HEADER ISOMERASE 11-AUG-10 3ODP TITLE CRYSTAL STRUCTURE OF A PUTATIVE TAGATOSE-6-PHOSPHATE KETOSE/ALDOSE TITLE 2 ISOMERASE (NT01CX_0292) FROM CLOSTRIDIUM NOVYI NT AT 2.35 A TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE TAGATOSE-6-PHOSPHATE KETOSE/ALDOSE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PREDICTED PHOSPHOSUGAR ISOMERASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM NOVYI; SOURCE 3 ORGANISM_TAXID: 386415; SOURCE 4 STRAIN: NT; SOURCE 5 GENE: NT01CX_0292; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-BIOLOGY, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 06-DEC-23 3ODP 1 REMARK REVDAT 4 20-SEP-23 3ODP 1 REMARK REVDAT 3 01-FEB-23 3ODP 1 REMARK SEQADV LINK REVDAT 2 20-JUL-11 3ODP 1 KEYWDS REVDAT 1 01-DEC-10 3ODP 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE TAGATOSE-6-PHOSPHATE JRNL TITL 2 KETOSE/ALDOSE ISOMERASE (NT01CX_0292) FROM CLOSTRIDIUM NOVYI JRNL TITL 3 NT AT 2.35 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 23616 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1215 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1639 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.3390 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3022 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 23 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 89.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : -0.70000 REMARK 3 B12 (A**2) : 0.23000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.234 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.284 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.475 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3117 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2055 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4220 ; 1.175 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5065 ; 0.859 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 397 ; 5.867 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;39.604 ;25.522 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 540 ;16.179 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;17.223 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 487 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3456 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 592 ; 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): 1956 ; 0.329 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 798 ; 0.074 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3147 ; 0.608 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1161 ; 1.121 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1070 ; 1.745 ; 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 : 7 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 20 REMARK 3 ORIGIN FOR THE GROUP (A): 17.1701 79.4901 43.6400 REMARK 3 T TENSOR REMARK 3 T11: 1.3901 T22: 0.6328 REMARK 3 T33: 1.6649 T12: -0.0047 REMARK 3 T13: -1.0042 T23: 0.3250 REMARK 3 L TENSOR REMARK 3 L11: 1.8521 L22: 5.9402 REMARK 3 L33: 2.3670 L12: -0.2455 REMARK 3 L13: 9.1383 L23: -3.6110 REMARK 3 S TENSOR REMARK 3 S11: -0.6285 S12: -0.2233 S13: 1.4126 REMARK 3 S21: -0.0166 S22: -0.0861 S23: -1.3267 REMARK 3 S31: -1.1164 S32: 0.2332 S33: 0.7146 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 21 A 49 REMARK 3 ORIGIN FOR THE GROUP (A): 5.5812 55.0885 46.5087 REMARK 3 T TENSOR REMARK 3 T11: 0.2431 T22: 0.9213 REMARK 3 T33: 0.8319 T12: 0.2925 REMARK 3 T13: -0.3559 T23: -0.5219 REMARK 3 L TENSOR REMARK 3 L11: 6.4267 L22: 12.6246 REMARK 3 L33: 4.3611 L12: 1.8170 REMARK 3 L13: 0.4025 L23: -0.1882 REMARK 3 S TENSOR REMARK 3 S11: -0.4482 S12: 1.3733 S13: -0.3267 REMARK 3 S21: -0.3310 S22: -1.0071 S23: 0.8845 REMARK 3 S31: -0.7444 S32: -1.1272 S33: 1.4553 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 50 A 89 REMARK 3 ORIGIN FOR THE GROUP (A): 16.0026 42.2611 54.5258 REMARK 3 T TENSOR REMARK 3 T11: 0.2233 T22: 0.3842 REMARK 3 T33: 0.9233 T12: 0.0611 REMARK 3 T13: 0.0806 T23: -0.3134 REMARK 3 L TENSOR REMARK 3 L11: 5.5202 L22: 2.8855 REMARK 3 L33: 4.6562 L12: -2.7955 REMARK 3 L13: 1.0589 L23: 0.8425 REMARK 3 S TENSOR REMARK 3 S11: -0.5659 S12: 0.6232 S13: -0.7654 REMARK 3 S21: 0.3660 S22: -0.5676 S23: 0.6268 REMARK 3 S31: -0.0389 S32: -0.3037 S33: 1.1335 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 90 A 140 REMARK 3 ORIGIN FOR THE GROUP (A): 24.4090 40.1294 44.9567 REMARK 3 T TENSOR REMARK 3 T11: 0.1709 T22: 0.7782 REMARK 3 T33: 0.7039 T12: 0.0914 REMARK 3 T13: 0.0297 T23: -0.2039 REMARK 3 L TENSOR REMARK 3 L11: 4.8434 L22: 1.8068 REMARK 3 L33: 4.2078 L12: -1.4109 REMARK 3 L13: 0.0814 L23: -0.2848 REMARK 3 S TENSOR REMARK 3 S11: -0.2941 S12: 1.3610 S13: -0.6712 REMARK 3 S21: -0.1691 S22: -0.8133 S23: 0.3393 REMARK 3 S31: 0.2085 S32: 0.3324 S33: 1.1074 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 141 A 193 REMARK 3 ORIGIN FOR THE GROUP (A): 14.3805 51.8133 42.0900 REMARK 3 T TENSOR REMARK 3 T11: 0.2685 T22: 0.8268 REMARK 3 T33: 0.6733 T12: 0.1691 REMARK 3 T13: -0.3195 T23: -0.2923 REMARK 3 L TENSOR REMARK 3 L11: 4.9171 L22: 3.8803 REMARK 3 L33: 2.3634 L12: -2.2080 REMARK 3 L13: 0.6305 L23: -1.0469 REMARK 3 S TENSOR REMARK 3 S11: -0.2093 S12: 1.7263 S13: -0.0835 REMARK 3 S21: -0.5472 S22: -0.9262 S23: 0.4554 REMARK 3 S31: -0.4730 S32: -0.3152 S33: 1.1355 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 194 A 356 REMARK 3 ORIGIN FOR THE GROUP (A): 18.9041 64.7749 64.7905 REMARK 3 T TENSOR REMARK 3 T11: 0.8580 T22: 0.1796 REMARK 3 T33: 0.8522 T12: 0.2221 REMARK 3 T13: -0.7053 T23: -0.1518 REMARK 3 L TENSOR REMARK 3 L11: 5.1344 L22: 3.1868 REMARK 3 L33: 4.2427 L12: -2.1825 REMARK 3 L13: 0.7397 L23: -0.6624 REMARK 3 S TENSOR REMARK 3 S11: -1.2109 S12: -0.2121 S13: 1.2096 REMARK 3 S21: 0.9319 S22: -0.0518 S23: -0.4096 REMARK 3 S31: -1.3905 S32: -0.2140 S33: 1.2627 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 391 REMARK 3 ORIGIN FOR THE GROUP (A): 30.0236 64.1802 44.1269 REMARK 3 T TENSOR REMARK 3 T11: 0.6396 T22: 0.8357 REMARK 3 T33: 1.1280 T12: -0.1969 REMARK 3 T13: -0.5188 T23: 0.6767 REMARK 3 L TENSOR REMARK 3 L11: 6.5893 L22: 5.4878 REMARK 3 L33: 5.6410 L12: -4.8455 REMARK 3 L13: -0.3708 L23: 2.3418 REMARK 3 S TENSOR REMARK 3 S11: -0.4875 S12: 1.5477 S13: 1.5807 REMARK 3 S21: -0.2355 S22: -0.5601 S23: -0.9358 REMARK 3 S31: -1.1864 S32: 0.8459 S33: 1.0476 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. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND REMARK 3 RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND REMARK 3 RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS REMARK 3 ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 6. PEG-200 (PG4) FRAGMENTS FROM THE REMARK 3 CRYSTALLIZATION SOLUTION ARE MODELED. 7. ASSIGNMENT OF PHOSPHATE REMARK 3 ION (PO4) WAS BASED ON ELECTRON DENSITY AND CONSERVATION OF THE REMARK 3 BINDING SITE IN 3I0Z AND OTHER HOMOLOG STRUCTURES. 8. THE TLS REMARK 3 GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER. 9. THE REMARK 3 RAMACHANDRAN OUTLIER RESIDUES 16 AND 308 ARE IN POOR DENSITY REMARK 3 REGION. REMARK 4 REMARK 4 3ODP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060985. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97871 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(111) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.15, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23656 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 77.391 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08400 REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.01000 REMARK 200 R SYM FOR SHELL (I) : 1.04200 REMARK 200 FOR SHELL : 0.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD + MOLECULAR REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: SHELX, SHELXD, AUTOSHARP, MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3I0Z REMARK 200 REMARK 200 REMARK: AN INITIAL SUBSTRUCTURE SOLUTION WAS FOUND USING SHELXD REMARK 200 AND SAD PHASES WERE REFINED WITH AUTOSHARP. AN ITERATIVE RESOLVE REMARK 200 RUN WAS ABLE TO TRACE ~70% OF THE STRUCTURE. HOWEVER, THE REMARK 200 CONNECTIVITY OF THE RESULTING MODEL WAS POOR. MOLECULAR REMARK 200 REPLACEMENT WITH MOLREP USING 3I0Z AS THE SEARCH MODEL PROVIDED REMARK 200 A MORE COMPLETE STARTING MODEL FOR SUBSEQUENT MODEL BUILDING AND REMARK 200 REFINEMENT. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50.00% PEG-200, 0.1M TRIS PH 7.0, REMARK 280 NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 80.00800 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 40.00400 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 40.00400 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 80.00800 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 300 REMARK: CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER REMARK 300 AS THE SIGNIFICANT OLIGOMERIZATION STATE. 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 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 120.01200 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 ARG A 392 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 TYR A 11 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 14 CG CD OE1 OE2 REMARK 470 LYS A 16 CD CE NZ REMARK 470 LYS A 22 CG CD CE NZ REMARK 470 LYS A 29 CG CD CE NZ REMARK 470 ARG A 42 CZ NH1 NH2 REMARK 470 LYS A 54 CD CE NZ REMARK 470 LYS A 132 CD CE NZ REMARK 470 GLU A 167 CG CD OE1 OE2 REMARK 470 GLU A 219 CG CD OE1 OE2 REMARK 470 LYS A 222 CG CD CE NZ REMARK 470 LYS A 223 CG CD CE NZ REMARK 470 LYS A 228 CE NZ REMARK 470 ASN A 310 CG OD1 ND2 REMARK 470 LYS A 312 CG CD CE NZ REMARK 470 LYS A 322 CG CD CE NZ REMARK 470 LYS A 336 CG CD CE NZ REMARK 470 LYS A 384 CG CD CE NZ 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 15 47.14 -81.82 REMARK 500 ARG A 15 48.48 -82.95 REMARK 500 LYS A 16 66.63 24.66 REMARK 500 ALA A 115 137.73 -173.15 REMARK 500 ARG A 116 -70.64 -69.47 REMARK 500 THR A 177 -86.76 -118.49 REMARK 500 ALA A 238 -115.20 57.83 REMARK 500 HIS A 271 42.87 -78.91 REMARK 500 LYS A 274 -31.37 -39.21 REMARK 500 ASN A 308 -172.05 50.64 REMARK 500 ASN A 310 -10.77 61.23 REMARK 500 HIS A 311 162.29 -48.67 REMARK 500 CYS A 374 72.34 -119.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PG4 A 400 REMARK 610 PG4 A 401 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 391683 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3ODP A 1 392 UNP A0Q2D8 A0Q2D8_CLONN 1 392 SEQADV 3ODP GLY A 0 UNP A0Q2D8 EXPRESSION TAG SEQRES 1 A 393 GLY MSE LYS ASN LEU LEU GLY TYR SER GLU ASP TYR LEU SEQRES 2 A 393 LYS GLU ARG LYS GLY TYR ILE THR ALA LYS GLU ILE CYS SEQRES 3 A 393 ASN GLN PRO LYS LEU TRP ARG GLU THR TYR GLU ILE ILE SEQRES 4 A 393 LEU SER GLN ARG GLU LYS LEU LYS SER PHE LEU ASP ASN SEQRES 5 A 393 PHE ALA LYS LYS PRO ASN ALA LYS ILE VAL ILE THR GLY SEQRES 6 A 393 ALA GLY SER SER ALA PHE VAL GLY ASN SER VAL VAL SER SEQRES 7 A 393 TYR LEU ASN ALA LYS GLU ASN ILE LYS ILE GLU ALA ILE SEQRES 8 A 393 ALA THR THR ASP ILE VAL SER HIS PRO PHE TYR TYR LEU SEQRES 9 A 393 LYS LYS ASP GLU PRO THR LEU LEU ILE SER CYS ALA ARG SEQRES 10 A 393 SER GLY ASN SER PRO GLU SER THR ALA ALA VAL THR LEU SEQRES 11 A 393 ALA GLU LYS ILE VAL ASP ASP ILE SER HIS LEU ILE ILE SEQRES 12 A 393 THR CYS ASN SER GLU GLY LYS LEU ALA LEU HIS ALA LYS SEQRES 13 A 393 ARG ASN TYR ASN SER PHE LEU LEU LEU MSE PRO GLU GLU SEQRES 14 A 393 SER ASN ASP LYS GLY PHE ALA MSE THR GLY SER PHE SER SEQRES 15 A 393 THR MSE LEU LEU SER CYS LEU LEU ILE PHE ASN LEU ASP SEQRES 16 A 393 LYS LEU GLU SER ILE GLY LYS GLN ILE GLU SER ILE SER SEQRES 17 A 393 MSE GLN GLY GLU LYS VAL LEU VAL ASN ASN VAL GLU LEU SEQRES 18 A 393 MSE LYS LYS ILE VAL GLY GLU LYS PHE LYS ARG THR VAL SEQRES 19 A 393 TYR LEU GLY ALA ALA ASN ALA PHE GLY LEU ALA LYS GLU SEQRES 20 A 393 SER ALA LEU LYS VAL LEU GLU LEU THR ALA GLY LYS ILE SEQRES 21 A 393 ALA THR LEU TYR ASP THR PRO LEU GLY PHE ARG HIS GLY SEQRES 22 A 393 PRO LYS SER ILE ILE ASP ASP GLU THR LEU ILE VAL ILE SEQRES 23 A 393 PHE PHE SER ASN ASP THR TYR ALA ARG GLU TYR GLU TYR SEQRES 24 A 393 ASP LEU LEU LYS GLU VAL TYR SER GLN ASN GLY ASN HIS SEQRES 25 A 393 LYS VAL LEU ALA ILE SER GLU TYR GLU ASP LYS LEU ILE SEQRES 26 A 393 GLU ASP ASN SER ASP TYR PHE ILE ALA ILE ASN LYS GLU SEQRES 27 A 393 GLU GLN GLU TYR GLU ASP ASP SER PHE LEU SER LEU ASP SEQRES 28 A 393 TYR LEU LEU ASN ALA GLN MSE TYR ALA PHE ILE ASN SER SEQRES 29 A 393 MSE GLU LEU GLY ILE GLY PRO ASP ASN PRO CYS PRO THR SEQRES 30 A 393 GLY GLU VAL ASN ARG VAL VAL LYS GLY VAL ILE ILE HIS SEQRES 31 A 393 ASP TYR ARG MODRES 3ODP MSE A 1 MET SELENOMETHIONINE MODRES 3ODP MSE A 165 MET SELENOMETHIONINE MODRES 3ODP MSE A 176 MET SELENOMETHIONINE MODRES 3ODP MSE A 183 MET SELENOMETHIONINE