HEADER HYDROLASE 26-JAN-11 2Y6U TITLE PEROXISOMAL ALPHA-BETA-HYDROLASE LPX1 (YOR084W) FROM SACCHAROMYCES TITLE 2 CEREVISIAE (CRYSTAL FORM II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOMAL MEMBRANE PROTEIN LPX1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LIPASE OF PEROXISOMES PROTEIN 1, LPX1-YOR084W; COMPND 5 EC: 3.1.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: CODON PLUS RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET21D; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PST281 KEYWDS HYDROLASE, PUTATIVE ESTERASE, PUTATIVE LIPASE EXPDTA X-RAY DIFFRACTION AUTHOR S.THOMS,H.H.NIEMANN REVDAT 5 20-DEC-23 2Y6U 1 REMARK REVDAT 4 25-SEP-19 2Y6U 1 REMARK REVDAT 3 24-JUL-19 2Y6U 1 REMARK LINK REVDAT 2 17-AUG-11 2Y6U 1 JRNL REVDAT 1 13-JUL-11 2Y6U 0 JRNL AUTH S.THOMS,J.HOFHUIS,C.THOING,J.GARTNER,H.H.NIEMANN JRNL TITL THE UNUSUAL EXTENDED C-TERMINAL HELIX OF THE PEROXISOMAL JRNL TITL 2 ALPHA-BETA-HYDROLASE LPX1 IS INVOLVED IN DIMER CONTACTS BUT JRNL TITL 3 DISPENSABLE FOR DIMERIZATION JRNL REF J.STRUCT.BIOL. V. 175 362 2011 JRNL REFN ISSN 1047-8477 JRNL PMID 21741480 JRNL DOI 10.1016/J.JSB.2011.06.008 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 41757 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2219 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3006 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 162 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2967 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : -0.02000 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): 0.102 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.910 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3163 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2164 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4318 ; 2.018 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5293 ; 1.088 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 421 ;22.017 ; 5.285 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;34.353 ;23.885 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 543 ;14.205 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;17.857 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 483 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3547 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 646 ; 0.001 ; 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): 1916 ; 1.222 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 762 ; 0.393 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3132 ; 2.030 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1247 ; 2.932 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1165 ; 4.345 ; 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 : 8 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 1 A 54 REMARK 3 ORIGIN FOR THE GROUP (A): -37.0282 -4.4623 8.7453 REMARK 3 T TENSOR REMARK 3 T11: 0.0667 T22: 0.1706 REMARK 3 T33: 0.1665 T12: -0.0144 REMARK 3 T13: 0.0060 T23: 0.0125 REMARK 3 L TENSOR REMARK 3 L11: 2.1773 L22: 3.6522 REMARK 3 L33: 2.3182 L12: 0.3618 REMARK 3 L13: 0.5202 