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 5 01-FEB-23 3KDW 1 REMARK SEQADV 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 EXPRESSION TAG SEQADV 3KDW GLY A -17 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW SER A -16 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW ASP A -15 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW LYS A -14 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW ILE A -13 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW HIS A -12 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW HIS A -11 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW HIS A -10 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW HIS A -9 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW HIS A -8 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW HIS A -7 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW GLU A -6 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW ASN A -5 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW LEU A -4 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW TYR A -3 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW PHE A -2 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW GLN A -1 UNP A6L4E1 EXPRESSION TAG SEQADV 3KDW GLY A 0 UNP A6L4E1 EXPRESSION TAG 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