HEADER HYDROLASE 10-JAN-08 3BWV TITLE CRYSTAL STRUCTURE OF DEOXYRIBONUCLEOTIDASE-LIKE PROTEIN (NP_764060.1) TITLE 2 FROM STAPHYLOCOCCUS EPIDERMIDIS ATCC 12228 AT 1.55 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE 5'(3')-DEOXYRIBONUCLEOTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.3.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS EPIDERMIDIS; SOURCE 3 ORGANISM_TAXID: 176280; SOURCE 4 STRAIN: ATCC 12228; SOURCE 5 GENE: NP_764060.1, SE_0505; 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 NP_764060.1, DEOXYRIBONUCLEOTIDASE-LIKE PROTEIN, STRUCTURAL GENOMICS, KEYWDS 2 JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, PSI-2, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 25-JAN-23 3BWV 1 REMARK SEQADV LINK REVDAT 5 24-JUL-19 3BWV 1 REMARK LINK REVDAT 4 25-OCT-17 3BWV 1 REMARK REVDAT 3 13-JUL-11 3BWV 1 VERSN REVDAT 2 24-FEB-09 3BWV 1 VERSN REVDAT 1 22-JAN-08 3BWV 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF DEOXYRIBONUCLEOTIDASE-LIKE PROTEIN JRNL TITL 2 (NP_764060.1) FROM STAPHYLOCOCCUS EPIDERMIDIS ATCC 12228 AT JRNL TITL 3 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 5.4.0066 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) : 29.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 43194 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2176 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) : 2792 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2700 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 181 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 27.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : -0.79000 REMARK 3 B33 (A**2) : 0.54000 REMARK 3 B12 (A**2) : -0.21000 REMARK 3 B13 (A**2) : -0.58000 REMARK 3 B23 (A**2) : 0.77000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.095 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.605 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2819 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1879 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3832 ; 1.634 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4576 ; 1.044 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 349 ; 5.971 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 144 ;35.647 ;24.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 476 ;13.772 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;21.593 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 422 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3154 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 602 ; 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): 1698 ; 1.004 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 680 ; 0.301 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2748 ; 1.748 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1121 ; 3.105 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1074 ; 4.812 ; 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 : 4 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 178 REMARK 3 ORIGIN FOR THE GROUP (A): 16.4425 19.0579 44.5968 REMARK 3 T TENSOR REMARK 3 T11: -0.0429 T22: -0.0424 REMARK 3 T33: -0.0632 T12: -0.0036 REMARK 3 T13: -0.0008 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 2.6255 L22: 1.8546 REMARK 3 L33: 1.5402 L12: -0.0568 REMARK 3 L13: -0.2049 L23: -0.5095 REMARK 3 S TENSOR REMARK 3 S11: 0.0451 S12: -0.0373 S13: -0.2010 REMARK 3 S21: 0.0031 S22: 0.0445 S23: 0.1524 REMARK 3 S31: 0.0587 S32: -0.0611 S33: -0.0896 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 300 A 300 REMARK 3 ORIGIN FOR THE GROUP (A): 15.9106 15.2850 41.5251 REMARK 3 T TENSOR REMARK 3 T11: -0.0237 T22: -0.0504 REMARK 3 T33: 0.0036 T12: -0.0243 REMARK 3 T13: -0.0392 T23: -0.0117 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 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 : B 3 B 178 REMARK 3 ORIGIN FOR THE GROUP (A): 16.8090 35.1872 