HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 26-FEB-10 3LYD TITLE CRYSTAL STRUCTURE OF PUTATIVE UNCHARACTERIZED PROTEIN FROM JONESIA TITLE 2 DENITRIFICANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: JONESIA DENITRIFICANS; SOURCE 3 ORGANISM_TAXID: 471856; SOURCE 4 STRAIN: ATCC 14870 / DSM 20603 / CIP 55134; SOURCE 5 GENE: JDEN_0139; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PMCSG19 KEYWDS JONESIA DENITRIFICANS, PSI-2, MCSG, GEBA, GENOMIC ENCYCLOPAEDIA OF KEYWDS 2 BACTERIA AND ARCHAEA, STRUCTURAL GENOMICS, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR C.CHANG,L.VOLKART,J.BEARDEN,D.WU,J.EISEN,C.KERFELD,A.JOACHIMIAK, AUTHOR 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 3 08-NOV-17 3LYD 1 REMARK REVDAT 2 13-JUL-11 3LYD 1 VERSN REVDAT 1 09-MAR-10 3LYD 0 JRNL AUTH C.CHANG,L.VOLKART,J.BEARDEN,D.WU,J.EISEN,C.KERFELD, JRNL AUTH 2 A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE UNCHARACTERIZED PROTEIN FROM JRNL TITL 2 JONESIA DENITRIFICANS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 52205 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2660 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3246 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 148 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2493 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 480 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 14.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : 0.27000 REMARK 3 B33 (A**2) : -0.37000 REMARK 3 B12 (A**2) : 0.00000 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): 0.072 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.384 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2805 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3880 ; 1.467 ; 1.926 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 363 ; 5.960 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 135 ;33.936 ;23.185 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 394 ;10.795 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;20.372 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 424 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2291 ; 0.009 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1746 ; 0.825 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2884 ; 1.441 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1059 ; 2.193 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 996 ; 3.350 ; 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 : 10 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 0 A 23 REMARK 3 ORIGIN FOR THE GROUP (A): 17.8422 17.4352 10.1763 REMARK 3 T TENSOR REMARK 3 T11: 0.0376 T22: 0.0211 REMARK 3 T33: 0.0125 T12: 0.0070 REMARK 3 T13: -0.0138 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 1.3502 L22: 0.8639 REMARK 3 L33: 1.4765 L12: 0.6291 REMARK 3 L13: -0.8543 L23: -0.4273 REMARK 3 S TENSOR REMARK 3 S11: 0.0079 S12: 0.0048 S13: 0.0040 REMARK 3 S21: -0.0527 S22: 0.0286 S23: -0.0037 REMARK 3 S31: 0.1512 S32: 0.0077 S33: -0.0365 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 24 A 59 REMARK 3 ORIGIN FOR THE GROUP (A): 28.3039 32.9221 7.6098 REMARK 3 T TENSOR REMARK 