HEADER HYDROLASE 24-APR-08 3CXM TITLE LEISHMANIA NAIFFI URACIL-DNA GLYCOSYLASE IN COMPLEX WITH 5-BROMOURACIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: URACIL-DNA GLYCOSYLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 129-373; COMPND 5 EC: 3.2.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA NAIFFI; SOURCE 3 ORGANISM_TAXID: 5678; SOURCE 4 GENE: SIMILAR TO LBRM18_V2.0540; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: AVA0421 KEYWDS BASE EXCISION REPAIR, BER, DNA DAMAGE REPAIR, LEISHMANIA, MSGPP, KEYWDS 2 SGPP, GLYCOSYLASE, HYDROLASE, 5-BROMOURACIL, STRUCTURAL GENOMICS, KEYWDS 3 STRUCTURAL GENOMICS OF PATHOGENIC PROTOZOA CONSORTIUM, DNA REPAIR, KEYWDS 4 GLYCOSIDASE, PSI-2, PROTEIN STRUCTURE INITIATIVE EXPDTA X-RAY DIFFRACTION AUTHOR E.T.LARSON,E.A.MERRITT,STRUCTURAL GENOMICS OF PATHOGENIC PROTOZOA AUTHOR 2 CONSORTIUM (SGPP) REVDAT 5 30-AUG-23 3CXM 1 REMARK SEQADV REVDAT 4 25-OCT-17 3CXM 1 REMARK REVDAT 3 13-JUL-11 3CXM 1 VERSN REVDAT 2 24-FEB-09 3CXM 1 VERSN REVDAT 1 06-MAY-08 3CXM 0 JRNL AUTH E.T.LARSON,E.A.MERRITT JRNL TITL STRUCTURES OF LEISHMANIA NAIFFI URACIL-DNA GLYCOSYLASE IN JRNL TITL 2 COMPLEX WITH SEVERAL LIGANDS IDENTIFIED WITH FRAGMENT JRNL TITL 3 COCKTAIL CRYSTALLOGRAPHY. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.4.0066 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 52760 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) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.160 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2693 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2932 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 162 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1933 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 240 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 21.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -0.52000 REMARK 3 B12 (A**2) : 0.17000 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): 0.050 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.053 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.276 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.977 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2108 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1471 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2883 ; 1.623 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3571 ; 0.974 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 267 ; 5.926 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;36.475 ;22.981 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 347 ;11.752 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;20.401 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 301 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2374 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 456 ; 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): 1257 ; 2.033 ; 4.