19.5333 REMARK 3 T TENSOR REMARK 3 T11: -0.0012 T22: -0.0453 REMARK 3 T33: -0.0388 T12: -0.0037 REMARK 3 T13: 0.0035 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 2.1807 L22: 1.1639 REMARK 3 L33: 1.3943 L12: -0.4027 REMARK 3 L13: 0.1575 L23: -0.5759 REMARK 3 S TENSOR REMARK 3 S11: 0.0158 S12: -0.0169 S13: 0.0008 REMARK 3 S21: -0.0287 S22: 0.0326 S23: 0.1476 REMARK 3 S31: -0.0099 S32: -0.0384 S33: -0.0483 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 : B 300 B 300 REMARK 3 ORIGIN FOR THE GROUP (A): 16.3695 38.4765 22.5175 REMARK 3 T TENSOR REMARK 3 T11: 0.0290 T22: -0.0212 REMARK 3 T33: -0.0711 T12: 0.0070 REMARK 3 T13: 0.0345 T23: -0.0936 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 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. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. REMARK 3 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. REMARK 3 4. MG AND CL MODELED BASED ON GEOMETRY AND CRYSTALLIZATION REMARK 3 CONDITIONS. REMARK 4 REMARK 4 3BWV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000046056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-07 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 : 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, 0.97908, 0.97959 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(111) BENT REMARK 200 (HORIZONTAL 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 : 43195 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 29.235 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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 (%): 34.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NANODROP, 17.6% PEG 3350, 0.4M REMARK 280 MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2000 ANGSTROM**2 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 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 LYS A 44 REMARK 465 HIS A 45 REMARK 465 MSE A 46 REMARK 465 ILE A 47 REMARK 465 PRO A 48 REMARK 465 GLU A 49 REMARK 465 HIS A 50 REMARK 465 GLU A 51 REMARK 465 MSE A 93 REMARK 465 ASP A 94 REMARK 465 LYS A 179 REMARK 465 GLY B 0 REMARK 465 MSE B 1 REMARK 465 THR B 2 REMARK 465 LYS B 44 REMARK 465 HIS B 45 REMARK 465 MSE B 46 REMARK 465 ILE B 47 REMARK 465 PRO B 48 REMARK 465 GLU B 49 REMARK 465 HIS B 50 REMARK 465 GLU B 51 REMARK 465 LYS B 179 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 THR A 2 OG1 CG2 REMARK 470 LYS A 34 CG CD CE NZ REMARK 470 GLU A 36 CG CD OE1 OE2 REMARK 470 LYS A 42 CE NZ REMARK 470 LEU A 43 CG CD1 CD2 REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 VAL A 95 CG1 CG2 REMARK 470 LYS A 138 CD CE NZ REMARK 470 GLU A 178 CG CD OE1 OE2 REMARK 470 ASP B 30 CG OD1 OD2 REMARK 470 LYS B 34 CD CE NZ REMARK 470 GLU B 36 CD OE1 OE2 REMARK 470 LYS B 42 CD CE NZ REMARK 470 LYS B 59 CG CD CE NZ REMARK 470 GLU B 75 CG CD OE1 OE2 REMARK 470 LYS B 78 CE NZ REMARK 470 ASP B 94 CG OD1 OD2 REMARK 470 GLU B 104 CD OE1 OE2 REMARK 470 LYS B 138 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 LYS A 41 CE LYS A 41 NZ 0.158 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 LEU A 132 CB - CG - CD2 ANGL. DEV. = -14.8 DEGREES REMARK 500 ASP B 134 CB - CG - OD1 ANGL. DEV. = 5.5 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 VAL A 13 -69.28 -136.49 REMARK 500 ASN A 32 50.05 -141.51 REMARK 500 VAL B 13 -62.65 -125.96 REMARK 500 VAL B 95 70.25 55.01 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 MG A 300 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 9 OD2 REMARK 620 2 ASP A 11 O 91.9 REMARK 620 3 ASP A 135 OD1 90.4 91.9 REMARK 620 4 HOH A 374 O 177.3 86.1 87.8 REMARK 620 5 HOH A 378 O 90.5 99.2 168.9 91.7 REMARK 620 6 HOH A 384 O 90.2 173.9 82.3 91.6 86.