HEADER HYDROLASE 03-APR-16 5B4B TITLE CRYSTAL STRUCTURE OF LPXH WITH LIPID X IN SPACEGROUP C2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-2,3-DIACYLGLUCOSAMINE HYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UDP-2,3-DIACYLGLUCOSAMINE PYROPHOSPHATASE LPXH, UDP-2,3- COMPND 5 DIACYLGLUCOSAMINE DIPHOSPHATASE; COMPND 6 EC: 3.6.1.54; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: PAO1; SOURCE 5 GENE: LPXH, PA1792; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS LPXH, LIPID A, LIPID X, UDP-2, 3-DIACYLGLUCOSAMINE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.OKADA,H.WAKABAYASHI,M.YAO,I.TANAKA REVDAT 3 08-NOV-23 5B4B 1 REMARK REVDAT 2 26-FEB-20 5B4B 1 REMARK REVDAT 1 28-SEP-16 5B4B 0 JRNL AUTH C.OKADA,H.WAKABAYASHI,M.KOBAYASHI,A.SHINODA,I.TANAKA,M.YAO JRNL TITL CRYSTAL STRUCTURES OF THE UDP-DIACYLGLUCOSAMINE JRNL TITL 2 PYROPHOSPHOHYDRASE LPXH FROM PSEUDOMONAS AERUGINOSA JRNL REF SCI REP V. 6 32822 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27609419 JRNL DOI 10.1038/SREP32822 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 62089 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3315 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4324 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 245 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3891 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 516 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.085 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.563 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4188 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4092 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5655 ; 1.451 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9381 ; 0.972 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 489 ; 5.436 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 208 ;31.044 ;21.250 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 690 ;12.250 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 61 ;15.672 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 605 ; 0.056 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4601 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1031 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1947 ; 1.895 ; 1.400 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1946 ; 1.886 ; 1.399 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2439 ; 2.683 ; 2.090 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2440 ; 2.682 ; 2.092 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2241 ; 3.504 ; 1.916 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2242 ; 3.503 ; 1.916 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3217 ; 5.365 ; 2.680 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 18715 ; 7.009 ;14.796 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 18209 ; 6.847 ;14.371 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 302 REMARK 3 ORIGIN FOR THE GROUP (A): -13.4777 -0.1630 -23.7607 REMARK 3 T TENSOR REMARK 3 T11: 0.0132 T22: 0.0043 REMARK 3 T33: 0.0029 T12: 0.0000 REMARK 3 T13: 0.0048 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.1163 L22: 0.1571 REMARK 3 L33: 0.1510 L12: 0.0584 REMARK 3 L13: 0.0920 L23: 0.0455 REMARK 3 S TENSOR REMARK 3 S11: -0.0011 S12: 0.0219 S13: -0.0032 REMARK 3 S21: 0.0176 S22: 0.0094 S23: 0.0107 REMARK 3 