L23: 1.3970 REMARK 3 S TENSOR REMARK 3 S11: 0.0357 S12: 0.0852 S13: -0.2381 REMARK 3 S21: 0.2079 S22: -0.1496 S23: 0.5407 REMARK 3 S31: 0.2504 S32: -0.3709 S33: 0.1139 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 : A 55 A 137 REMARK 3 ORIGIN FOR THE GROUP (A): -31.4446 -3.5166 5.3957 REMARK 3 T TENSOR REMARK 3 T11: 0.0154 T22: 0.1122 REMARK 3 T33: 0.0496 T12: 0.0015 REMARK 3 T13: -0.0124 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 2.4550 L22: 3.4397 REMARK 3 L33: 3.0669 L12: 0.1719 REMARK 3 L13: 0.1290 L23: 1.2115 REMARK 3 S TENSOR REMARK 3 S11: 0.0005 S12: 0.2213 S13: -0.1772 REMARK 3 S21: -0.0528 S22: -0.0126 S23: 0.2372 REMARK 3 S31: 0.1391 S32: -0.2227 S33: 0.0121 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 138 A 283 REMARK 3 ORIGIN FOR THE GROUP (A): -21.9590 6.2272 -0.2924 REMARK 3 T TENSOR REMARK 3 T11: 0.1416 T22: 0.1528 REMARK 3 T33: 0.1032 T12: -0.0034 REMARK 3 T13: 0.0082 T23: 0.0251 REMARK 3 L TENSOR REMARK 3 L11: 1.8989 L22: 1.6313 REMARK 3 L33: 2.8178 L12: -0.2958 REMARK 3 L13: 0.6350 L23: -0.2479 REMARK 3 S TENSOR REMARK 3 S11: -0.0432 S12: 0.3874 S13: 0.3271 REMARK 3 S21: -0.2836 S22: -0.0156 S23: -0.0553 REMARK 3 S31: -0.4295 S32: 0.1285 S33: 0.0588 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 284 A 316 REMARK 3 ORIGIN FOR THE GROUP (A): -10.5905 -7.7053 3.7526 REMARK 3 T TENSOR REMARK 3 T11: 0.0410 T22: 0.1396 REMARK 3 T33: 0.0756 T12: 0.0412 REMARK 3 T13: 0.0127 T23: -0.0567 REMARK 3 L TENSOR REMARK 3 L11: 5.3565 L22: 3.0915 REMARK 3 L33: 6.3397 L12: 0.8049 REMARK 3 L13: -0.3807 L23: 0.1002 REMARK 3 S TENSOR REMARK 3 S11: 0.0258 S12: 0.2278 S13: 0.0133 REMARK 3 S21: -0.0911 S22: -0.0208 S23: -0.1605 REMARK 3 S31: 0.0374 S32: 0.3792 S33: -0.0050 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 317 A 348 REMARK 3 ORIGIN FOR THE GROUP (A): -20.1730 -14.0208 -3.5877 REMARK 3 T TENSOR REMARK 3 T11: 0.0948 T22: 0.1771 REMARK 3 T33: 0.1182 T12: 0.0179 REMARK 3 T13: 0.0056 T23: -0.1050 REMARK 3 L TENSOR REMARK 3 L11: 3.3117 L22: 3.0491 REMARK 3 L33: 5.0939 L12: 0.4349 REMARK 3 L13: -0.7485 L23: -0.0217 REMARK 3 S TENSOR REMARK 3 S11: -0.0643 S12: 0.4054 S13: -0.4264 REMARK 3 S21: -0.3048 S22: -0.0094 S23: -0.1252 REMARK 3 S31: 0.5581 S32: 0.1224 S33: 0.0737 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 349 A 356 REMARK 3 ORIGIN FOR THE GROUP (A): -32.6812 -26.0021 19.8660 REMARK 3 T TENSOR REMARK 3 T11: 0.9901 T22: 1.3119 REMARK 3 T33: 1.0034 T12: -0.1287 REMARK 3 T13: 0.0350 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 1.7967 L22: 4.4578 REMARK 3 L33: 0.0689 L12: 2.8258 REMARK 3 L13: 0.3425 L23: 0.5323 REMARK 3 S TENSOR REMARK 3 S11: 0.2662 S12: -0.2612 S13: -0.2574 REMARK 3 S21: 0.1908 S22: -0.3356 S23: -0.4469 REMARK 3 S31: 0.0793 S32: -0.0478 S33: 0.0695 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 357 A 376 REMARK 3 ORIGIN FOR THE GROUP (A): -30.3424 -24.7320 36.9585 REMARK 3 T TENSOR REMARK 3 T11: 0.2685 T22: 0.0821 REMARK 3 T33: 0.1929 T12: -0.0451 REMARK 3 T13: 0.0164 T23: 0.0930 REMARK 3 L TENSOR REMARK 3 L11: 21.0558 