HEADER SUGAR BINDING PROTEIN 23-OCT-09 3KDW TITLE CRYSTAL STRUCTURE OF PUTATIVE SUGAR BINDING PROTEIN (YP_001300177.1) TITLE 2 FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.70 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE SUGAR BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES VULGATUS ATCC 8482; SOURCE 3 ORGANISM_TAXID: 435590; SOURCE 4 STRAIN: ATCC 8482 / DSM 1447 / NCTC 11154; SOURCE 5 GENE: BVU_2916; 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 PUTATIVE SUGAR BINDING PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, KEYWDS 3 SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 4 17-JUL-19 3KDW 1 REMARK LINK REVDAT 3 25-OCT-17 3KDW 1 REMARK REVDAT 2 13-JUL-11 3KDW 1 VERSN REVDAT 1 24-NOV-09 3KDW 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE SUGAR BINDING PROTEIN JRNL TITL 2 (YP_001300177.1) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.70 JRNL TITL 3 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 31866 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1609 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2172 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1626 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 253 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 24.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.19000 REMARK 3 B22 (A**2) : -0.19000 REMARK 3 B33 (A**2) : 0.28000 REMARK 3 B12 (A**2) : -0.09000 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): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.086 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.124 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1831 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1246 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2508 ; 1.518 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3043 ; 1.041 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 244 ; 4.456 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;35.239 ;24.111 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 333 ;13.217 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;13.321 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 274 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2044 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 377 ; 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): 1085 ; 0.827 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 439 ; 0.284 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1759 ; 1.504 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 746 ; 2.528 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 728 ; 3.986 ; 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 : 5 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 -5 A 25 REMARK 3 ORIGIN FOR THE GROUP (A): 34.5170 28.5240 22.7720 REMARK 3 T TENSOR REMARK 3 T11: 0.1045 T22: 0.2206 REMARK 3 T33: 0.1542 T12: 0.0135 REMARK 3 T13: 0.0373 T23: 0.0116 REMARK 3 L TENSOR REMARK 3 L11: 10.5527 L22: 0.7455 REMARK 3 L33: 3.8708 L12: 1.7724 REMARK 3 L13: -4.1117 L23: 0.2971 REMARK 3 S TENSOR REMARK 3 S11: 0.0542 S12: 0.6656 S13: 0.0022 REMARK 3 S21: -0.0304 S22: 0.0939 S23: -0.0562 REMARK 3 S31: -0.1502 S32: -0.1741 S33: -0.1481 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 26 A 49 REMARK 3 ORIGIN FOR THE GROUP (A): 25.3220 31.6420 21.1730 REMARK 3 T TENSOR REMARK 3 T11: 0.0798 T22: 0.2048 REMARK 3 T33: 0.0574 T12: 0.0102 REMARK 3 T13: 0.0204 T23: 0.0370 REMARK 3 L TENSOR REMARK 3 L11: 2.8787 L22: 5.6607 REMARK 3 L33: 1.6719 L12: -0.0050 REMARK 3 L13: 0.2216 L23: 0.2768 REMARK 3 S TENSOR REMARK 3 S11: 0.0078 S12: 0.4084 S13: 0.0918 REMARK 3 S21: -0.5509 S22: -0.1255 S23: 0.0745 REMARK 3 S31: -0.0470 S32: -0.1235 S33: 0.1178 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 98 REMARK 3 ORIGIN FOR THE GROUP (A): 15.6190 22.3520 30.7760 REMARK 3 T TENSOR REMARK 3 T11: 0.0576 T22: 0.1094 REMARK 3 T33: 0.1165 T12: -0.0179 REMARK 3 T13: -0.0020 T23: -0.0370 REMARK 3 L TENSOR REMARK 3 L11: 4.6903 L22: 1.8130 REMARK 3 L33: 1.2201 L12: 1.8711 REMARK 3 L13: -1.1104 L23: -0.6919 REMARK 3 S TENSOR REMARK 3 S11: -0.1087 S12: 0.3367 S13: -0.2945 REMARK 3 S21: -0.1542 S22: 0.0761 S23: 0.0427 REMARK 3 S31: 0.1778 S32: -0.1867 S33: 0.0326 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 99 A 189 REMARK 3 ORIGIN FOR