HEADER UNKNOWN FUNCTION 05-JUN-08 3DDE TITLE CRYSTAL STRUCTURE OF A DOMAIN OF UNKNOWN FUNCTION WITH A HEME TITLE 2 OXYGENASE-LIKE FOLD (SDEN_3740) FROM SHEWANELLA DENITRIFICANS OS217 TITLE 3 AT 2.30 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TENA/THI-4 PROTEIN, DOMAIN OF UNKNOWN FUNCTION WITH A HEME COMPND 3 OXYGENASE-LIKE FOLD; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA DENITRIFICANS OS217; SOURCE 3 ORGANISM_TAXID: 318161; SOURCE 4 GENE: YP_564736.1, SDEN_3740; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-2, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 7 01-FEB-23 3DDE 1 REMARK SEQADV REVDAT 6 24-JUL-19 3DDE 1 REMARK LINK REVDAT 5 25-OCT-17 3DDE 1 REMARK REVDAT 4 13-JUL-11 3DDE 1 VERSN REVDAT 3 23-MAR-11 3DDE 1 HEADER TITLE KEYWDS REVDAT 2 24-FEB-09 3DDE 1 VERSN REVDAT 1 24-JUN-08 3DDE 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF DOMAIN OF UNKNOWN FUNCTION WITH A HEME JRNL TITL 2 OXYGENASE-LIKE FOLD (YP_564736.1) FROM SHEWANELLA JRNL TITL 3 DENITRIFICANS OS-217 AT 2.30 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 23503 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1206 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1583 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3555 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 47.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.08000 REMARK 3 B22 (A**2) : -1.74000 REMARK 3 B33 (A**2) : -1.34000 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): 0.370 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.243 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.212 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.745 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3770 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2381 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5142 ; 1.340 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5838 ; 1.001 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 483 ; 2.884 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;33.655 ;24.465 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 574 ;11.435 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;19.040 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 588 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4243 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 759 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 921 ; 0.210 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2275 ; 0.169 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1861 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1572 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 82 ; 0.150 ; 0.200 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): 6 ; 0.151 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 17 ; 0.264 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.169 ; 0.200 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): 2587 ; 0.679 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 953 ; 0.260 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3802 ; 1.001 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1566 ; 0.700 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1335 ; 1.028 ; 3.000 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 14 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2 A 30 2 REMARK 3 1 B 2 B 30 2 REMARK 3 2 A 31 A 34 6 REMARK 