L22: 6.2058 REMARK 3 L33: 3.3985 L12: 3.4366 REMARK 3 L13: 2.3717 L23: 0.2505 REMARK 3 S TENSOR REMARK 3 S11: 0.1364 S12: -0.0200 S13: -0.5760 REMARK 3 S21: 0.0730 S22: 0.0522 S23: -0.0088 REMARK 3 S31: 0.3392 S32: -0.0630 S33: -0.1887 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 377 A 381 REMARK 3 ORIGIN FOR THE GROUP (A): -12.1012 -22.9028 39.6455 REMARK 3 T TENSOR REMARK 3 T11: 0.5158 T22: 0.3141 REMARK 3 T33: 0.5725 T12: 0.0966 REMARK 3 T13: -0.1326 T23: 0.0302 REMARK 3 L TENSOR REMARK 3 L11: 30.1350 L22: 3.4901 REMARK 3 L33: 10.4515 L12: -2.4376 REMARK 3 L13: 8.3774 L23: -5.8449 REMARK 3 S TENSOR REMARK 3 S11: 1.0868 S12: -0.5199 S13: -1.7782 REMARK 3 S21: -0.3553 S22: -0.4039 S23: 0.2429 REMARK 3 S31: 0.7993 S32: 0.5684 S33: -0.6829 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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. REMARK 4 REMARK 4 2Y6U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1290045782. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-09 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 : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X12 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44068 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 48.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2Y6V REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION. DROP CONTAINED 2.5 UL REMARK 280 PROTEIN (2.0 MG/ML), 0.5 UL ADDITIVE (0.1 M UREA) AND 2 UL REMARK 280 RESERVOIR (8 % PEG 8000, 0.1 M HEPES, PH 7.0) REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 83.68000 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 41.84000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.84000 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 83.68000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.4 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 41.84000 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 GLU A 2 REMARK 465 ALA A 243 REMARK 465 SER A 244 REMARK 465 GLY A 245 REMARK 465 ASP A 246 REMARK 465 ASP A 247 REMARK 465 GLU A 248 REMARK 465 ASP A 249 REMARK 465 GLY A 250 REMARK 465 THR A 382 REMARK 465 THR A 383 REMARK 465 LYS A 384 REMARK 465 GLN A 385 REMARK 465 LYS A 386 REMARK 465 LEU A 387 REMARK 465 ALA A 388 REMARK 465 ALA A 389 REMARK 465 ALA A 390 REMARK 465 LEU A 391 REMARK 465 GLU A 392 REMARK 465 HIS A 393 REMARK 465 HIS A 394 REMARK 465 HIS A 395 REMARK 465 HIS A 396 REMARK 465 HIS A 397 REMARK 465 HIS A 398 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 69 CG GLU A 69 CD 0.095 REMARK 500 ARG A 119 CZ ARG A 119 NH1 -0.079 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 119 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 119 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 MET A 269 CG - SD - CE ANGL. DEV. = 16.8 DEGREES REMARK 500 ARG A 336 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 336 NE - CZ - NH2 ANGL. DEV. = -5.0 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 MET A 63 -145.20 -110.40 REMARK 500 VAL A 76 114.98 -32.10 REMARK 500 ALA A 80 -91.42 -42.13 REMARK 