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 495 ; 0.682 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2038 ; 3.259 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 851 ; 4.406 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 832 ; 7.073 ;10.000 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 130 A 166 REMARK 3 ORIGIN FOR THE GROUP (A): -43.3390 26.9530 11.0550 REMARK 3 T TENSOR REMARK 3 T11: 0.1151 T22: 0.1250 REMARK 3 T33: -0.0036 T12: 0.0346 REMARK 3 T13: -0.0132 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 1.5143 L22: 0.5696 REMARK 3 L33: 1.3557 L12: 0.2029 REMARK 3 L13: 0.3555 L23: 0.0690 REMARK 3 S TENSOR REMARK 3 S11: -0.0996 S12: 0.0306 S13: 0.1695 REMARK 3 S21: 0.0288 S22: 0.0953 S23: 0.0117 REMARK 3 S31: -0.2577 S32: -0.0963 S33: 0.0043 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 167 A 174 REMARK 3 ORIGIN FOR THE GROUP (A): -50.3470 18.1220 23.6780 REMARK 3 T TENSOR REMARK 3 T11: 0.0865 T22: 0.2271 REMARK 3 T33: 0.0076 T12: 0.0361 REMARK 3 T13: 0.0203 T23: 0.0353 REMARK 3 L TENSOR REMARK 3 L11: 8.1473 L22: 5.2460 REMARK 3 L33: 13.3327 L12: -0.1775 REMARK 3 L13: 0.3126 L23: -4.2060 REMARK 3 S TENSOR REMARK 3 S11: 0.0222 S12: -0.3076 S13: -0.1082 REMARK 3 S21: 0.1941 S22: 0.2807 S23: 0.2780 REMARK 3 S31: -0.1079 S32: -0.9143 S33: -0.3029 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 175 A 195 REMARK 3 ORIGIN FOR THE GROUP (A): -36.9570 25.4170 22.0950 REMARK 3 T TENSOR REMARK 3 T11: 0.1200 T22: 0.0812 REMARK 3 T33: -0.0117 T12: 0.0261 REMARK 3 T13: -0.0029 T23: -0.0169 REMARK 3 L TENSOR REMARK 3 L11: 1.8434 L22: 1.4602 REMARK 3 L33: 3.7375 L12: 1.0354 REMARK 3 L13: -1.0954 L23: -1.6172 REMARK 3 S TENSOR REMARK 3 S11: -0.0789 S12: 0.0595 S13: 0.0125 REMARK 3 S21: 0.1047 S22: 0.1255 S23: -0.0131 REMARK 3 S31: -0.1957 S32: -0.2218 S33: -0.0466 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 196 A 226 REMARK 3 ORIGIN FOR THE GROUP (A): -27.8570 22.4210 24.7330 REMARK 3 T TENSOR REMARK 3 T11: 0.1558 T22: 0.1643 REMARK 3 T33: 0.0489 T12: -0.0115 REMARK 3 T13: -0.0148 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 1.3327 L22: 1.3649 REMARK 3 L33: 1.7578 L12: 1.1562 REMARK 3 L13: -1.1988 L23: -0.7688 REMARK 3 S TENSOR REMARK 3 S11: 0.0423 S12: -0.1542 S13: -0.0706 REMARK 3 S21: 0.1346 S22: -0.0866 S23: -0.1063 REMARK 3 S31: -0.1722 S32: 0.1940 S33: 0.0442 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 227 A 250 REMARK 3 ORIGIN FOR THE GROUP (A): -13.5040 20.8630 27.7200 REMARK 3 T TENSOR REMARK 3 T11: 0.0626 T22: 0.1630 REMARK 3 T33: 0.0631 T12: -0.0476 REMARK 3 T13: -0.0151 T23: 0.1052 REMARK 3 L TENSOR REMARK 3 L11: 3.4428 L22: 1.3061 REMARK 3 L33: 1.0744 L12: 0.3415 REMARK 3 L13: -0.4487 L23: 0.5159 REMARK 3 S TENSOR REMARK 3 S11: -0.0008 S12: -0.6369 S13: -0.5671 REMARK 3 S21: 0.1040 S22: -0.1107 S23: -0.2618 REMARK 3 S31: 0.0859 S32: 0.2552 S33: 0.1115 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 251 A 302 REMARK 3 ORIGIN FOR THE GROUP (A): -31.7010 20.8010 15.8320 REMARK 3 T TENSOR REMARK 3 T11: 0.1460 T22: 0.1392 REMARK 3 T33: 0.0358 T12: 0.0032 REMARK 3 T13: 0.0002 