3 2 B 31 B 34 6 REMARK 3 3 A 35 A 84 2 REMARK 3 3 B 35 B 84 2 REMARK 3 4 A 85 A 85 6 REMARK 3 4 B 85 B 85 6 REMARK 3 5 A 86 A 100 2 REMARK 3 5 B 86 B 100 2 REMARK 3 6 A 101 A 101 6 REMARK 3 6 B 101 B 101 6 REMARK 3 7 A 102 A 139 2 REMARK 3 7 B 102 B 139 2 REMARK 3 8 A 140 A 145 6 REMARK 3 8 B 140 B 145 6 REMARK 3 9 A 146 A 167 2 REMARK 3 9 B 146 B 167 2 REMARK 3 10 A 168 A 176 6 REMARK 3 10 B 168 B 176 6 REMARK 3 11 A 177 A 186 2 REMARK 3 11 B 177 B 186 2 REMARK 3 12 A 187 A 187 6 REMARK 3 12 B 187 B 187 6 REMARK 3 13 A 188 A 220 2 REMARK 3 13 B 188 B 220 2 REMARK 3 14 A 221 A 232 6 REMARK 3 14 B 221 B 232 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1166 ; 0.030 ; 0.050 REMARK 3 MEDIUM POSITIONAL 1 A (A): 1316 ; 0.140 ; 0.500 REMARK 3 LOOSE POSITIONAL 1 A (A): 445 ; 0.720 ; 5.000 REMARK 3 TIGHT THERMAL 1 A (A**2): 1166 ; 0.100 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1316 ; 0.410 ; 2.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 445 ; 1.520 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 233 REMARK 3 ORIGIN FOR THE GROUP (A): -11.4519 24.3746 -55.1856 REMARK 3 T TENSOR REMARK 3 T11: -0.2774 T22: 0.3143 REMARK 3 T33: -0.1720 T12: -0.1777 REMARK 3 T13: 0.0076 T23: 0.1689 REMARK 3 L TENSOR REMARK 3 L11: 2.9290 L22: 2.6017 REMARK 3 L33: 8.2529 L12: 0.2539 REMARK 3 L13: 1.7380 L23: 0.8097 REMARK 3 S TENSOR REMARK 3 S11: 0.0797 S12: -1.0379 S13: -0.3445 REMARK 3 S21: 0.1791 S22: 0.0451 S23: 0.4534 REMARK 3 S31: 1.0321 S32: -1.7508 S33: -0.1248 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 232 REMARK 3 ORIGIN FOR THE GROUP (A): -8.1745 21.0874 -93.4003 REMARK 3 T TENSOR REMARK 3 T11: -0.0015 T22: -0.3342 REMARK 3 T33: -0.2201 T12: -0.1504 REMARK 3 T13: -0.1451 T23: 0.0369 REMARK 3 L TENSOR REMARK 3 L11: 2.0207 L22: 5.0676 REMARK 3 L33: 2.2690 L12: -0.5264 REMARK 3 L13: -0.4499 L23: 0.5920 REMARK 3 S TENSOR REMARK 3 S11: 0.0219 S12: 0.1188 S13: -0.2459 REMARK 3 S21: -1.0114 S22: -0.0115 S23: 0.4333 REMARK 3 S31: 0.2203 S32: -0.2351 S33: -0.0105 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. REMARK 3 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY REMARK 3 OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 REMARK 3 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. REMARK 3 4. NITRATE, 1,2-ETHANEDIOL, PEG AND PGE WERE MODELED BASED REMARK 3 ON CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS. REMARK 3 5. AMINO ACID SER 225 IN CHAINS A AND B REMARK 3 ARE RAMACHADRAN OUTLIERS IN A REGION REMARK 3 OF ELECTRON DENSITY THAT IS DIFFICULT TO MODEL. REMARK 3 6. THERE IS UNMODELED ELECTRON DENSITY NEAR AMINO ACIDS GLU 83, REMARK 3 HIS 86, GLU 140 AND HIS 170 IN BOTH PROTOMERS. REMARK 4 REMARK 4 3DDE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047898. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-08 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 : 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) : 0.91162,0.97932,0.97918 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, TOROID REMARK 200 FOCUSING MIRROR 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23523 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 29.173 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20.0% POLYETHYLENE GLYCOL 3350, 0.269M REMARK 280 MAGNESIUM NITRATE, NANODROP, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 46.40500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.40500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.00000 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 300 REMARK: AUTHORS STATE THAT THE PROTOMER MAY FORM A TETRAMER BASED REMARK 300 ON CRYSTAL PACKING ANALYSIS. SIZE-EXCLUSION CHROMATOGRAPHY COUPLED REMARK 300 WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER REMARK 300 AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION. 