HEADER METAL BINDING PROTEIN 12-DEC-06 2O8Q TITLE CRYSTAL STRUCTURE OF A PROTEIN WITH A CUPIN-LIKE FOLD AND UNKNOWN TITLE 2 FUNCTION (BXE_C0505) FROM BURKHOLDERIA XENOVORANS LB400 AT 1.55 A TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA XENOVORANS; SOURCE 3 ORGANISM_TAXID: 266265; SOURCE 4 STRAIN: LB400; SOURCE 5 GENE: YP_555756.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS CPUIN-LIKE FOLD, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL KEYWDS 2 GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, METAL BINDING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 7 25-JAN-23 2O8Q 1 REMARK SEQADV LINK REVDAT 6 25-OCT-17 2O8Q 1 REMARK REVDAT 5 18-OCT-17 2O8Q 1 REMARK REVDAT 4 13-JUL-11 2O8Q 1 VERSN REVDAT 3 28-JUL-10 2O8Q 1 HEADER TITLE KEYWDS REVDAT 2 24-FEB-09 2O8Q 1 VERSN REVDAT 1 26-DEC-06 2O8Q 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN (YP_555756.1) FROM JRNL TITL 2 BURKHOLDERIA XENOVORANS LB400 AT 1.55 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 57868 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2939 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3968 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 238 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1900 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 231 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 21.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.05000 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): 0.059 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.061 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.898 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2081 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1399 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2820 ; 1.837 ; 1.933 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3378 ; 1.006 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 262 ; 9.118 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;27.541 ;23.558 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 308 ;12.652 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;19.630 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 295 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2398 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 460 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 382 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1486 ; 0.209 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 970 ; 0.183 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1146 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 173 ; 0.183 ; 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): 20 ; 0.280 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 62 ; 0.373 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.240 ; 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): 1305 ; 2.062 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 525 ; 0.516 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2049 ; 3.183 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 878 ; 4.504 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 771 ; 6.464 ;11.000 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 : 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 0 A 128 REMARK 3 ORIGIN FOR THE GROUP (A): 34.6380 19.8428 23.6197 REMARK 3 T TENSOR REMARK 3 T11: -0.0417 T22: -0.0378 REMARK 3 T33: -0.0431 T12: 0.0007 REMARK 3 T13: 0.0366 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 1.8629 L22: 1.2727 REMARK 3 L33: 1.3598 L12: 0.2744 REMARK 3 L13: -0.9599 L23: -0.2704 REMARK 3 S TENSOR REMARK 3 S11: -0.0071 S12: 0.1220 S13: 0.0451 REMARK 3 S21: -0.1551 S22: 0.0188 S23: -0.1713 REMARK 3 S31: -0.0548 S32: 0.0596 S33: -0.0117 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 1 B 127 REMARK 3 ORIGIN FOR THE GROUP (A): 32.0135 7.4884 40.5619 REMARK 3 T TENSOR REMARK 3 T11: -0.0496 T22: -0.0396 REMARK 3 T33: -0.0395 T12: 0.0409 REMARK 3 T13: -0.0009 T23: 0.0255 REMARK 3 L TENSOR REMARK 3 L11: 1.2046 L22: 2.0120 REMARK 3 L33: 1.2570 L12: 0.3174 REMARK 3 L13: -0.3619 L23: -0.2264 REMARK 3 S TENSOR REMARK 3 S11: -0.0521 S12: -0.1354 S13: -0.1365 REMARK 3 S21: 0.0670 S22: 0.0268 S23: -0.1265 REMARK 3 S31: 0.1877 S32: 0.1167 S33: 0.0253 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: (1). HYDROGENS HAVE BEEN ADDED IN REMARK 3 RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS REMARK 3 ONLY. (3). 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL REMARK 3 S-MET INCORPORATION. (4). A NI ATOM ON EACH OF THE TWO SUBUNITS REMARK 3 IN THE ASYMMETRIC UNIT IS COORDINATED TO THE SIDE CHAIN OF HIS REMARK 3 58, HIS 60, HIS 100, AND THREE WATERS. ANOMALOUS DIFFERENCE REMARK 3 FOURIERS AND X-RAY FLUORESCENCE EXPERIMENTS SUPPORT THE REMARK 3 ASSIGNMENT THE NI IONS. (5). RESIDUES 20-21 AND 50-54 ON THE A REMARK 3 SUBUNIT AND 20-22 ON THE B SUBUNIT ARE DISORDERED AND WERE NOT REMARK 3 MODELED. REMARK 4 REMARK 4 2O8Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040828. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-06; 20-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 9.0; 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SSRL; APS REMARK 200 BEAMLINE : BL1-5; 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000017; 0.97921, 0.97888, REMARK 200 0.94645 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR; SI(111) DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : 1M LONG RH COATED BENT REMARK 200 CYLINDRICAL MIRROR FORHORIZONTAL REMARK 200 AND VERTICAL FOCUSSING; REMARK 200 ADJUSTABLE FOCUSING MIRRORS IN K- REMARK 200 B GEOMETRY REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; MARMOSAIC 300 REMARK 200 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57924 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 29.683 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.96500 REMARK 200 R SYM FOR SHELL (I) : 0.96500 REMARK 200 FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHELXD, SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: REMARK 200 TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. A 2.35 REMARK 200 ANGSTROM MAD REMARK 200 DATA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE AND TRACE AN REMARK 200 INITIAL MODEL. TH REMARK 200 E MODEL WAS THEN REFINED USING THE AMPLITUDES FROM A SECOND REMARK 200 CRYSTAL THAT DIFFRAC REMARK 200 TED TO AN ENHANCED RESOLUTION OF 1.55 ANGSTROM. THE 2.35 ANGSTROM REMARK 200 MAD PHASES FRO REMARK 200 M THE FIRST CRYSTAL WERE USED AS PHASE RESTRAINTS DURING THE REMARK 200 REFINEMENT. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0% DIOXANE, 10.0% PEG-20000, 0.1M REMARK 280 BICINE PH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, REMARK 280 TEMPERATURE 277K. 0.2M (NH4)2TARTRATE, 20.0% PEG-3350, NO BUFFER REMARK 280 PH 6.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 51.12750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.12750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.37300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.12750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.12750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.37300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.12750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.12750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.37300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.12750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.12750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.37300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 300 SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT REMARK 300 SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A REMARK 300 BIOLOGICALLY 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 74.74600 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 20 REMARK 465 LEU A 21 REMARK 465 GLY A 50 REMARK 465 LYS A 51 REMARK 465 GLU A 52 REMARK 465 ALA A 53 REMARK 465 LYS A 54 REMARK 465 GLU A 129 REMARK 465 ALA A 130 REMARK 465 ARG A 131 REMARK 465 LYS A 132 REMARK 465 PRO A 133 REMARK 465 GLY B 0 REMARK 465 GLY B 20 REMARK 465 LEU B 21 REMARK 465 ARG B 22 REMARK 465 GLY B 50 REMARK 465 LYS B 51 REMARK 465 GLU B 128 REMARK 465 GLU B 129 REMARK 465 ALA B 130 REMARK 465 ARG B 131 REMARK 465 LYS B 132 REMARK 465 PRO B 133 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 2 CD CE NZ REMARK 470 GLN A 4 CD OE1 NE2 REMARK 470 PHE A 24 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 126 CG OD1 OD2 REMARK 470 LEU A 127 CG CD1 CD2 REMARK 470 LYS B 12 CD CE NZ REMARK 470 ARG B 19 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 52 CG CD OE1 OE2 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 LYS A 12 N - CA - C ANGL. DEV. = 21.5 DEGREES REMARK 500 GLY A 63 N - CA - C ANGL. DEV. = -17.0 DEGREES REMARK 500 MSE B 1 CB - CG - SE ANGL. DEV. = 18.1 DEGREES REMARK 500 GLY B 63 N - CA - C ANGL. DEV. = -16.4 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 13 -73.68 75.66 REMARK 500 ASP A 13 -65.30 76.93 REMARK 500 SER A 15 -169.08 -72.81 REMARK 500 LYS B 2 136.46 174.27 REMARK 500 ALA B 53 164.25 174.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 12 ASP A 13 43.39 REMARK 500 LYS A 12 ASP A 13 39.73 REMARK 500 MSE B 1 LYS B 2 124.47 REMARK 500 ALA B 53 LYS B 54 -70.58 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 NI A 300 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 58 NE2 REMARK 620 2 HIS A 60 NE2 94.7 REMARK 620 3 HIS A 100 NE2 87.4 96.1 REMARK 620 4 HOH A 340 O 89.7 90.7 172.8 REMARK 620 5 HOH A 346 O 91.6 171.6 89.7 83.8 REMARK 620 6 HOH A 377 O 178.7 86.2 91.6 91.2 87.