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 0.7091 L22: 0.9279 REMARK 3 L33: 0.9895 L12: 0.5547 REMARK 3 L13: -0.0315 L23: -0.0061 REMARK 3 S TENSOR REMARK 3 S11: -0.0447 S12: 0.0810 S13: -0.0551 REMARK 3 S21: -0.0520 S22: 0.0329 S23: -0.0813 REMARK 3 S31: -0.0915 S32: 0.0728 S33: 0.0118 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 303 A 338 REMARK 3 ORIGIN FOR THE GROUP (A): -21.5630 13.9790 11.1400 REMARK 3 T TENSOR REMARK 3 T11: 0.0937 T22: 0.0453 REMARK 3 T33: 0.2440 T12: -0.0214 REMARK 3 T13: 0.0764 T23: -0.0964 REMARK 3 L TENSOR REMARK 3 L11: 3.9182 L22: 0.9275 REMARK 3 L33: 3.2095 L12: -0.3076 REMARK 3 L13: 0.5862 L23: -0.8933 REMARK 3 S TENSOR REMARK 3 S11: -0.0362 S12: 0.3374 S13: -0.9702 REMARK 3 S21: -0.1329 S22: 0.0088 S23: -0.0540 REMARK 3 S31: 0.1250 S32: 0.1958 S33: 0.0273 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 339 A 371 REMARK 3 ORIGIN FOR THE GROUP (A): -12.8320 24.2190 16.4230 REMARK 3 T TENSOR REMARK 3 T11: 0.1164 T22: 0.1568 REMARK 3 T33: 0.1142 T12: -0.0399 REMARK 3 T13: 0.0186 T23: 0.0168 REMARK 3 L TENSOR REMARK 3 L11: 2.1069 L22: 1.5813 REMARK 3 L33: 1.5327 L12: 0.6033 REMARK 3 L13: -0.3815 L23: -0.1553 REMARK 3 S TENSOR REMARK 3 S11: -0.0625 S12: -0.0252 S13: -0.3009 REMARK 3 S21: -0.1262 S22: -0.1282 S23: -0.2161 REMARK 3 S31: 0.0249 S32: 0.0600 S33: 0.1907 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: 1. ATOM RECORD CONTAINS RESIDUAL B REMARK 3 FACTORS ONLY. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 3CXM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91724 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52821 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 97.2 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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 1EUI REMARK 200 REMARK 200 REMARK: REMARK 200 1. THE BLU-ICE SOFTWARE PACKAGE WAS USED FOR DATA COLLECTION. THE REMARK 200 REFERENCE IS: MCPHILLIPS T.M., MCPHILLIPS S.E., CHIU H.J., COHEN REMARK 200 A.E., DEACON A.M., ELLIS P.J., GARMAN E., GONZALEZ A., SAUTER N.K., REMARK 200 PHIZACKERLEY R.P., SOLTIS S.M., KUHN P., BLU-ICE AND THE REMARK 200 DISTRIBUTED CONTROL SYSTEM: SOFTWARE FOR DATA ACQUISITION AND REMARK 200 INSTRUMENT CONTROL AT MACROMOLECULAR CRYSTALLOGRAPHY BEAMLINES. REMARK 200 J.SYNCHROTRON RADIAT. 2002 NOV 1, 9(PT 6):401-6. EPUB 2002 NOV 1. REMARK 200 PMID: 12409628. REMARK 200 2. THE TLS MOTION DETERMINATION SERVER (HTTP:// REMARK 200 SKULD.BMSC.WASHINGTON.EDU/~TLSMD/) WAS USED FOR SELECTION OF THE REMARK 200 TLS GROUPS USED IN REFINEMENT. THE REFERENCE IS: PAINTER J. AND REMARK 200 MERRITT E.A., TLSMD WEB SERVER FOR THE GENERATION OF MULTI-GROUP REMARK 200 TLS MODELS. J.APPL.CRYST. 2006 FEB, 39(PT 1):109-111. EPUB 2006 REMARK 200 JAN 12. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3 M POTASSIUM PHOSPHATE DIBASIC, 0.1 REMARK 280 M SODIUM ACETATE PH 4.5, 5 MM DTT, PH 8.