S31: -0.0047 S32: 0.0138 S33: -0.0084 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 301 REMARK 3 ORIGIN FOR THE GROUP (A): -50.0991 -7.6551 -17.9945 REMARK 3 T TENSOR REMARK 3 T11: 0.0066 T22: 0.0200 REMARK 3 T33: 0.0111 T12: 0.0013 REMARK 3 T13: 0.0026 T23: 0.0143 REMARK 3 L TENSOR REMARK 3 L11: 0.4373 L22: 0.1368 REMARK 3 L33: 0.1957 L12: -0.1979 REMARK 3 L13: -0.0722 L23: -0.0199 REMARK 3 S TENSOR REMARK 3 S11: 0.0330 S12: -0.0267 S13: -0.0169 REMARK 3 S21: -0.0131 S22: -0.0133 S23: -0.0036 REMARK 3 S31: -0.0300 S32: -0.0045 S33: -0.0197 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 REMARK 4 REMARK 4 5B4B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-APR-16. REMARK 100 THE DEPOSITION ID IS D_1300000508. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-10 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 : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65538 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.57500 REMARK 200 FOR SHELL : 1.970 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: 5B49 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 131MM DL-MALIC ACID PH7.0, 17.5% PEG REMARK 280 3350, 10% (V/V) GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 71.76700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.24200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 71.76700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.24200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 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 241 REMARK 465 GLU A 242 REMARK 465 HIS A 243 REMARK 465 HIS A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 MET B 1 REMARK 465 HIS B 244 REMARK 465 HIS B 245 REMARK 465 HIS B 246 REMARK 465 HIS B 247 REMARK 465 HIS B 248 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 636 O HOH A 682 2.05 REMARK 500 O HOH B 408 O HOH B 611 2.10 REMARK 500 O HOH B 562 O HOH B 625 2.10 REMARK 500 O HOH B 410 O HOH B 503 2.12 REMARK 500 O HOH A 610 O HOH A 629 2.13 REMARK 500 O HOH A 504 O HOH A 624 2.16 REMARK 500 O48 LP5 A 301 O HOH A 401 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 525 O HOH B 560 2454 2.09 REMARK 500 O HOH A 524 O HOH B 410 3555 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 31 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP A 81 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 234 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES 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 ARG A 29 -49.73 -130.14 REMARK 500 LEU A 39 54.22 -95.36 REMARK 500 HIS A 195 -46.81 72.57 REMARK 500 LEU B 39 53.38 -97.02 REMARK 500 ASP B 81 35.14 -140.10 REMARK 500 HIS B 195 -46.40 73.11 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 A 691 DISTANCE = 6.21 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LP5 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LP5 B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5B49 RELATED DB: PDB REMARK 900 RELATED ID: 5B4A RELATED DB: PDB REMARK 900 RELATED ID: 5B4C RELATED DB: PDB REMARK 900 RELATED ID: 5B4D RELATED DB: PDB DBREF 5B4B A 1 240 UNP Q9I2V0 LPXH_PSEAE 1 240 DBREF 5B4B B 1 240 UNP Q9I2V0 LPXH_PSEAE 1 240 SEQADV 5B4B LEU A 241 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B GLU A 242 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B HIS A 243 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B