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.8 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 66.00000 REMARK 350 BIOMT3 2 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 GLY A 0 REMARK 465 MSE A 1 REMARK 465 LEU A 234 REMARK 465 ARG A 235 REMARK 465 ASP A 236 REMARK 465 ASN A 237 REMARK 465 ALA A 238 REMARK 465 GLY B 0 REMARK 465 MSE B 1 REMARK 465 PHE B 233 REMARK 465 LEU B 234 REMARK 465 ARG B 235 REMARK 465 ASP B 236 REMARK 465 ASN B 237 REMARK 465 ALA B 238 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 LYS A 8 CG CD CE NZ REMARK 470 GLU A 10 CD OE1 OE2 REMARK 470 GLN A 11 CG CD OE1 NE2 REMARK 470 LYS A 34 CG CD CE NZ REMARK 470 LYS A 37 CG CD CE NZ REMARK 470 LYS A 66 CD CE NZ REMARK 470 LYS A 71 CD CE NZ REMARK 470 LYS A 108 CD CE NZ REMARK 470 ASN A 141 CG OD1 ND2 REMARK 470 TYR A 143 CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 151 CD CE NZ REMARK 470 LYS A 165 CG CD CE NZ REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 ASP A 174 CG OD1 OD2 REMARK 470 LYS A 176 CE NZ REMARK 470 GLU A 179 CG CD OE1 OE2 REMARK 470 GLU A 183 CG CD OE1 OE2 REMARK 470 GLU A 193 CD OE1 OE2 REMARK 470 LYS A 218 CD CE NZ REMARK 470 LYS B 8 CG CD CE NZ REMARK 470 GLN B 11 CG CD OE1 NE2 REMARK 470 LYS B 34 CG CD CE NZ REMARK 470 LYS B 37 CD CE NZ REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 LYS B 71 CG CD CE NZ REMARK 470 LYS B 108 CD CE NZ REMARK 470 ASN B 141 OD1 ND2 REMARK 470 LYS B 151 CD CE NZ REMARK 470 LYS B 165 CE NZ REMARK 470 HIS B 170 ND1 CD2 CE1 NE2 REMARK 470 LYS B 172 CG CD CE NZ REMARK 470 ASP B 174 CG OD1 OD2 REMARK 470 LYS B 176 CE NZ REMARK 470 GLU B 179 CG CD OE1 OE2 REMARK 470 GLU B 183 CG CD OE1 OE2 REMARK 470 GLU B 193 CD OE1 OE2 REMARK 470 LYS B 218 CG CD CE NZ 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 SER A 96 CB SER A 96 OG 0.093 REMARK 500 PHE A 233 C PHE A 233 O 0.139 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 211 NE - CZ - NH2 ANGL. DEV. = -3.4 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 ASP A 32 -85.00 -121.74 REMARK 500 LYS A 34 114.01 -178.36 REMARK 500 ASN A 141 41.69 -104.55 REMARK 500 ASP A 158 60.01 38.38 REMARK 500 MSE A 164 32.71 -144.68 REMARK 500 SER A 225 -69.96 103.41 REMARK 500 ASP B 32 -122.87 -125.02 REMARK 500 LYS B 34 135.45 -174.22 REMARK 500 ASP B 158 60.77 38.89 REMARK 500 MSE B 164 34.27 -142.70 REMARK 500 ILE B 168 10.54 -143.02 REMARK 500 SER B 225 -118.05 -170.33 REMARK 500 SER B 228 36.72 -84.60 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 NO3 B 239 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 240 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE B 241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 239 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 240 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 370140 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE 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 3DDE A 1 238 UNP Q12HR3 Q12HR3_SHEDO 1 238 