500 SER A 134 -15.75 -43.83 REMARK 500 SER A 145 -122.02 64.07 REMARK 500 GLN A 158 83.18 -154.13 REMARK 500 LEU A 161 -63.17 -99.27 REMARK 500 VAL A 172 -58.96 -125.22 REMARK 500 HIS A 228 130.79 -39.95 REMARK 500 PRO A 252 156.43 -45.48 REMARK 500 PHE A 272 -17.68 -140.48 REMARK 500 GLN A 351 62.84 101.39 REMARK 500 GLN A 357 66.59 -101.73 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 A2033 DISTANCE = 6.35 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1382 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Y6V RELATED DB: PDB REMARK 900 PEROXISOMAL ALPHA-BETA-HYDROLASE LPX1 (YOR084W) FROM SACCHAROMYCES REMARK 900 CEREVISIAE (CRYSTAL FORM I) REMARK 999 REMARK 999 SEQUENCE REMARK 999 C-TERMINAL ELEVEN RESIDUES ARE CLONING ARTEFACT (AAALE) REMARK 999 AND HEXA-HISTIDINE TAG. DBREF 2Y6U A 1 387 UNP Q12405 LPX1_YEAST 1 387 SEQADV 2Y6U ALA A 388 UNP Q12405 EXPRESSION TAG SEQADV 2Y6U ALA A 389 UNP Q12405 EXPRESSION TAG SEQADV 2Y6U ALA A 390 UNP Q12405 EXPRESSION TAG SEQADV 2Y6U LEU A 391 UNP Q12405 EXPRESSION TAG SEQADV 2Y6U GLU A 392 UNP Q12405 EXPRESSION TAG SEQADV 2Y6U HIS A 393 UNP Q12405 EXPRESSION TAG SEQADV 2Y6U HIS A 394 UNP Q12405 EXPRESSION TAG SEQADV 2Y6U HIS A 395 UNP Q12405 EXPRESSION TAG SEQADV 2Y6U HIS A 396 UNP Q12405 EXPRESSION TAG SEQADV 2Y6U HIS A 397 UNP Q12405 EXPRESSION TAG SEQADV 2Y6U HIS A 398 UNP Q12405 EXPRESSION TAG SEQRES 1 A 398 MET GLU GLN ASN ARG PHE LYS LYS GLU THR LYS THR CME SEQRES 2 A 398 SER ALA SER TRP PRO ARG ALA PRO GLN SER THR LEU CSO SEQRES 3 A 398 ALA THR ASP ARG LEU GLU LEU THR TYR ASP VAL TYR THR SEQRES 4 A 398 SER ALA GLU ARG GLN ARG ARG SER ARG THR ALA THR ARG SEQRES 5 A 398 LEU ASN LEU VAL PHE LEU HIS GLY SER GLY MET SER LYS SEQRES 6 A 398 VAL VAL TRP GLU TYR TYR LEU PRO ARG LEU VAL ALA ALA SEQRES 7 A 398 ASP ALA GLU GLY ASN TYR ALA ILE ASP LYS VAL LEU LEU SEQRES 8 A 398 ILE ASP GLN VAL ASN HIS GLY ASP SER ALA VAL ARG ASN SEQRES 9 A 398 ARG GLY ARG LEU GLY THR ASN PHE ASN TRP ILE ASP GLY SEQRES 10 A 398 ALA ARG ASP VAL LEU LYS ILE ALA THR CSO GLU LEU GLY SEQRES 11 A 398 SER ILE ASP SER HIS PRO ALA LEU ASN VAL VAL ILE GLY SEQRES 12 A 398 HIS SER MET GLY GLY PHE GLN ALA LEU ALA CYS ASP VAL SEQRES 13 A 398 LEU GLN PRO ASN LEU PHE HIS LEU LEU ILE LEU ILE GLU SEQRES 14 A 398 PRO VAL VAL ILE THR ARG LYS ALA ILE GLY ALA GLY ARG SEQRES 15 A 398 PRO GLY LEU PRO PRO ASP SER PRO GLN ILE PRO GLU ASN SEQRES 16 A 398 LEU TYR ASN SER LEU ARG LEU LYS THR CSO ASP HIS PHE SEQRES 17 A 398 ALA ASN GLU SER GLU TYR VAL LYS TYR MET ARG ASN GLY SEQRES 18 A 398 SER PHE PHE THR ASN ALA HIS SER GLN ILE LEU GLN ASN SEQRES 19 A 398 ILE ILE ASP PHE GLU ARG THR LYS ALA SER GLY ASP ASP SEQRES 20 A 398 GLU ASP GLY GLY PRO VAL ARG THR LYS MET GLU GLN ALA SEQRES 21 A 398 GLN ASN LEU LEU CYS TYR MET ASN MET GLN THR PHE ALA SEQRES 22 A 398 PRO PHE LEU ILE SER ASN VAL LYS PHE VAL ARG LYS ARG SEQRES 23 A 398 THR ILE HIS ILE VAL GLY ALA ARG SER ASN TRP CSO PRO SEQRES 24 A 398 PRO GLN ASN GLN LEU PHE LEU GLN LYS THR LEU GLN ASN SEQRES 25 A 398 TYR HIS LEU ASP VAL ILE PRO GLY GLY SER HIS