3 T11: 0.0156 T22: 0.0122 REMARK 3 T33: 0.0566 T12: 0.0073 REMARK 3 T13: -0.0103 T23: -0.0115 REMARK 3 L TENSOR REMARK 3 L11: 2.1382 L22: 0.8526 REMARK 3 L33: 0.5235 L12: 0.3824 REMARK 3 L13: 0.3931 L23: -0.0134 REMARK 3 S TENSOR REMARK 3 S11: -0.0777 S12: -0.0195 S13: 0.2687 REMARK 3 S21: -0.0330 S22: 0.0314 S23: -0.0798 REMARK 3 S31: -0.0124 S32: 0.0361 S33: 0.0463 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 60 A 77 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7612 41.1777 6.6060 REMARK 3 T TENSOR REMARK 3 T11: 0.0799 T22: 0.1456 REMARK 3 T33: 0.1492 T12: 0.0314 REMARK 3 T13: 0.0076 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 2.3799 L22: 4.8265 REMARK 3 L33: 0.5800 L12: 3.1003 REMARK 3 L13: 0.5391 L23: 0.1150 REMARK 3 S TENSOR REMARK 3 S11: 0.0540 S12: -0.1652 S13: 0.1818 REMARK 3 S21: 0.1406 S22: -0.0601 S23: 0.3015 REMARK 3 S31: -0.0299 S32: -0.1055 S33: 0.0062 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 78 A 136 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4188 38.0991 1.5481 REMARK 3 T TENSOR REMARK 3 T11: 0.0367 T22: 0.0276 REMARK 3 T33: 0.0302 T12: 0.0099 REMARK 3 T13: -0.0239 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 0.2084 L22: 1.5181 REMARK 3 L33: 0.6282 L12: 0.4141 REMARK 3 L13: 0.0025 L23: 0.2330 REMARK 3 S TENSOR REMARK 3 S11: -0.0428 S12: -0.0209 S13: 0.0093 REMARK 3 S21: -0.1078 S22: 0.0252 S23: -0.0331 REMARK 3 S31: -0.0701 S32: -0.0579 S33: 0.0177 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 137 A 157 REMARK 3 ORIGIN FOR THE GROUP (A): 26.0441 34.1096 -3.5916 REMARK 3 T TENSOR REMARK 3 T11: 0.0402 T22: 0.0280 REMARK 3 T33: 0.0282 T12: -0.0091 REMARK 3 T13: 0.0221 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 1.7365 L22: 7.1032 REMARK 3 L33: 1.1012 L12: 1.4077 REMARK 3 L13: -0.1242 L23: 0.4571 REMARK 3 S TENSOR REMARK 3 S11: -0.0239 S12: 0.0658 S13: 0.1343 REMARK 3 S21: -0.4760 S22: 0.0752 S23: -0.2048 REMARK 3 S31: -0.1048 S32: 0.0946 S33: -0.0513 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 : B 0 B 23 REMARK 3 ORIGIN FOR THE GROUP (A): 24.0413 18.2478 11.7813 REMARK 3 T TENSOR REMARK 3 T11: 0.0599 T22: 0.0376 REMARK 3 T33: 0.0397 T12: 0.0098 REMARK 3 T13: -0.0064 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 0.4347 L22: 0.5809 REMARK 3 L33: 0.5746 L12: 0.1870 REMARK 3 L13: 0.1094 L23: -0.1362 REMARK 3 S TENSOR REMARK 3 S11: 0.0018 S12: -0.0020 S13: 0.0289 REMARK 3 S21: -0.0481 S22: 0.0332 S23: -0.0311 REMARK 3 S31: 0.1764 S32: 0.0412 S33: -0.0349 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 : B 24 B 59 REMARK 3 ORIGIN FOR THE GROUP (A): 5.6842 21.6357 21.7100 REMARK 3 T TENSOR REMARK 3 T11: 0.0289 T22: 0.0599 REMARK 3 T33: 0.0232 T12: -0.0122 REMARK 3 T13: -0.0087 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11: 1.1678 L22: 0.1899 REMARK 3 L33: 0.5442 L12: -0.4441 REMARK 3 L13: -0.2116 L23: 0.1056 REMARK 3 S TENSOR REMARK 3 S11: -0.0037 S12: -0.0758 S13: -0.0423 REMARK 3 S21: 0.0043 S22: -0.0027 S23: 0.0305 REMARK 3 S31: 0.0779 S32: -0.0480 S33: 0.0064 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 : B 60 B 77 REMARK 3 ORIGIN FOR THE GROUP (A): 18.0663 36.6592 29.2909 