THE GROUP (A): 14.2290 39.4820 36.5750 REMARK 3 T TENSOR REMARK 3 T11: 0.0860 T22: 0.0951 REMARK 3 T33: 0.1225 T12: 0.0008 REMARK 3 T13: -0.0052 T23: 0.0156 REMARK 3 L TENSOR REMARK 3 L11: 1.1158 L22: 0.6134 REMARK 3 L33: 1.0976 L12: -0.6911 REMARK 3 L13: -0.1122 L23: -0.0448 REMARK 3 S TENSOR REMARK 3 S11: 0.0267 S12: 0.0901 S13: 0.1419 REMARK 3 S21: -0.0152 S22: -0.0087 S23: -0.0490 REMARK 3 S31: -0.1777 S32: -0.0329 S33: -0.0180 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 190 A 220 REMARK 3 ORIGIN FOR THE GROUP (A): -1.4650 53.8790 35.1410 REMARK 3 T TENSOR REMARK 3 T11: 0.1244 T22: 0.0517 REMARK 3 T33: 0.1322 T12: 0.0403 REMARK 3 T13: -0.0132 T23: 0.0163 REMARK 3 L TENSOR REMARK 3 L11: 1.8244 L22: 5.1178 REMARK 3 L33: 1.4097 L12: -1.2225 REMARK 3 L13: 0.9078 L23: -1.4282 REMARK 3 S TENSOR REMARK 3 S11: -0.1812 S12: -0.0387 S13: 0.2145 REMARK 3 S21: -0.1721 S22: 0.2047 S23: 0.0878 REMARK 3 S31: -0.1655 S32: -0.0546 S33: -0.0234 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS REMARK 3 ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE REMARK 3 ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REMARK 3 REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. REMARK 3 CHLORIDE (CL), (4S)-2-METHYL-2,4-PENTANEDIOL (MPD) (4R)-2-METHYL- REMARK 3 2,4-PENTANEDIOL (MRD), AND PHOSPHATE (PO4) FROM THE PROTEIN/ REMARK 3 CRYSTALLIZATION SOLUTION HAVE BEEN MODELED INTO THE SOLVENT REMARK 3 STRUCTURE. 5. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD REMARK 3 SERVER. REMARK 4 REMARK 4 3KDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055869. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91837,0.97929 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31900 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 28.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2000M (NH4)2HPO4, 50.0000% MPD, 0.1M REMARK 280 TRIS PH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 29.04267 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 58.08533 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 58.08533 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 29.04267 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 AND ANALYTICAL SIZE EXCLUSION REMARK 300 CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE REMARK 300 ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN REMARK 300 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -192.0 KCAL/MOL 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 87.12800 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 MSE A -18 REMARK 465 GLY A -17 REMARK 465 SER A -16 REMARK 465 ASP A -15 REMARK 465 LYS A -14 REMARK 465 ILE A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 GLU A -6 REMARK 465 LYS A 221 REMARK 465 ILE A 222 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 ASN A -5 CG OD1 ND2 REMARK 470 LYS A 39 CD CE NZ REMARK 470 LYS A 43 CD CE NZ REMARK 470 LYS A 47 CE NZ REMARK 470 LYS A 126 CE NZ REMARK 470 LYS A 145 NZ REMARK 470 LYS A 155 CE NZ REMARK 470 LYS A 206 CD CE NZ REMARK 470 LYS A 209 CD CE NZ REMARK 470 LYS A 216 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 GLU A 171 CB GLU A 171 CG -0.114 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE CRYSTALLIZATION REAGENT CONTAINED A RACEMIC MIXTURE (4R/4S) OF REMARK 600 2-METHYL-2,4-PENTANEDIOL (MPD) ONE OF THE SOLVENT SITES HAS BEEN REMARK 600 MODELED AS MIXTURE OF BOTH ENANTIOMERS RESID 301 (4S - MPD) AND REMARK 600 RESID 302 (4R - MRD). REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 310 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 393277 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE THIS CONSTRUCT (RESIDUES 21-222) WAS EXPRESSED WITH THE N- REMARK 999 TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. DBREF 3KDW A 21 222 UNP A6L4E1 A6L4E1_BACV8 21 222 SEQADV 3KDW MSE A -18 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW GLY A -17 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW SER A -16 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW ASP A -15 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW LYS A -14 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW ILE A -13 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW HIS A -12 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW HIS A -11 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW HIS A -10 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW HIS A -9 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW HIS A -8 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW HIS A -7 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW GLU A -6 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW ASN A -5 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW LEU A -4 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW TYR A -3 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW PHE A -2 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW GLN A -1 UNP A6L4E1 LEADER SEQUENCE SEQADV 3KDW GLY A 0 UNP A6L4E1 LEADER SEQUENCE SEQRES 1 A 221 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS GLU SEQRES 2 A 221 ASN LEU TYR PHE GLN GLY ALA VAL ASP LEU ASP ARG GLU SEQRES 3 A 221 GLY ARG ASP PRO ALA TYR VAL GLU SER ILE VAL LYS ARG SEQRES 4 A 221 SER GLN LYS ILE VAL ASP LYS LEU GLU LEU THR ASP THR SEQRES 5 A 221 VAL ALA ALA ARG GLU VAL THR THR ILE ILE ALA ASN ARG SEQRES 6 A 221 TYR PHE LYS LEU ASN ASP ILE TYR GLU THR ARG ASP ALA SEQRES 7 A 221 LYS VAL LYS LEU ALA LYS GLU THR LEU THR GLY ASP ALA SEQRES 8 A 221 LYS GLN GLU ALA VAL LYS ALA ALA GLU ALA GLU LYS ASP SEQRES 9 A 221 ALA ALA LEU TYR ARG THR HIS PHE ALA PHE PRO ALA ASP SEQRES 10 A 221 LEU SER LEU TYR LEU ASP ALA LYS GLN ILE ASP ALA VAL SEQRES 11 A 221 LYS ASP GLY MSE THR TYR GLY VAL VAL MSE VAL THR TYR SEQRES 12 A 221 LYS ALA THR VAL ASP MSE ILE PRO THR LEU LYS GLU GLU SEQRES 13 A 221 GLU LYS ALA GLN ILE MSE ALA TRP LEU VAL GLU ALA ARG SEQRES 14 A 221 GLU PHE ALA MSE ASP ALA GLU ASN SER ASN LYS LYS HIS SEQRES 15 A 221 ALA ALA PHE GLY LYS TYR LYS GLY ARG ILE ASN ASN TYR SEQRES 16 A 221 LEU SER LYS ARG GLY TYR ASP LEU VAL LYS GLU ARG LYS SEQRES 17 A 221 ALA TRP TYR GLU ARG ILE LYS ALA ARG GLY GLY LYS ILE MODRES 3KDW MSE A 135 MET SELENOMETHIONINE MODRES 3KDW MSE A 141 MET SELENOMETHIONINE MODRES 3KDW MSE A 150 MET SELENOMETHIONINE MODRES 3KDW MSE A 163 MET SELENOMETHIONINE MODRES 3KDW MSE A 174 MET SELENOMETHIONINE HET MSE A 135 8 HET MSE A 141 13 HET MSE A 150 8 HET MSE A 163 8 HET MSE A 174 8 HET CL A 300 1 HET MPD A 301 8 HET MRD A 302 8 HET MPD A 303 8 HET PO4 A 304 5 HET PO4 A 305 5 HET PO4 A 306 5 HET PO4 A 307 5 HET PO4 A 308 5 HET PO4 A 309 5 HET PO4 A 310 5 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM PO4 PHOSPHATE ION FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 CL CL 1- FORMUL 3 MPD 2(C6 H14 O2) FORMUL 4 MRD C6 H14 O2 FORMUL 6 PO4 7(O4 P 3-) FORMUL 13 HOH *253(H2 O) HELIX 1 1 ASP A 30 GLU A 49 1 20 HELIX 2 2 ASP A 52 LEU A 88 1 37 HELIX 3 3 THR A 89 PHE A 113 1 25 HELIX 4 4 PHE A 113 SER A 120 1 8 HELIX 5 5 ASP A 124 MSE A 135 1 12 HELIX 6 6 GLY A 138 ILE A 151 1 14 HELIX 7 7 LYS A 155 MSE A 174 1 20 HELIX 8 8 ASN A 178 ARG A 200 1 23 HELIX 9 9 ASP A 203 ARG A 218 1 16 LINK C GLY A 134 N MSE A 135 1555 1555 1.32 LINK C MSE A 135 N THR A 136 1555 1555 1.33 LINK C VAL A 140 N MSE A 141 1555 1555 1.33 LINK C MSE A 141 N VAL A 142 1555 1555 1.34 LINK C ASP A 149 N MSE A 150 1555 1555 1.33 LINK C MSE A 150 N ILE A 151 1555 1555 1.32 LINK C ILE A 162 N MSE A 163 1555 1555 1.32 LINK C MSE A 163 N ALA A 164 1555 1555 1.34 LINK C ALA A 173 N MSE A 174 1555 1555 1.33 LINK C MSE A 174 N ASP A 175 1555 1555 1.34 SITE 1 AC1 3 GLN A -1 ARG A 26 HOH A 433 SITE 1 AC2 4 HOH A 411 HOH A 422 HOH A 594 HOH A 611 SITE 1 AC3 7 LYS A 104 ARG A 110 PHE A 172 HOH A 411 SITE 2 AC3 7 HOH A 422 HOH A 594 HOH A 611 SITE 1 AC4 3 THR A 147 ASN A 194 ARG A 208 SITE 1 AC5 3 LEU A 24 ASN A 195 HOH A 523 SITE 1 AC6 4 ARG A 40 HOH A 438 HOH A 478 HOH A 531 SITE 1 AC7 8 LEU A 50 THR A 51 ASP A 52 LYS A 85 SITE 2 AC7 8 GLN A 127 HOH A 482 HOH A 524 HOH A 550 SITE 1 AC8 6 ASP A 129 ASP A 133 MSE A 141 ARG A 170 SITE 2 AC8 6 HOH A 399 HOH A 400 SITE 1 AC9 7 LYS A 155 GLU A 157 ASN A 178 SER A 179 SITE 2 AC9 7 HOH A 389 HOH A 398 HOH A 579 SITE 1 BC1 3 TYR A 144 GLU A 156 HOH A 401 SITE 1 BC2 3 SER A 120 TYR A 122 LEU A 123 CRYST1 75.303 75.303 87.128 90.00 90.00 120.00 P 31 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 0.013280 0.007667 0.000000 0.00000 SCALE2 0.000000 0.015334 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011477 0.00000 MASTER 473 0 16 9 0 0 15 6 0 0 0 17 END