LEU VAL SEQRES 26 A 398 ASN VAL GLU ALA PRO ASP LEU VAL ILE GLU ARG ILE ASN SEQRES 27 A 398 HIS HIS ILE HIS GLU PHE VAL LEU THR SER PRO LEU GLN SEQRES 28 A 398 SER SER HIS ILE PRO GLN LEU THR LEU GLU GLU ARG ALA SEQRES 29 A 398 VAL MET PHE ASP ARG ALA PHE ASP SER PHE LYS ASN GLU SEQRES 30 A 398 ALA LEU VAL LYS THR THR LYS GLN LYS LEU ALA ALA ALA SEQRES 31 A 398 LEU GLU HIS HIS HIS HIS HIS HIS MODRES 2Y6U CME A 13 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE MODRES 2Y6U CSO A 26 CYS S-HYDROXYCYSTEINE MODRES 2Y6U CSO A 127 CYS S-HYDROXYCYSTEINE MODRES 2Y6U CSO A 205 CYS S-HYDROXYCYSTEINE MODRES 2Y6U CSO A 298 CYS S-HYDROXYCYSTEINE HET CME A 13 10 HET CSO A 26 7 HET CSO A 127 11 HET CSO A 205 7 HET CSO A 298 11 HET GOL A1382 6 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM CSO S-HYDROXYCYSTEINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CME C5 H11 N O3 S2 FORMUL 1 CSO 4(C3 H7 N O3 S) FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *280(H2 O) HELIX 1 1 SER A 64 LEU A 75 5 12 HELIX 2 2 HIS A 97 ASN A 104 1 8 HELIX 3 3 ASN A 113 LEU A 129 1 17 HELIX 4 4 SER A 145 GLN A 158 1 14 HELIX 5 5 PRO A 193 LYS A 203 1 11 HELIX 6 6 ASN A 210 GLY A 221 1 12 HELIX 7 7 HIS A 228 GLU A 239 1 12 HELIX 8 8 GLU A 258 CYS A 265 1 8 HELIX 9 9 ASN A 268 THR A 271 5 4 HELIX 10 10 PHE A 272 VAL A 280 1 9 HELIX 11 11 LYS A 281 VAL A 283 5 3 HELIX 12 12 PRO A 299 LEU A 310 1 12 HELIX 13 13 LEU A 324 ALA A 329 1 6 HELIX 14 14 ALA A 329 SER A 348 1 20 HELIX 15 15 THR A 359 LEU A 379 1 21 SHEET 1 AA 8 PHE A 6 SER A 14 0 SHEET 2 AA 8 GLU A 32 SER A 40 -1 O LEU A 33 N CME A 13 SHEET 3 AA 8 TYR A 84 ILE A 92 -1 O ASP A 87 N SER A 40 SHEET 4 AA 8 THR A 51 LEU A 58 1 O THR A 51 N ALA A 85 SHEET 5 AA 8 ALA A 137 HIS A 144 1 O LEU A 138 N ASN A 54 SHEET 6 AA 8 LEU A 164 ILE A 168 1 O LEU A 164 N VAL A 141 SHEET 7 AA 8 ARG A 286 GLY A 292 1 O ARG A 286 N LEU A 165 SHEET 8 AA 8 TYR A 313 ILE A 318 1 O HIS A 314 N HIS A 289 SHEET 1 AB 3 HIS A 207 PHE A 208 0 SHEET 2 AB 3 VAL A 253 THR A 255 -1 O VAL A 253 N PHE A 208 SHEET 3 AB 3 ARG A 240 THR A 241 -1 O THR A 241 N ARG A 254 LINK C THR A 12 N CME A 13 1555 1555 1.31 LINK C CME A 13 N SER A 14 1555 1555 1.31 LINK C LEU A 25 N CSO A 26 1555 1555 1.34 LINK C CSO A 26 N ALA A 27 1555 1555 1.33 LINK C THR A 126 N CSO A 127 1555 1555 1.32 LINK C CSO A 127 N GLU A 128 1555 1555 1.32 LINK C THR A 204 N CSO A 205 1555 1555 1.35 LINK C CSO A 205 N ASP A 206 1555 1555 1.31 LINK C TRP A 297 N CSO A 298 1555 1555 1.32 LINK C CSO A 298 N PRO A 299 1555 1555 1.38 CISPEP 1 TRP A 17 PRO A 18 0 -3.44 CISPEP 2 HIS A 135 PRO A 136 0 -1.47 CISPEP 3 ALA A 180 GLY A 181 0 23.49 CISPEP 4 LEU A 350 GLN A 351 0 10.68 SITE 1 AC1 10 THR A 204 CSO A 205 TYR A 217 MET A 218 SITE 2 AC1 10 PHE A 224 GLU A 239 ASN A 262 HOH A2163 SITE 3 AC1 10 HOH A2184 HOH A2194 CRYST1 87.156 87.156 125.520 90.00 90.00 120.00 P 32 2 1 6 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 0.011474 0.006624 0.000000 0.00000 SCALE2 0.000000 0.013249 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007967 0.00000