REMARK 3 T TENSOR REMARK 3 T11: 0.1307 T22: 0.0879 REMARK 3 T33: 0.2187 T12: 0.0191 REMARK 3 T13: 0.0784 T23: 0.0098 REMARK 3 L TENSOR REMARK 3 L11: 5.2049 L22: 1.6770 REMARK 3 L33: 2.7121 L12: -2.9503 REMARK 3 L13: -3.1352 L23: 1.7648 REMARK 3 S TENSOR REMARK 3 S11: 0.3528 S12: 0.1246 S13: 0.4512 REMARK 3 S21: -0.1729 S22: -0.0396 S23: -0.2355 REMARK 3 S31: -0.2494 S32: 0.0386 S33: -0.3132 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 78 B 136 REMARK 3 ORIGIN FOR THE GROUP (A): 14.2581 27.3706 30.6589 REMARK 3 T TENSOR REMARK 3 T11: 0.0283 T22: 0.0304 REMARK 3 T33: 0.0126 T12: 0.0079 REMARK 3 T13: -0.0062 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 0.8063 L22: 0.6370 REMARK 3 L33: 0.9704 L12: -0.0712 REMARK 3 L13: -0.3175 L23: 0.2038 REMARK 3 S TENSOR REMARK 3 S11: 0.0353 S12: 0.0381 S13: 0.0618 REMARK 3 S21: 0.0594 S22: -0.0194 S23: 0.0205 REMARK 3 S31: 0.0121 S32: -0.0996 S33: -0.0159 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 137 B 157 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7188 17.1488 31.3239 REMARK 3 T TENSOR REMARK 3 T11: 0.0530 T22: 0.0513 REMARK 3 T33: 0.0068 T12: -0.0230 REMARK 3 T13: -0.0040 T23: 0.0058 REMARK 3 L TENSOR REMARK 3 L11: 2.2033 L22: 1.6135 REMARK 3 L33: 1.8853 L12: -0.9193 REMARK 3 L13: -1.4920 L23: 0.8136 REMARK 3 S TENSOR REMARK 3 S11: -0.0832 S12: -0.1249 S13: -0.0659 REMARK 3 S21: 0.1402 S22: 0.0434 S23: 0.0476 REMARK 3 S31: 0.2305 S32: -0.0782 S33: 0.0398 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3LYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000057884. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97962 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52288 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 47.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.37100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.230 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000, SHELXD, MLPHARE, DM, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MGCL2, 0.1M BIS-TRIS, 25% REMARK 280 PEG3350, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.77550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.74000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.43950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.74000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.77550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.43950 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 SER B -2 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 GLN A 44 CG CD OE1 NE2 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 270 O HOH A 346 1.66 REMARK 500 NH2 ARG A 55 O HOH A 246 1.93 REMARK 500 OE1 GLU A 10 O HOH A 423 2.03 REMARK 500 O HOH A 444 O HOH A 451 2.08 REMARK 500 O HOH A 310 O HOH A 347 2.09 REMARK 500 OE1 GLN B 75 O HOH B 398 2.13 REMARK 500 OH TYR A 141 O HOH A 391 2.13 REMARK 500 O HOH B 261 O HOH B 459 2.14 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 183 O HOH B 389 4455 1.98 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 THR B 74 -5.85 -51.32 REMARK 500 HIS B 104 18.40 59.