HIS A 244 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B HIS A 245 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B HIS A 246 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B HIS A 247 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B HIS A 248 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B LEU B 241 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B GLU B 242 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B HIS B 243 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B HIS B 244 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B HIS B 245 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B HIS B 246 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B HIS B 247 UNP Q9I2V0 EXPRESSION TAG SEQADV 5B4B HIS B 248 UNP Q9I2V0 EXPRESSION TAG SEQRES 1 A 248 MET SER VAL LEU PHE ILE SER ASP LEU HIS LEU GLU ALA SEQRES 2 A 248 GLU ARG PRO ASP ILE THR ARG ALA PHE LEU SER PHE LEU SEQRES 3 A 248 ASP GLU ARG ALA ARG ARG ALA GLU ALA LEU TYR ILE LEU SEQRES 4 A 248 GLY ASP PHE PHE GLU ALA TRP ILE GLY ASP ASP GLY MET SEQRES 5 A 248 ASP ALA PHE GLN ARG SER ILE ALA GLN SER LEU ARG GLN SEQRES 6 A 248 VAL ALA ASP GLY GLY THR ARG ILE TYR LEU MET HIS GLY SEQRES 7 A 248 ASN ARG ASP PHE LEU ILE GLY LYS ALA PHE CYS ARG GLU SEQRES 8 A 248 ALA GLY CYS THR LEU LEU PRO ASP PRO SER VAL ILE ASP SEQRES 9 A 248 LEU TYR GLY GLU PRO VAL LEU LEU MET HIS GLY ASP SER SEQRES 10 A 248 LEU CYS THR ARG ASP GLU ALA TYR MET ARG LEU ARG ARG SEQRES 11 A 248 TRP LEU ARG ASN PRO LEU THR LEU TRP VAL LEU ARG HIS SEQRES 12 A 248 LEU PRO LEU ALA THR ARG HIS LYS LEU ALA ARG LYS LEU SEQRES 13 A 248 ARG LYS GLU SER ARG ALA GLN THR ARG MET LYS ALA VAL SEQRES 14 A 248 ASP ILE ILE ASP VAL THR PRO GLU GLU VAL PRO ARG VAL SEQRES 15 A 248 MET ARG GLY HIS GLY VAL ARG THR LEU ILE HIS GLY HIS SEQRES 16 A 248 THR HIS ARG PRO ALA GLU HIS PRO LEU ASP ILE ASP GLY SEQRES 17 A 248 GLN PRO ALA ARG ARG ILE VAL LEU GLY ASP TRP ASP ARG SEQRES 18 A 248 GLN GLY TRP ALA LEU GLU ILE ASP ALA ASN GLY HIS ARG SEQRES 19 A 248 GLN ALA PRO PHE PRO LEU LEU GLU HIS HIS HIS HIS HIS SEQRES 20 A 248 HIS SEQRES 1 B 248 MET SER VAL LEU PHE ILE SER ASP LEU HIS LEU GLU ALA SEQRES 2 B 248 GLU ARG PRO ASP ILE THR ARG ALA PHE LEU SER PHE LEU SEQRES 3 B 248 ASP GLU ARG ALA ARG ARG ALA GLU ALA LEU TYR ILE LEU SEQRES 4 B 248 GLY ASP PHE PHE GLU ALA TRP ILE GLY ASP ASP GLY MET SEQRES 5 B 248 ASP ALA PHE GLN ARG SER ILE ALA GLN SER LEU ARG GLN SEQRES 6 B 248 VAL ALA ASP GLY GLY THR ARG ILE TYR LEU MET HIS GLY SEQRES 7 B 248 ASN ARG ASP PHE LEU ILE GLY LYS ALA PHE CYS ARG GLU SEQRES 8 B 248 ALA GLY CYS THR LEU LEU PRO ASP PRO SER VAL ILE ASP SEQRES 9 B 248 LEU TYR GLY GLU PRO VAL LEU LEU MET HIS GLY ASP SER SEQRES 10 B 248 LEU CYS THR ARG ASP GLU ALA TYR MET ARG LEU ARG ARG SEQRES 11 B 248 TRP LEU ARG ASN PRO LEU THR LEU TRP VAL LEU ARG HIS SEQRES 12 B 248 LEU PRO LEU ALA THR ARG HIS LYS LEU ALA ARG LYS LEU SEQRES 13 B 248 ARG LYS GLU SER ARG ALA GLN THR ARG MET LYS ALA VAL SEQRES 14 B 248 ASP ILE ILE ASP VAL THR PRO GLU GLU VAL PRO ARG VAL SEQRES 15 B 248 MET ARG GLY HIS GLY VAL ARG THR LEU ILE HIS GLY HIS SEQRES 16 B 248 THR HIS ARG PRO ALA GLU HIS PRO LEU ASP ILE ASP GLY SEQRES 17 B 248 GLN PRO ALA ARG ARG ILE VAL LEU GLY ASP TRP ASP ARG SEQRES 18 B 248 GLN GLY TRP ALA LEU GLU ILE ASP ALA ASN GLY HIS ARG SEQRES 19 