DBREF 3DDE B 1 238 UNP Q12HR3 Q12HR3_SHEDO 1 238 SEQADV 3DDE GLY A 0 UNP Q12HR3 EXPRESSION TAG SEQADV 3DDE GLY B 0 UNP Q12HR3 EXPRESSION TAG SEQRES 1 A 239 GLY MSE SER ILE ILE ASP LEU THR LYS LEU GLU GLN LYS SEQRES 2 A 239 VAL ALA THR MSE TRP ASP SER ILE LEU THR ASN SER PRO SEQRES 3 A 239 PHE ILE HIS GLU VAL LEU ASP GLY LYS ALA THR LYS ALA SEQRES 4 A 239 LEU TYR ALA ILE TYR MSE THR GLU THR TYR HIS TYR THR SEQRES 5 A 239 LYS HIS ASN ALA LYS ASN GLN ALA LEU VAL GLY ILE MSE SEQRES 6 A 239 GLY LYS ASP LEU PRO GLY LYS TYR LEU SER PHE CYS PHE SEQRES 7 A 239 HIS HIS ALA HIS GLU GLU ALA GLY HIS GLU LEU MSE ALA SEQRES 8 A 239 LEU SER ASP ILE ALA SER ILE GLY PHE ASP ARG GLU ASP SEQRES 9 A 239 VAL LEU SER SER LYS PRO LEU PRO ALA THR GLU THR LEU SEQRES 10 A 239 ILE ALA TYR LEU TYR TRP ILE SER ALA THR GLY ASN PRO SEQRES 11 A 239 VAL GLN ARG LEU GLY TYR SER TYR TRP ALA GLU ASN VAL SEQRES 12 A 239 TYR GLY TYR ILE ASP PRO VAL LEU LYS ALA ILE GLN SER SEQRES 13 A 239 THR LEU ASP LEU THR PRO GLN SER MSE LYS PHE PHE ILE SEQRES 14 A 239 ALA HIS SER LYS ILE ASP ALA LYS HIS ALA GLU GLU VAL SEQRES 15 A 239 ASN GLU MSE LEU HIS GLU VAL CYS LYS THR GLN GLU ASP SEQRES 16 A 239 VAL ASP SER VAL VAL ALA VAL MSE GLU ASN SER LEU VAL SEQRES 17 A 239 LEU THR ALA ARG ILE LEU ASP ASP VAL TRP LYS GLU TYR SEQRES 18 A 239 GLN LEU PHE GLN SER GLY ALA SER ASP ARG TYR ALA PHE SEQRES 19 A 239 LEU ARG ASP ASN ALA SEQRES 1 B 239 GLY MSE SER ILE ILE ASP LEU THR LYS LEU GLU GLN LYS SEQRES 2 B 239 VAL ALA THR MSE TRP ASP SER ILE LEU THR ASN SER PRO SEQRES 3 B 239 PHE ILE HIS GLU VAL LEU ASP GLY LYS ALA THR LYS ALA SEQRES 4 B 239 LEU TYR ALA ILE TYR MSE THR GLU THR TYR HIS TYR THR SEQRES 5 B 239 LYS HIS ASN ALA LYS ASN GLN ALA LEU VAL GLY ILE MSE SEQRES 6 B 239 GLY LYS ASP LEU PRO GLY LYS TYR LEU SER PHE CYS PHE SEQRES 7 B 239 HIS HIS ALA HIS GLU GLU ALA GLY HIS GLU LEU MSE ALA SEQRES 8 B 239 LEU SER ASP ILE ALA SER ILE GLY PHE ASP ARG GLU ASP SEQRES 9 B 239 VAL LEU SER SER LYS PRO LEU PRO ALA THR GLU THR LEU SEQRES 10 B 239 ILE ALA TYR LEU TYR TRP ILE SER ALA THR GLY ASN PRO SEQRES 11 B 239 VAL GLN ARG LEU GLY TYR SER TYR TRP ALA GLU ASN VAL SEQRES 12 B 239 TYR GLY TYR ILE ASP PRO VAL LEU LYS ALA ILE GLN SER SEQRES 13 B 239 THR LEU ASP LEU THR PRO GLN SER MSE LYS PHE PHE ILE SEQRES 14 B 239 ALA HIS SER LYS ILE ASP ALA LYS HIS ALA GLU GLU VAL SEQRES 15 B 239 ASN GLU MSE LEU HIS GLU VAL CYS LYS THR GLN GLU ASP SEQRES 16 B 239 VAL ASP SER VAL VAL ALA VAL MSE GLU ASN SER LEU VAL SEQRES 17 B 239 LEU THR ALA ARG ILE LEU ASP ASP VAL TRP LYS GLU TYR SEQRES 18 B 239 GLN LEU PHE GLN SER GLY ALA SER ASP ARG TYR ALA PHE SEQRES 19 B 239 LEU ARG ASP ASN ALA MODRES 3DDE MSE A 16 MET SELENOMETHIONINE MODRES 3DDE MSE A 44 MET SELENOMETHIONINE MODRES 3DDE MSE A 64 MET SELENOMETHIONINE MODRES 3DDE MSE A 89 MET SELENOMETHIONINE MODRES 3DDE MSE A 164 MET SELENOMETHIONINE MODRES 3DDE MSE A 184 MET SELENOMETHIONINE MODRES 3DDE MSE A 202 MET SELENOMETHIONINE MODRES 3DDE MSE B 16 MET SELENOMETHIONINE MODRES 3DDE MSE B 44 MET SELENOMETHIONINE MODRES 3DDE MSE B 64 MET SELENOMETHIONINE MODRES 3DDE MSE B 89 MET SELENOMETHIONINE MODRES 3DDE MSE B 164 MET SELENOMETHIONINE MODRES 3DDE MSE B 184 MET SELENOMETHIONINE MODRES 3DDE MSE B 202 MET SELENOMETHIONINE HET MSE A 16 8 HET MSE A 44 8 HET MSE A 64 8 HET MSE A 89 13 HET MSE A 164 8 HET MSE A 184 8 HET MSE A 202 8 HET MSE B 16 8 HET MSE B 44 8 HET MSE B 64 8 HET MSE