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 86 OE2 REMARK 620 2 HOH A 269 O 94.6 REMARK 620 3 HOH A 361 O 87.3 95.4 REMARK 620 4 HOH A 349 O 85.7 174.8 89.8 REMARK 620 5 HOH A 180 O 81.8 90.7 167.9 84.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 227 O REMARK 620 2 HOH A 253 O 95.5 REMARK 620 3 HOH A 424 O 170.5 91.6 REMARK 620 4 HOH A 382 O 74.3 93.5 111.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC37305 RELATED DB: TARGETDB DBREF 3LYD A 1 158 UNP C7QYG7 C7QYG7_JONDD 1 158 DBREF 3LYD B 1 158 UNP C7QYG7 C7QYG7_JONDD 1 158 SEQADV 3LYD SER A -2 UNP C7QYG7 EXPRESSION TAG SEQADV 3LYD ASN A -1 UNP C7QYG7 EXPRESSION TAG SEQADV 3LYD ALA A 0 UNP C7QYG7 EXPRESSION TAG SEQADV 3LYD SER B -2 UNP C7QYG7 EXPRESSION TAG SEQADV 3LYD ASN B -1 UNP C7QYG7 EXPRESSION TAG SEQADV 3LYD ALA B 0 UNP C7QYG7 EXPRESSION TAG SEQRES 1 A 161 SER ASN ALA MSE PRO SER ILE ARG TYR PRO SER THR GLU SEQRES 2 A 161 PHE PRO ALA LEU THR GLY PHE THR VAL PRO ILE PRO GLU SEQRES 3 A 161 THR TRP GLN PRO ASP PRO THR MSE GLY THR GLN PHE ALA SEQRES 4 A 161 ALA ARG PRO HIS THR PRO PRO GLN GLY PHE THR PRO ASN SEQRES 5 A 161 ILE ILE GLY THR VAL ARG ARG ALA ALA THR GLY ALA LEU SEQRES 6 A 161 HIS ASN GLN ARG THR GLU LEU ASP GLN ARG ALA THR GLN SEQRES 7 A 161 LEU PRO ASP TYR ALA GLU ARG GLY ARG THR GLU THR THR SEQRES 8 A 161 VAL ASP GLY PHE PRO ALA TYR HIS ILE GLU TYR ALA TYR SEQRES 9 A 161 ARG HIS HIS GLY THR ILE THR ILE ALA GLN MSE ILE THR SEQRES 10 A 161 LEU VAL GLU VAL SER HIS PRO HIS ALA VAL ASP ILE ILE SEQRES 11 A 161 GLN LEU THR ALA THR CYS ALA GLY ASP GLN THR ALA ASP SEQRES 12 A 161 TYR TRP ASP THR PHE ARG LEU MSE HIS ALA ASP LEU THR SEQRES 13 A 161 VAL GLN PRO HIS GLY SEQRES 1 B 161 SER ASN ALA MSE PRO SER ILE ARG TYR PRO SER THR GLU SEQRES 2 B 161 PHE PRO ALA LEU THR GLY PHE THR VAL PRO ILE PRO GLU SEQRES 3 B 161 THR TRP GLN PRO ASP PRO THR MSE GLY THR GLN PHE ALA SEQRES 4 B 161 ALA ARG PRO HIS THR PRO PRO GLN GLY PHE THR PRO ASN SEQRES 5 B 161 ILE ILE GLY THR VAL ARG ARG ALA ALA THR GLY ALA LEU SEQRES 6 B 161 HIS ASN GLN ARG THR GLU LEU ASP GLN ARG ALA THR GLN SEQRES 7 B 161 LEU PRO ASP TYR ALA GLU ARG GLY ARG THR GLU THR THR SEQRES 8 B 161 VAL ASP GLY PHE PRO ALA TYR HIS ILE GLU TYR ALA TYR SEQRES 9 B 161 ARG HIS HIS GLY THR ILE THR ILE ALA GLN MSE ILE THR SEQRES 10 B 161 LEU VAL GLU VAL SER HIS PRO HIS ALA VAL ASP ILE ILE SEQRES 11 B 161 GLN LEU THR ALA THR CYS ALA GLY ASP GLN THR ALA ASP SEQRES 12 B 161 TYR TRP ASP THR PHE ARG LEU MSE HIS ALA ASP LEU THR SEQRES 13 B 161 VAL GLN PRO HIS GLY MODRES 3LYD MSE A 1 MET SELENOMETHIONINE MODRES 3LYD MSE A 31 MET SELENOMETHIONINE MODRES 3LYD MSE A 112 MET SELENOMETHIONINE MODRES 3LYD MSE A 148 MET SELENOMETHIONINE MODRES 3LYD MSE B 1 MET SELENOMETHIONINE MODRES 3LYD MSE B 31 MET SELENOMETHIONINE MODRES 3LYD MSE B 112 MET SELENOMETHIONINE MODRES 3LYD MSE B 148 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 31 8 HET MSE A 112 8 HET MSE A 148 8 HET MSE B 1 8 HET MSE B 31 16 HET MSE B 112 8 HET MSE B 148 8 HET MG A 201 1 HET MG A 202 1 HET EDO A 203 4 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 3 MG 2(MG 2+) FORMUL 5 EDO C2 H6 O2 FORMUL 6 HOH *480(H2 O) HELIX 1 1 GLY A 60 THR A 74 1 15 HELIX 2 2 GLN A 137 ASP A 151 1 15 HELIX 3 3 GLY B 60 