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K 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 35.23433 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 70.46867 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 52.85150 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 88.08583 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 17.61717 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 MET A -22 REMARK 465 ALA A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 MET A -14 REMARK 465 GLY A -13 REMARK 465 THR A -12 REMARK 465 LEU A -11 REMARK 465 GLU A -10 REMARK 465 ALA A -9 REMARK 465 GLN A -8 REMARK 465 THR A -7 REMARK 465 GLN A -6 REMARK 465 GLY A -5 REMARK 465 PRO A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 MET A -1 REMARK 465 MET A 0 REMARK 465 SER A 129 REMARK 465 LEU A 372 REMARK 465 HIS A 373 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 TRP A 135 -26.43 -147.20 REMARK 500 LYS A 199 -21.54 -144.57 REMARK 500 GLN A 205 -85.17 -95.03 REMARK 500 GLN A 213 -65.79 -126.01 REMARK 500 HIS A 215 29.78 -145.43 REMARK 500 PHE A 219 -14.69 68.35 REMARK 500 MET A 263 78.13 -104.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URB A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: LNAI002302AAC RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 1. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT REMARK 999 THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE REMARK 999 TIME OF DEPOSITION. REMARK 999 2. THE GENE USED IN THIS STUDY WAS CLONED FROM L. NAIFFI REMARK 999 GENOMIC DNA USING PRIMERS DESIGNED FOR RESIDUES 129 TO 373 REMARK 999 OF THE AVAILABLE L. BRAZILIENSIS SEQUENCE (UNIPROT ID REMARK 999 A4H9F6_LEIBR). ACCORDINGLY, THE NUMBERING OF THE L. NAIFFI REMARK 999 PROTEIN USED HERE FOLLOWS THAT OF THE L. BRAZILIENSIS REMARK 999 HOMOLOG DESPITE THE LACK OF KNOWLEDGE OF THE FULL-LENGTH REMARK 999 L. NAIFFI SEQUENCE. DBREF 3CXM A 129 373 PDB 3CXM 3CXM 129 373 SEQADV 3CXM MET A -22 PDB 3CXM EXPRESSION TAG SEQADV 3CXM ALA A -21 PDB 3CXM EXPRESSION TAG SEQADV 3CXM HIS A -20 PDB 3CXM EXPRESSION TAG SEQADV 3CXM HIS A -19 PDB 3CXM EXPRESSION TAG SEQADV 3CXM HIS A -18 PDB 3CXM EXPRESSION TAG SEQADV 3CXM HIS A -17 PDB 3CXM EXPRESSION TAG SEQADV 3CXM HIS A -16 PDB 3CXM EXPRESSION TAG SEQADV 3CXM HIS A -15 PDB 3CXM EXPRESSION TAG SEQADV 3CXM MET A -14 PDB 3CXM EXPRESSION TAG SEQADV 3CXM GLY A -13 PDB 3CXM EXPRESSION TAG SEQADV 3CXM THR A -12 PDB 3CXM EXPRESSION TAG SEQADV 3CXM LEU A -11 PDB 3CXM EXPRESSION TAG SEQADV 3CXM GLU A -10 PDB 3CXM EXPRESSION TAG SEQADV 3CXM ALA A -9 PDB 3CXM EXPRESSION TAG SEQADV 3CXM GLN A -8 PDB 3CXM EXPRESSION TAG SEQADV 3CXM THR A -7 PDB 3CXM EXPRESSION TAG SEQADV 3CXM GLN A -6 PDB 3CXM EXPRESSION TAG SEQADV 3CXM GLY A -5 PDB 3CXM EXPRESSION TAG SEQADV 3CXM PRO A -4 PDB 3CXM EXPRESSION TAG SEQADV 3CXM GLY A -3 PDB 3CXM EXPRESSION TAG SEQADV 3CXM SER A -2 PDB 3CXM EXPRESSION TAG SEQADV 3CXM MET A -1 PDB 3CXM EXPRESSION TAG SEQADV 3CXM MET A 0 PDB 3CXM EXPRESSION TAG SEQRES 1 A 268 MET ALA HIS HIS HIS HIS HIS HIS MET GLY THR LEU GLU SEQRES 2 A 268 ALA GLN THR GLN GLY PRO GLY SER