEU PHE PRO LEU HIS TRP ARG SER SEQRES 9 A 180 PHE PRO SER GLY ASP THR ALA MET ALA PHE THR ILE ALA SEQRES 10 A 180 THR VAL LEU SER HIS GLY GLU LYS LEU HIS ILE LYS ALA SEQRES 11 A 180 ILE LEU PHE LEU TYR ALA PHE LEU ILE GLY TYR GLU ARG SEQRES 12 A 180 ILE TYR ALA GLY VAL HIS PHE PRO LEU ASP VAL PHE VAL SEQRES 13 A 180 GLY ALA LEU ILE GLY ILE ILE CYS GLY ILE ILE SER LEU SEQRES 14 A 180 LYS TYR SER LYS GLY GLY VAL TYR GLU ARG ASN HET SO4 A 201 5 HET BOG A 202 9 HET BOG A 203 18 HET BOG A 204 9 HET BOG A 205 18 HET BOG A 206 18 HETNAM SO4 SULFATE ION HETNAM BOG OCTYL BETA-D-GLUCOPYRANOSIDE HETSYN BOG BETA-OCTYLGLUCOSIDE; OCTYL BETA-D-GLUCOSIDE; OCTYL D- HETSYN 2 BOG GLUCOSIDE; OCTYL GLUCOSIDE FORMUL 2 SO4 O4 S 2- FORMUL 3 BOG 5(C14 H28 O6) FORMUL 8 HOH *55(H2 O) HELIX 1 AA1 PHE A 6 ALA A 19 1 14 HELIX 2 AA2 HIS A 21 ALA A 32 1 12 HELIX 3 AA3 TYR A 33 TYR A 38 5 6 HELIX 4 AA4 VAL A 39 ARG A 51 1 13 HELIX 5 AA5 LYS A 54 ASN A 77 1 24 HELIX 6 AA6 ARG A 80 LEU A 85 1 6 HELIX 7 AA7 SER A 101 HIS A 116 1 16 HELIX 8 AA8 LYS A 119 ALA A 140 1 22 HELIX 9 AA9 PHE A 144 TYR A 165 1 22 CISPEP 1 PHE A 99 PRO A 100 0 -7.95 CRYST1 80.030 80.196 80.440 90.00 90.00 90.00 C 2 2 21 8 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 0.012495 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012469 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012432 0.00000