THR B 74 1 15 HELIX 4 4 GLN B 137 ASP B 151 1 15 SHEET 1 A 3 SER A 3 TYR A 6 0 SHEET 2 A 3 GLY B 16 PRO B 20 -1 O PHE B 17 N TYR A 6 SHEET 3 A 3 THR B 153 GLN B 155 -1 O GLN B 155 N GLY B 16 SHEET 1 B 3 THR A 153 GLN A 155 0 SHEET 2 B 3 GLY A 16 PRO A 20 -1 N GLY A 16 O GLN A 155 SHEET 3 B 3 SER B 3 TYR B 6 -1 O TYR B 6 N PHE A 17 SHEET 1 C 7 TRP A 25 PRO A 27 0 SHEET 2 C 7 PHE A 35 PRO A 39 -1 O ARG A 38 N GLN A 26 SHEET 3 C 7 ASN A 49 ALA A 57 -1 O GLY A 52 N PHE A 35 SHEET 4 C 7 VAL A 124 ALA A 134 -1 O THR A 130 N ILE A 51 SHEET 5 C 7 ILE A 107 SER A 119 -1 N ALA A 110 O CYS A 133 SHEET 6 C 7 PHE A 92 HIS A 103 -1 N TYR A 101 O ILE A 109 SHEET 7 C 7 ALA A 80 VAL A 89 -1 N ALA A 80 O ALA A 100 SHEET 1 D 7 TRP B 25 PRO B 27 0 SHEET 2 D 7 PHE B 35 PRO B 39 -1 O ARG B 38 N GLN B 26 SHEET 3 D 7 ASN B 49 ALA B 57 -1 O GLY B 52 N PHE B 35 SHEET 4 D 7 VAL B 124 ALA B 134 -1 O THR B 130 N ILE B 51 SHEET 5 D 7 ILE B 107 SER B 119 -1 N ALA B 110 O CYS B 133 SHEET 6 D 7 PHE B 92 HIS B 103 -1 N HIS B 103 O ILE B 107 SHEET 7 D 7 ALA B 80 VAL B 89 -1 N THR B 85 O HIS B 96 LINK C MSE A 1 N PRO A 2 1555 1555 1.36 LINK C THR A 30 N MSE A 31 1555 1555 1.34 LINK C MSE A 31 N GLY A 32 1555 1555 1.33 LINK C GLN A 111 N MSE A 112 1555 1555 1.33 LINK C MSE A 112 N ILE A 113 1555 1555 1.33 LINK C LEU A 147 N MSE A 148 1555 1555 1.33 LINK C MSE A 148 N HIS A 149 1555 1555 1.33 LINK C ALA B 0 N MSE B 1 1555 1555 1.33 LINK C MSE B 1 N PRO B 2 1555 1555 1.36 LINK C THR B 30 N AMSE B 31 1555 1555 1.33 LINK C THR B 30 N BMSE B 31 1555 1555 1.33 LINK C AMSE B 31 N GLY B 32 1555 1555 1.34 LINK C BMSE B 31 N GLY B 32 1555 1555 1.33 LINK C GLN B 111 N MSE B 112 1555 1555 1.32 LINK C MSE B 112 N ILE B 113 1555 1555 1.33 LINK C LEU B 147 N MSE B 148 1555 1555 1.33 LINK C MSE B 148 N HIS B 149 1555 1555 1.33 LINK OE2 GLU A 86 MG MG A 201 1555 1555 2.07 LINK MG MG A 202 O HOH A 227 1555 1555 1.94 LINK MG MG A 201 O HOH A 269 1555 1555 1.99 LINK MG MG A 202 O HOH A 253 1555 1555 2.08 LINK MG MG A 201 O HOH A 361 1555 1555 2.14 LINK MG MG A 202 O HOH A 424 1555 1555 2.14 LINK MG MG A 201 O HOH A 349 1555 1555 2.16 LINK MG MG A 201 O HOH A 180 1555 1555 2.20 LINK MG MG A 202 O HOH A 382 1555 1555 2.95 CISPEP 1 TYR A 6 PRO A 7 0 -0.95 CISPEP 2 TYR B 6 PRO B 7 0 2.14 SITE 1 AC1 6 GLU A 86 HOH A 180 HOH A 269 HOH A 294 SITE 2 AC1 6 HOH A 349 HOH A 361 SITE 1 AC2 7 ASP A 90 HOH A 227 HOH A 253 HOH A 382 SITE 2 AC2 7 HOH A 424 HOH B 263 HOH B 292 SITE 1 AC3 4 THR A 87 THR A 88 HOH A 461 ASP B 78 CRYST1 41.551 70.879 99.480 90.00 90.00 90.00 P 21 21 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 0.024067 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014109 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010052 0.00000 HETATM 1 N MSE A 1 6.043 6.351 29.781 1.00 26.45 N HETATM 2 CA MSE A 1 6.162 7.424 28.760 1.00 25.75 C HETATM 3 C MSE A 1 6.781 6.897 27.451 1.00 25.05 C HETATM 4 O MSE A 1 7.937 6.453 27.456 1.00 26.05 O HETATM 5 CB MSE A 1 6.994 8.597 29.309 1.00 26.28 C HETATM 6 CG MSE A 1 6.504 9.183 30.604 1.00 26.21 C HETATM 7 SE MSE A 1 6.352 11.127 30.622 0.50 35.05 SE HETATM 8 CE MSE A 1 8.200 11.698 30.907 1.00 31.83 C