MET MET SER VAL SER SEQRES 3 A 268 SER SER ARG TRP LEU ALA GLY LEU ILE THR ASN PRO GLU SEQRES 4 A 268 TRP ARG ASP PHE LEU ALA PRO ILE THR ALA ASP SER TRP SEQRES 5 A 268 ARG LYS GLY ALA PHE ILE ARG ILE GLU ARG PHE LEU ASP SEQRES 6 A 268 GLU GLU LYS GLU LYS GLY ARG VAL ILE LEU PRO PRO ALA SEQRES 7 A 268 ALA ASP ILE PHE ASN ALA PHE ASN SER CYS PRO PHE ARG SEQRES 8 A 268 GLY LEU LYS VAL VAL LEU LEU GLY GLN ASP PRO TYR HIS SEQRES 9 A 268 ASP LEU HIS GLN ALA HIS GLY LEU CYS PHE SER VAL LEU SEQRES 10 A 268 PRO GLU VAL PRO LEU PRO PRO SER LEU ARG ASN ILE TYR SEQRES 11 A 268 LYS GLU LEU THR THR ASP ILE ALA GLY PHE GLN ALA PRO SEQRES 12 A 268 LYS HIS GLY TYR LEU GLN SER TRP SER GLU GLN GLY MET SEQRES 13 A 268 LEU MET LEU ASN ALA THR LEU THR VAL GLU ALA HIS LYS SEQRES 14 A 268 ALA ASN SER HIS SER LYS THR SER GLY TRP ALA ALA PHE SEQRES 15 A 268 THR ASP ALA VAL ILE GLN HIS LEU SER GLN HIS HIS PRO SEQRES 16 A 268 ASN ARG LEU VAL PHE LEU LEU TRP GLY GLY TYR ALA GLN SEQRES 17 A 268 GLN LYS LYS ARG LEU ILE ASP ALA ASN ARG HIS VAL VAL SEQRES 18 A 268 LEU GLU ASN VAL HIS PRO SER PRO LEU SER ALA ASN ARG SEQRES 19 A 268 GLY TRP PHE GLY CYS ARG CYS PHE SER ALA CYS ASN GLU SEQRES 20 A 268 ALA LEU GLN ARG MET SER HIS LEU PRO MET HIS TRP GLN SEQRES 21 A 268 LEU PRO LEU ASN ALA PRO LEU HIS HET BR A 403 1 HET URB A 401 9 HET URA A 402 8 HET GOL A 404 6 HETNAM BR BROMIDE ION HETNAM URB 5-BROMOPYRIMIDINE-2,4(1H,3H)-DIONE HETNAM URA URACIL HETNAM GOL GLYCEROL HETSYN URB 5-BROMOURACIL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 BR BR 1- FORMUL 3 URB C4 H3 BR N2 O2 FORMUL 4 URA C4 H4 N2 O2 FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *240(H2 O) HELIX 1 1 LEU A 136 ILE A 140 5 5 HELIX 2 2 ASN A 142 ALA A 154 1 13 HELIX 3 3 GLY A 160 LYS A 175 1 16 HELIX 4 4 PRO A 182 ILE A 186 5 5 HELIX 5 5 PHE A 187 SER A 192 1 6 HELIX 6 6 PRO A 228 ILE A 242 1 15 HELIX 7 7 LEU A 253 GLU A 258 1 6 HELIX 8 8 GLY A 283 HIS A 299 1 17 HELIX 9 9 GLY A 309 GLN A 314 1 6 HELIX 10 10 LYS A 315 ILE A 319 5 5 HELIX 11 11 SER A 333 ASN A 338 1 6 HELIX 12 12 ARG A 345 MET A 357 1 13 SHEET 1 A 2 ILE A 179 LEU A 180 0 SHEET 2 A 2 VAL A 270 GLU A 271 -1 O VAL A 270 N LEU A 180 SHEET 1 B 4 MET A 261 ASN A 265 0 SHEET 2 B 4 VAL A 200 GLY A 204 1 N VAL A 200 O LEU A 262 SHEET 3 B 4 VAL A 304 TRP A 308 1 O LEU A 306 N VAL A 201 SHEET 4 B 4 VAL A 325 ASN A 329 1 O VAL A 325 N PHE A 305 CISPEP 1 LEU A 180 PRO A 181 0 -12.39 SITE 1 AC1 2 PRO A 229 SER A 230 SITE 1 AC2 10 GLY A 204 GLN A 205 ASP A 206 TYR A 208 SITE 2 AC2 10 CYS A 218 PHE A 219 ASN A 265 HIS A 331 SITE 3 AC2 10 HOH A 600 HOH A 658 SITE 1 AC3 9 GLY A 204 GLN A 205 ASP A 206 TYR A 208 SITE 2 AC3 9 CYS A 218 PHE A 219 ASN A 265 HOH A 600 SITE 3 AC3 9 HOH A 658 SITE 1 AC4 4 HIS A 273 PRO A 361 HIS A 363 HOH A 513 CRYST1 75.320 75.320 105.703 90.00 90.00 120.00 P 61 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 0.013277 0.007665 0.000000 0.00000 SCALE2 0.000000 0.015331 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009460 0.00000