B 248 GLN ALA PRO PHE PRO LEU LEU GLU HIS HIS HIS HIS HIS SEQRES 20 B 248 HIS HET LP5 A 301 96 HET GOL A 302 6 HET LP5 B 301 48 HETNAM LP5 (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5- HETNAM 2 LP5 ((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY) HETNAM 3 LP5 TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 LP5 2(C34 H66 N O12 P) FORMUL 4 GOL C3 H8 O3 FORMUL 6 HOH *516(H2 O) HELIX 1 AA1 ARG A 15 ARG A 29 1 15 HELIX 2 AA2 ALA A 30 ALA A 33 5 4 HELIX 3 AA3 GLY A 48 MET A 52 5 5 HELIX 4 AA4 ASP A 53 GLY A 69 1 17 HELIX 5 AA5 GLY A 85 GLY A 93 1 9 HELIX 6 AA6 GLY A 115 CYS A 119 5 5 HELIX 7 AA7 ASP A 122 ARG A 133 1 12 HELIX 8 AA8 ASN A 134 HIS A 143 1 10 HELIX 9 AA9 PRO A 145 ARG A 165 1 21 HELIX 10 AB1 ALA A 168 ASP A 173 1 6 HELIX 11 AB2 GLU A 177 GLY A 187 1 11 HELIX 12 AB3 ARG B 15 ARG B 29 1 15 HELIX 13 AB4 ALA B 30 ALA B 33 5 4 HELIX 14 AB5 GLY B 48 MET B 52 5 5 HELIX 15 AB6 ASP B 53 GLY B 69 1 17 HELIX 16 AB7 GLY B 85 GLY B 93 1 9 HELIX 17 AB8 GLY B 115 CYS B 119 5 5 HELIX 18 AB9 ASP B 122 ARG B 133 1 12 HELIX 19 AC1 ASN B 134 ARG B 142 1 9 HELIX 20 AC2 PRO B 145 ARG B 165 1 21 HELIX 21 AC3 ALA B 168 ASP B 173 1 6 HELIX 22 AC4 GLU B 177 GLY B 187 1 11 SHEET 1 AA1 6 CYS A 94 LEU A 97 0 SHEET 2 AA1 6 ARG A 72 MET A 76 1 N LEU A 75 O LEU A 97 SHEET 3 AA1 6 ALA A 35 LEU A 39 1 N ILE A 38 O MET A 76 SHEET 4 AA1 6 VAL A 3 ILE A 6 1 N LEU A 4 O TYR A 37 SHEET 5 AA1 6 GLY A 223 ASP A 229 -1 O ILE A 228 N VAL A 3 SHEET 6 AA1 6 GLY A 232 PHE A 238 -1 O ARG A 234 N GLU A 227 SHEET 1 AA2 5 SER A 101 LEU A 105 0 SHEET 2 AA2 5 GLU A 108 LEU A 112 -1 O LEU A 112 N SER A 101 SHEET 3 AA2 5 THR A 190 HIS A 193 1 O ILE A 192 N LEU A 111 SHEET 4 AA2 5 GLN A 209 VAL A 215 1 O ILE A 214 N LEU A 191 SHEET 5 AA2 5 ALA A 200 ILE A 206 -1 N HIS A 202 O ARG A 213 SHEET 1 AA3 6 THR B 95 LEU B 97 0 SHEET 2 AA3 6 ARG B 72 MET B 76 1 N LEU B 75 O LEU B 97 SHEET 3 AA3 6 ALA B 35 LEU B 39 1 N ILE B 38 O MET B 76 SHEET 4 AA3 6 VAL B 3 ILE B 6 1 N LEU B 4 O TYR B 37 SHEET 5 AA3 6 GLY B 223 ILE B 228 -1 O ILE B 228 N VAL B 3 SHEET 6 AA3 6 HIS B 233 PHE B 238 -1 O ARG B 234 N GLU B 227 SHEET 1 AA4 5 SER B 101 LEU B 105 0 SHEET 2 AA4 5 GLU B 108 LEU B 112 -1 O LEU B 112 N SER B 101 SHEET 3 AA4 5 THR B 190 HIS B 193 1 O THR B 190 N LEU B 111 SHEET 4 AA4 5 GLN B 209 VAL B 215 1 O ILE B 214 N LEU B 191 SHEET 5 AA4 5 ALA B 200 ILE B 206 -1 N HIS B 202 O ARG B 213 CISPEP 1 ASP A 99 PRO A 100 0 7.19 CISPEP 2 ASP B 99 PRO B 100 0 3.74 SITE 1 AC1 22 ALA A 45 TRP A 46 ASN A 79 ARG A 80 SITE 2 AC1 22 ASP A 122 ALA A 124 TYR A 125 LEU A 156 SITE 3 AC1 22 ARG A 157 SER A 160 GLN A 163 THR A 164 SITE 4 AC1 22 LYS A 167 HIS A 195 HOH A 401 HOH A 402 SITE 5 AC1 22 HOH A 404 HOH A 405 HOH A 421 HOH A 455 SITE 6 AC1 22 HOH A 541 TRP B 139 SITE 1 AC2 7 ASP A 50 ARG A 121 ASP A 170 ASP A 173 SITE 2 AC2 7 VAL A 174 HOH A 448 HOH A 473 SITE 1 AC3 19 LEU A 136 TRP B 46 ASN B 79 ARG B 80 SITE 2 AC3 19 ASP B 122 ALA B 124 TYR B 125 ARG B 149 SITE 3 AC3 19 SER B 160 GLN B 163 THR B 164 LYS B 167 SITE 4 AC3 19 HIS B 195 HOH B 404 HOH B 406 HOH B 413 SITE 5 AC3 19 HOH B 442 HOH B 472 HOH B 481 CRYST1 143.534 42.484 100.756 90.00 125.12 90.00 C 1 2 1 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 0.006967 0.000000 0.004900 0.00000 SCALE2 0.000000 0.023538 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012134 