MODRES 3ODP MSE A 208 MET SELENOMETHIONINE MODRES 3ODP MSE A 221 MET SELENOMETHIONINE MODRES 3ODP MSE A 357 MET SELENOMETHIONINE MODRES 3ODP MSE A 364 MET SELENOMETHIONINE HET MSE A 1 13 HET MSE A 165 8 HET MSE A 176 8 HET MSE A 183 8 HET MSE A 208 8 HET MSE A 221 8 HET MSE A 357 8 HET MSE A 364 8 HET PG4 A 400 10 HET PG4 A 401 10 HET PO4 A 402 5 HETNAM MSE SELENOMETHIONINE HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM PO4 PHOSPHATE ION FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 PG4 2(C8 H18 O5) FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *23(H2 O) HELIX 1 1 GLU A 9 ARG A 15 1 7 HELIX 2 2 GLY A 17 ASN A 26 1 10 HELIX 3 3 ASN A 26 LYS A 54 1 29 HELIX 4 4 GLY A 66 SER A 74 1 9 HELIX 5 5 VAL A 75 GLU A 83 1 9 HELIX 6 6 ALA A 91 VAL A 96 1 6 HELIX 7 7 HIS A 98 TYR A 102 5 5 HELIX 8 8 SER A 120 VAL A 134 1 15 HELIX 9 9 GLY A 148 HIS A 153 1 6 HELIX 10 10 ALA A 154 ARG A 156 5 3 HELIX 11 11 PRO A 166 ASN A 170 5 5 HELIX 12 12 THR A 177 ILE A 190 1 14 HELIX 13 13 LYS A 195 ASN A 217 1 23 HELIX 14 14 ASN A 217 GLY A 226 1 10 HELIX 15 15 ALA A 238 THR A 255 1 18 HELIX 16 16 THR A 265 ARG A 270 1 6 HELIX 17 17 HIS A 271 ILE A 277 5 7 HELIX 18 18 ASP A 290 GLN A 307 1 18 HELIX 19 19 ASP A 321 ASP A 326 1 6 HELIX 20 20 ASP A 343 PHE A 346 5 4 HELIX 21 21 LEU A 347 GLY A 367 1 21 SHEET 1 A 2 ASN A 3 LEU A 4 0 SHEET 2 A 2 TYR A 7 SER A 8 -1 O TYR A 7 N LEU A 4 SHEET 1 B 5 LYS A 86 ALA A 89 0 SHEET 2 B 5 LYS A 59 THR A 63 1 N ILE A 60 O LYS A 86 SHEET 3 B 5 THR A 109 ALA A 115 1 O ILE A 112 N THR A 63 SHEET 4 B 5 ILE A 137 THR A 143 1 O ILE A 142 N SER A 113 SHEET 5 B 5 SER A 160 LEU A 164 1 O LEU A 163 N ILE A 141 SHEET 1 C 5 ALA A 260 ASP A 264 0 SHEET 2 C 5 ARG A 231 LEU A 235 1 N THR A 232 O ALA A 260 SHEET 3 C 5 THR A 281 PHE A 286 1 O VAL A 284 N VAL A 233 SHEET 4 C 5 LYS A 312 TYR A 319 1 O ILE A 316 N ILE A 285 SHEET 5 C 5 TYR A 330 ASN A 335 1 O TYR A 330 N ALA A 315 LINK C GLY A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N LYS A 2 1555 1555 1.33 LINK C LEU A 164 N MSE A 165 1555 1555 1.33 LINK C MSE A 165 N PRO A 166 1555 1555 1.34 LINK C ALA A 175 N MSE A 176 1555 1555 1.33 LINK C MSE A 176 N THR A 177 1555 1555 1.33 LINK C THR A 182 N MSE A 183 1555 1555 1.33 LINK C MSE A 183 N LEU A 184 1555 1555 1.34 LINK C SER A 207 N MSE A 208 1555 1555 1.33 LINK C MSE A 208 N GLN A 209 1555 1555 1.33 LINK C LEU A 220 N MSE A 221 1555 1555 1.33 LINK C MSE A 221 N LYS A 222 1555 1555 1.33 LINK C GLN A 356 N MSE A 357 1555 1555 1.33 LINK C MSE A 357 N TYR A 358 1555 1555 1.33 LINK C SER A 363 N MSE A 364 1555 1555 1.34 LINK C MSE A 364 N GLU A 365 1555 1555 1.33 SITE 1 AC1 6 ALA A 81 GLU A 83 ASN A 84 LYS A 104 SITE 2 AC1 6 GLU A 107 PG4 A 401 SITE 1 AC2 10 LYS A 59 ASN A 80 ALA A 81 LYS A 86 SITE 2 AC2 10 GLU A 88 PHE A 100 TYR A 101 TYR A 102 SITE 3 AC2 10 LYS A 104 PG4 A 400 SITE 1 AC3 6 SER A 68 ALA A 115 ARG A 116 SER A 117 SITE 2 AC3 6 GLY A 118 SER A 120 CRYST1 89.364 89.364 120.012 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 0.011190 0.006461 0.000000 0.00000 SCALE2 0.000000 0.012921 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008332 0.00000