B 89 16 HET MSE B 164 8 HET MSE B 184 8 HET MSE B 202 8 HET PEG A 239 7 HET PEG A 240 7 HET NO3 B 239 4 HET EDO B 240 4 HET PGE B 241 10 HET PEG B 242 7 HETNAM MSE SELENOMETHIONINE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM NO3 NITRATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM PGE TRIETHYLENE GLYCOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 14(C5 H11 N O2 SE) FORMUL 3 PEG 3(C4 H10 O3) FORMUL 5 NO3 N O3 1- FORMUL 6 EDO C2 H6 O2 FORMUL 7 PGE C6 H14 O4 FORMUL 9 HOH *74(H2 O) HELIX 1 1 ASP A 5 SER A 24 1 20 HELIX 2 2 SER A 24 ASP A 32 1 9 HELIX 3 3 THR A 36 LYS A 52 1 17 HELIX 4 4 HIS A 53 GLY A 65 1 13 HELIX 5 5 PRO A 69 ALA A 84 1 16 HELIX 6 6 HIS A 86 ILE A 97 1 12 HELIX 7 7 ASP A 100 SER A 106 1 7 HELIX 8 8 LEU A 110 THR A 126 1 17 HELIX 9 9 ASN A 128 GLN A 131 5 4 HELIX 10 10 ARG A 132 ASN A 141 1 10 HELIX 11 11 VAL A 142 LEU A 157 1 16 HELIX 12 12 THR A 160 SER A 163 5 4 HELIX 13 13 MSE A 164 CYS A 189 1 26 HELIX 14 14 THR A 191 PHE A 223 1 33 HELIX 15 15 ASP B 5 SER B 24 1 20 HELIX 16 16 SER B 24 ASP B 32 1 9 HELIX 17 17 THR B 36 LYS B 52 1 17 HELIX 18 18 HIS B 53 GLY B 65 1 13 HELIX 19 19 PRO B 69 ALA B 84 1 16 HELIX 20 20 HIS B 86 ILE B 97 1 12 HELIX 21 21 ASP B 100 SER B 106 1 7 HELIX 22 22 LEU B 110 THR B 126 1 17 HELIX 23 23 ASN B 128 VAL B 130 5 3 HELIX 24 24 GLN B 131 GLU B 140 1 10 HELIX 25 25 VAL B 142 LEU B 157 1 16 HELIX 26 26 THR B 160 SER B 163 5 4 HELIX 27 27 MSE B 164 ALA B 169 1 6 HELIX 28 28 HIS B 170 CYS B 189 1 20 HELIX 29 29 THR B 191 GLN B 224 1 34 LINK C THR A 15 N MSE A 16 1555 1555 1.33 LINK C MSE A 16 N TRP A 17 1555 1555 1.33 LINK C TYR A 43 N MSE A 44 1555 1555 1.34 LINK C MSE A 44 N THR A 45 1555 1555 1.33 LINK C ILE A 63 N MSE A 64 1555 1555 1.34 LINK C MSE A 64 N GLY A 65 1555 1555 1.33 LINK C LEU A 88 N MSE A 89 1555 1555 1.33 LINK C MSE A 89 N ALA A 90 1555 1555 1.33 LINK C SER A 163 N MSE A 164 1555 1555 1.33 LINK C MSE A 164 N LYS A 165 1555 1555 1.34 LINK C GLU A 183 N MSE A 184 1555 1555 1.33 LINK C MSE A 184 N LEU A 185 1555 1555 1.34 LINK C VAL A 201 N MSE A 202 1555 1555 1.33 LINK C MSE A 202 N GLU A 203 1555 1555 1.33 LINK C THR B 15 N MSE B 16 1555 1555 1.33 LINK C MSE B 16 N TRP B 17 1555 1555 1.34 LINK C TYR B 43 N MSE B 44 1555 1555 1.34 LINK C MSE B 44 N THR B 45 1555 1555 1.32 LINK C ILE B 63 N MSE B 64 1555 1555 1.33 LINK C MSE B 64 N GLY B 65 1555 1555 1.34 LINK C LEU B 88 N AMSE B 89 1555 1555 1.33 LINK C LEU B 88 N BMSE B 89 1555 1555 1.33 LINK C AMSE B 89 N ALA B 90 1555 1555 1.33 LINK C BMSE B 89 N ALA B 90 1555 1555 1.33 LINK C SER B 163 N MSE B 164 1555 1555 1.33 LINK C MSE B 164 N LYS B 165 1555 1555 1.34 LINK C GLU B 183 N MSE B 184 1555 1555 1.32 LINK C MSE B 184 N LEU B 185 1555 1555 1.33 LINK C VAL B 201 N MSE B 202 1555 1555 1.33 LINK C MSE B 202 N GLU B 203 1555 1555 1.33 SITE 1 AC1 6 ASN B 54 ARG B 132 TYR B 135 SER B 136 SITE 2 AC1 6 GLU B 140 HOH B 285 SITE 1 AC2 4 ASP B 5 LYS B 8 LEU B 9 LYS B 12 SITE 1 AC3 2 TYR B 43 TYR B 50 SITE 1 AC4 3 TYR A 121 HOH A 268 ILE B 63 SITE 1 AC5 7 GLU B 114 TYR B 119 TRP B 122 ILE B 123 SITE 2 AC5 7 THR B 126 GLY B 127 GLN B 131 SITE 1 AC6 2 ILE A 63 TYR B 121 CRYST1 92.810 66.000 84.380 90.00 90.00 90.00 P 21 21 2 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 0.010775 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015152 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011851 0.00000