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 300 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 58 NE2 REMARK 620 2 HIS B 60 NE2 96.1 REMARK 620 3 HIS B 100 NE2 87.7 96.5 REMARK 620 4 HOH B 362 O 89.3 89.1 173.9 REMARK 620 5 HOH B 393 O 177.8 86.0 91.5 91.4 REMARK 620 6 HOH B 413 O 90.9 170.4 90.4 84.3 87.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 369680 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV REMARK 999 PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET REMARK 999 SEQUENCE. DBREF 2O8Q A 1 133 UNP Q13HN3 Q13HN3_BURXL 1 133 DBREF 2O8Q B 1 133 UNP Q13HN3 Q13HN3_BURXL 1 133 SEQADV 2O8Q GLY A 0 UNP Q13HN3 EXPRESSION TAG SEQADV 2O8Q MSE A 1 UNP Q13HN3 MET 1 MODIFIED RESIDUE SEQADV 2O8Q MSE A 39 UNP Q13HN3 MET 39 MODIFIED RESIDUE SEQADV 2O8Q MSE A 85 UNP Q13HN3 MET 85 MODIFIED RESIDUE SEQADV 2O8Q GLY B 0 UNP Q13HN3 EXPRESSION TAG SEQADV 2O8Q MSE B 1 UNP Q13HN3 MET 1 MODIFIED RESIDUE SEQADV 2O8Q MSE B 39 UNP Q13HN3 MET 39 MODIFIED RESIDUE SEQADV 2O8Q MSE B 85 UNP Q13HN3 MET 85 MODIFIED RESIDUE SEQRES 1 A 134 GLY MSE LYS LEU GLN THR THR ILE GLN HIS GLU PRO LYS SEQRES 2 A 134 ASP GLY SER GLY PHE ASP ARG GLY LEU ARG GLU PHE PHE SEQRES 3 A 134 GLU TYR ARG ASP THR GLY VAL ASN GLU ALA THR GLY GLY SEQRES 4 A 134 MSE PHE GLY ALA HIS VAL ILE ARG ALA ILE PRO GLY LYS SEQRES 5 A 134 GLU ALA LYS PRO THR TRP HIS THR HIS THR VAL GLY PHE SEQRES 6 A 134 GLN LEU PHE TYR VAL LEU ARG GLY TRP VAL GLU PHE GLU SEQRES 7 A 134 TYR GLU ASP ILE GLY ALA VAL MSE LEU GLU ALA GLY GLY SEQRES 8 A 134 SER ALA PHE GLN PRO PRO GLY VAL ARG HIS ARG GLU LEU SEQRES 9 A 134 ARG HIS SER ASP ASP LEU GLU VAL LEU GLU ILE VAL SER SEQRES 10 A 134 PRO ALA GLY PHE ALA THR SER VAL VAL ASP LEU GLU GLU SEQRES 11 A 134 ALA ARG LYS PRO SEQRES 1 B 134 GLY MSE LYS LEU GLN THR THR ILE GLN HIS GLU PRO LYS SEQRES 2 B 134 ASP GLY SER GLY PHE ASP ARG GLY LEU ARG GLU PHE PHE SEQRES 3 B 134 GLU TYR ARG ASP THR GLY VAL ASN GLU ALA THR GLY GLY SEQRES 4 B 134 MSE PHE GLY ALA HIS VAL ILE ARG ALA ILE PRO GLY LYS SEQRES 5 B 134 GLU ALA LYS PRO THR TRP HIS THR HIS THR VAL GLY PHE SEQRES 6 B 134 GLN LEU PHE TYR VAL LEU ARG GLY TRP VAL GLU PHE GLU SEQRES 7 B 134 TYR GLU ASP ILE GLY ALA VAL MSE LEU GLU ALA GLY GLY SEQRES 8 B 134 SER ALA PHE GLN PRO PRO GLY VAL ARG HIS ARG GLU LEU SEQRES 9 B 134 ARG HIS SER ASP ASP LEU GLU VAL LEU GLU ILE VAL SER SEQRES 10 B 134 PRO ALA GLY PHE ALA THR SER VAL VAL ASP LEU GLU GLU SEQRES 11 B 134 ALA ARG LYS PRO MODRES 2O8Q MSE A 1 MET SELENOMETHIONINE MODRES 2O8Q MSE A 39 MET SELENOMETHIONINE MODRES 2O8Q MSE A 85 MET SELENOMETHIONINE MODRES 2O8Q MSE B 1 MET SELENOMETHIONINE MODRES 2O8Q MSE B 39 MET SELENOMETHIONINE MODRES 2O8Q MSE B 85 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 39 16 HET MSE A 85 8 HET MSE B 1 8 HET MSE B 39 16 HET MSE B 85 8 HET NI A 300 1 HET EDO A 301 4 HET EDO A 302 4 HET EDO A 303 4 HET EDO A 304 4 HET NI B 300 1 HET EDO B 301 4 HET EDO B 302 4 HET EDO B 303 4 HET EDO B 304 4 HETNAM MSE SELENOMETHIONINE HETNAM NI NICKEL (II) ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 NI 2(NI 2+) FORMUL 4 EDO 8(C2 H6 O2) FORMUL 13 HOH *231(H2 O) HELIX 1 1 GLY A 31 GLY A 37 1 7 HELIX 