0.00000 CONECT 3943 3945 CONECT 3944 3946 CONECT 3945 3943 3947 3949 3951 CONECT 3946 3944 3948 3950 3952 CONECT 3947 3945 CONECT 3948 3946 CONECT 3949 3945 CONECT 3950 3946 CONECT 3951 3945 3953 CONECT 3952 3946 3954 CONECT 3953 3951 3955 3997 CONECT 3954 3952 3956 3998 CONECT 3955 3953 3957 3991 CONECT 3956 3954 3958 3992 CONECT 3957 3955 3959 CONECT 3958 3956 3960 CONECT 3959 3957 3961 3989 CONECT 3960 3958 3962 3990 CONECT 3961 3959 3963 CONECT 3962 3960 3964 CONECT 3963 3961 3965 3967 CONECT 3964 3962 3966 3968 CONECT 3965 3963 CONECT 3966 3964 CONECT 3967 3963 3969 CONECT 3968 3964 3970 CONECT 3969 3967 3971 CONECT 3970 3968 3972 CONECT 3971 3969 3973 CONECT 3972 3970 3974 CONECT 3973 3971 3975 CONECT 3974 3972 3976 CONECT 3975 3973 3977 CONECT 3976 3974 3978 CONECT 3977 3975 3979 CONECT 3978 3976 3980 CONECT 3979 3977 3981 CONECT 3980 3978 3982 CONECT 3981 3979 3983 CONECT 3982 3980 3984 CONECT 3983 3981 3985 CONECT 3984 3982 3986 CONECT 3985 3983 3987 CONECT 3986 3984 3988 CONECT 3987 3985 CONECT 3988 3986 CONECT 3989 3959 CONECT 3990 3960 CONECT 3991 3955 3993 4005 CONECT 3992 3956 3994 4006 CONECT 3993 3991 3995 4003 CONECT 3994 3992 3996 4004 CONECT 3995 3993 3997 3999 CONECT 3996 3994 3998 4000 CONECT 3997 3953 3995 CONECT 3998 3954 3996 CONECT 3999 3995 4001 CONECT 4000 3996 4002 CONECT 4001 3999 CONECT 4002 4000 CONECT 4003 3993 CONECT 4004 3994 CONECT 4005 3991 4007 CONECT 4006 3992 4008 CONECT 4007 4005 4009 4011 CONECT 4008 4006 4010 4012 CONECT 4009 4007 CONECT 4010 4008 CONECT 4011 4007 4013 CONECT 4012 4008 4014 CONECT 4013 4011 4015 4017 CONECT 4014 4012 4016 4018 CONECT 4015 4013 CONECT 4016 4014 CONECT 4017 4013 4019 CONECT 4018 4014 4020 CONECT 4019 4017 4021 CONECT 4020 4018 4022 CONECT 4021 4019 4023 CONECT 4022 4020 4024 CONECT 4023 4021 4025 CONECT 4024 4022 4026 CONECT 4025 4023 4027 CONECT 4026 4024 4028 CONECT 4027 4025 4029 CONECT 4028 4026 4030 CONECT 4029 4027 4031 CONECT 4030 4028 4032 CONECT 4031 4029 4033 CONECT 4032 4030 4034 CONECT 4033 4031 4035 CONECT 4034 4032 4036 CONECT 4035 4033 4037 CONECT 4036 4034 4038 CONECT 4037 4035 CONECT 4038 4036 CONECT 4039 4040 4041 CONECT 4040 4039 CONECT 4041 4039 4042 4043 CONECT 4042 4041 CONECT 4043 4041 4044 CONECT 4044 4043 CONECT 4045 4046 CONECT 4046 4045 4047 4048 4049 CONECT 4047 4046 CONECT 4048 4046 CONECT 4049 4046 4050 CONECT 4050 4049 4051 4072 CONECT 4051 4050 4052 4069 CONECT 4052 4051 4053 CONECT 4053 4052 4054 4068 CONECT 4054 4053 4055 CONECT 4055 4054 4056 4057 CONECT 4056 4055 CONECT 4057 4055 4058 CONECT 4058 4057 4059 CONECT 4059 4058 4060 CONECT 4060 4059 4061 CONECT 4061 4060 4062 CONECT 4062 4061 4063 CONECT 4063 4062 4064 CONECT 4064 4063 4065 CONECT 4065 4064 4066 CONECT 4066 4065 4067 CONECT 4067 4066 CONECT 4068 4053 CONECT 4069 4051 4070 4076 CONECT 4070 4069 4071 4075 CONECT 4071 4070 4072 4073 CONECT 4072 4050 4071 CONECT 4073 4071 4074 CONECT 4074 4073 CONECT 4075 4070 CONECT 4076 4069 4077 CONECT 4077 4076 4078 4079 CONECT 4078 4077 CONECT 4079 4077 4080 CONECT 4080 4079 4081 4082 CONECT 4081 4080 CONECT 4082 4080 4083 CONECT 4083 4082 4084 CONECT 4084 4083 4085 CONECT 4085 4084 4086 CONECT 4086 4085 4087 CONECT 4087 4086 4088 CONECT 4088 4087 4089 CONECT 4089 4088 4090 CONECT 4090 4089 4091 CONECT 4091 4090 4092 CONECT 4092 4091 MASTER 422 0 3 22 22 0 13 6 4509 2 150 40 END