2 2 GLY B 31 GLY B 37 1 7 SHEET 1 A 6 THR A 6 GLN A 8 0 SHEET 2 A 6 SER A 91 PHE A 93 -1 O PHE A 93 N THR A 6 SHEET 3 A 6 GLN A 65 ARG A 71 -1 N PHE A 67 O ALA A 92 SHEET 4 A 6 GLU A 110 VAL A 115 -1 O GLU A 110 N LEU A 70 SHEET 5 A 6 GLY A 41 ALA A 47 -1 N ILE A 45 O VAL A 111 SHEET 6 A 6 PHE A 25 ASP A 29 -1 N GLU A 26 O ARG A 46 SHEET 1 B 2 HIS A 58 HIS A 60 0 SHEET 2 B 2 THR A 122 VAL A 124 -1 O SER A 123 N THR A 59 SHEET 1 C 3 GLY A 82 GLU A 87 0 SHEET 2 C 3 TRP A 73 TYR A 78 -1 N VAL A 74 O LEU A 86 SHEET 3 C 3 HIS A 100 HIS A 105 -1 O ARG A 104 N GLU A 75 SHEET 1 D 6 THR B 6 GLN B 8 0 SHEET 2 D 6 SER B 91 PHE B 93 -1 O PHE B 93 N THR B 6 SHEET 3 D 6 GLN B 65 ARG B 71 -1 N PHE B 67 O ALA B 92 SHEET 4 D 6 GLU B 110 VAL B 115 -1 O LEU B 112 N TYR B 68 SHEET 5 D 6 GLY B 41 ALA B 47 -1 N ILE B 45 O VAL B 111 SHEET 6 D 6 PHE B 25 ASP B 29 -1 N GLU B 26 O ARG B 46 SHEET 1 E 2 HIS B 58 HIS B 60 0 SHEET 2 E 2 THR B 122 VAL B 124 -1 O SER B 123 N THR B 59 SHEET 1 F 3 GLY B 82 GLU B 87 0 SHEET 2 F 3 TRP B 73 TYR B 78 -1 N VAL B 74 O LEU B 86 SHEET 3 F 3 HIS B 100 HIS B 105 -1 O ARG B 104 N GLU B 75 LINK C GLY A 0 N MSE A 1 1555 1555 1.34 LINK C MSE A 1 N LYS A 2 1555 1555 1.35 LINK C GLY A 38 N AMSE A 39 1555 1555 1.33 LINK C GLY A 38 N BMSE A 39 1555 1555 1.32 LINK C AMSE A 39 N PHE A 40 1555 1555 1.35 LINK C BMSE A 39 N PHE A 40 1555 1555 1.33 LINK C VAL A 84 N MSE A 85 1555 1555 1.32 LINK C MSE A 85 N LEU A 86 1555 1555 1.33 LINK C MSE B 1 N LYS B 2 1555 1555 1.32 LINK C GLY B 38 N AMSE B 39 1555 1555 1.32 LINK C GLY B 38 N BMSE B 39 1555 1555 1.32 LINK C BMSE B 39 N PHE B 40 1555 1555 1.34 LINK C AMSE B 39 N PHE B 40 1555 1555 1.34 LINK C BVAL B 84 N MSE B 85 1555 1555 1.34 LINK C AVAL B 84 N MSE B 85 1555 1555 1.33 LINK C MSE B 85 N LEU B 86 1555 1555 1.33 LINK NE2 HIS A 58 NI NI A 300 1555 1555 2.09 LINK NE2 HIS A 60 NI NI A 300 1555 1555 2.08 LINK NE2 HIS A 100 NI NI A 300 1555 1555 2.15 LINK NI NI A 300 O HOH A 340 1555 1555 2.15 LINK NI NI A 300 O HOH A 346 1555 1555 2.15 LINK NI NI A 300 O HOH A 377 1555 1555 2.13 LINK NE2 HIS B 58 NI NI B 300 1555 1555 2.10 LINK NE2 HIS B 60 NI NI B 300 1555 1555 2.10 LINK NE2 HIS B 100 NI NI B 300 1555 1555 2.14 LINK NI NI B 300 O HOH B 362 1555 1555 2.16 LINK NI NI B 300 O HOH B 393 1555 1555 2.20 LINK NI NI B 300 O HOH B 413 1555 1555 2.13 CISPEP 1 SER A 116 PRO A 117 0 -5.61 CISPEP 2 SER B 116 PRO B 117 0 -7.93 SITE 1 AC1 6 HIS A 58 HIS A 60 HIS A 100 HOH A 340 SITE 2 AC1 6 HOH A 346 HOH A 377 SITE 1 AC2 6 HIS B 58 HIS B 60 HIS B 100 HOH B 362 SITE 2 AC2 6 HOH B 393 HOH B 413 SITE 1 AC3 2 PHE B 25 TYR B 27 SITE 1 AC4 1 HIS A 58 SITE 1 AC5 6 GLY A 14 SER A 15 GLY A 16 PHE A 17 SITE 2 AC5 6 GLU B 26 ARG B 46 SITE 1 AC6 5 MSE A 39 SER A 116 GLY B 63 PHE B 64 SITE 2 AC6 5 SER B 116 SITE 1 AC7 4 GLY B 16 PHE B 17 ASP B 18 HOH B 324 SITE 1 AC8 4 THR A 5 ILE A 7 ILE A 81 HOH A 407 SITE 1 AC9 5 GLU A 34 HOH A 326 GLN B 4 THR B 6 SITE 2 AC9 5 HOH B 391 CRYST1 102.255 102.255 74.746 90.00 90.00 90.00 P 42 21 2 16 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 0.009780 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009780 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013380 0.00000