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 300 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 9 OD2 REMARK 620 2 ASP B 11 O 91.1 REMARK 620 3 ASP B 135 OD1 89.4 94.4 REMARK 620 4 HOH B 383 O 87.4 178.4 86.0 REMARK 620 5 HOH B 386 O 177.3 89.9 88.1 91.7 REMARK 620 6 HOH B 387 O 93.4 96.2 169.0 83.5 89.0 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 MG A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 376319 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT USED FOR REFINEMENT WAS EXPRESSED WITH REMARK 999 A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMARK 999 REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) REMARK 999 FOLLOWED BY THE TARGET SEQUENCE. DBREF 3BWV A 1 179 UNP Q8CTG7 53DR_STAES 1 179 DBREF 3BWV B 1 179 UNP Q8CTG7 53DR_STAES 1 179 SEQADV 3BWV GLY A 0 UNP Q8CTG7 EXPRESSION TAG SEQADV 3BWV GLY B 0 UNP Q8CTG7 EXPRESSION TAG SEQRES 1 A 180 GLY MSE THR ARG GLN ARG ILE ALA ILE ASP MSE ASP GLU SEQRES 2 A 180 VAL LEU ALA ASP THR LEU GLY ALA VAL VAL LYS ALA VAL SEQRES 3 A 180 ASN GLU ARG ALA ASP LEU ASN ILE LYS MSE GLU SER LEU SEQRES 4 A 180 ASN GLY LYS LYS LEU LYS HIS MSE ILE PRO GLU HIS GLU SEQRES 5 A 180 GLY LEU VAL MSE ASP ILE LEU LYS GLU PRO GLY PHE PHE SEQRES 6 A 180 ARG ASN LEU ASP VAL MSE PRO HIS ALA GLN GLU VAL VAL SEQRES 7 A 180 LYS GLN LEU ASN GLU HIS TYR ASP ILE TYR ILE ALA THR SEQRES 8 A 180 ALA ALA MSE ASP VAL PRO THR SER PHE HIS ASP LYS TYR SEQRES 9 A 180 GLU TRP LEU LEU GLU TYR PHE PRO PHE LEU ASP PRO GLN SEQRES 10 A 180 HIS PHE VAL PHE CYS GLY ARG LYS ASN ILE ILE LEU ALA SEQRES 11 A 180 ASP TYR LEU ILE ASP ASP ASN PRO LYS GLN LEU GLU ILE SEQRES 12 A 180 PHE GLU GLY LYS SER ILE MSE PHE THR ALA SER HIS ASN SEQRES 13 A 180 VAL TYR GLU HIS ARG PHE GLU ARG VAL SER GLY TRP ARG SEQRES 14 A 180 ASP VAL LYS ASN TYR PHE ASN SER ILE GLU LYS SEQRES 1 B 180 GLY MSE THR ARG GLN ARG ILE ALA ILE ASP MSE ASP GLU SEQRES 2 B 180 VAL LEU ALA ASP THR LEU GLY ALA VAL VAL LYS ALA VAL SEQRES 3 B 180 ASN GLU ARG ALA ASP LEU ASN ILE LYS MSE GLU SER LEU SEQRES 4 B 180 ASN GLY LYS LYS LEU LYS HIS MSE ILE PRO GLU HIS GLU SEQRES 5 B 180 GLY LEU VAL MSE ASP ILE LEU LYS GLU PRO GLY PHE PHE SEQRES 6 B 180 ARG ASN LEU ASP VAL MSE PRO HIS ALA GLN GLU VAL VAL SEQRES 7 B 180 LYS GLN LEU ASN GLU HIS TYR ASP ILE TYR ILE ALA THR SEQRES 8 B 180 ALA ALA MSE ASP VAL PRO THR SER PHE HIS ASP LYS TYR SEQRES 9 B 180 GLU TRP LEU LEU GLU TYR PHE PRO PHE LEU ASP PRO GLN SEQRES 10 B 180 HIS PHE VAL PHE CYS GLY ARG LYS ASN ILE ILE LEU ALA SEQRES 11 B 180 ASP TYR LEU ILE ASP ASP ASN PRO LYS GLN LEU GLU ILE SEQRES 12 B 180 PHE GLU GLY LYS SER ILE MSE PHE THR ALA SER HIS ASN SEQRES 13 B 180 VAL TYR GLU HIS ARG PHE GLU ARG VAL SER GLY TRP ARG SEQRES 14 B 180 ASP VAL LYS ASN TYR PHE ASN SER ILE GLU LYS MODRES 3BWV MSE A 10 MET SELENOMETHIONINE MODRES 3BWV MSE A 35 MET SELENOMETHIONINE MODRES 3BWV MSE A 55 MET SELENOMETHIONINE MODRES 3BWV MSE A 70 MET SELENOMETHIONINE MODRES 3BWV MSE A 149 MET SELENOMETHIONINE MODRES 3BWV MSE B 10 MET SELENOMETHIONINE MODRES 3BWV MSE B 35 MET SELENOMETHIONINE MODRES 3BWV MSE B 55 MET SELENOMETHIONINE MODRES 3BWV MSE B 70 MET SELENOMETHIONINE MODRES 3BWV MSE B 93 MET SELENOMETHIONINE MODRES 3BWV MSE B 149 MET SELENOMETHIONINE HET MSE A 10 13 HET MSE A 35 8 HET MSE A 55 8 HET MSE A 70 8 HET MSE A 149 8 HET MSE B 10 13 HET MSE B 35 8 HET MSE B 55 8 HET MSE B 70 8 HET MSE B 93 8 HET MSE B 149 13 HET MG A 300 1 HET MG B 300 1 HET CL B 301 1 HET CL B 302 1 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 3 MG 2(MG 2+) FORMUL 5 CL 2(CL 1-) FORMUL 7 HOH *181(H2 O) HELIX 1 1 ASP A 16 ALA A 29 1 14 HELIX 2 2 LYS A 34 LEU A 38 5 5 HELIX 3 3 GLY A 52 GLU A 60 1 9 HELIX 4 4 GLY A 62 ASN A 66 5 5 HELIX 5 5 HIS A 72 ASN A 81 1 10 HELIX 6 6 THR A 97 PHE A 110 1 14 HELIX 7 7 ASP A 114 GLN A 116 5 3 HELIX 8 8 ARG A 123 ILE A 127 5 5 HELIX 9 9 ASN A 136 PHE A 143 1 8 HELIX 10 10 ALA A 152 VAL A 156 5 5 HELIX 11 11 GLY A 166 GLU A 178 1 13 HELIX 12 12 ASP B 16 ALA B 29 1 14 HELIX 13 13 LYS B 34 ASN B 39 5 6 HELIX 14 14 GLY B 52 GLU B 60 1 9 HELIX 15 15 HIS B 72 ASN B 81 1 10 HELIX 16 16 VAL B 95 THR B 97 5 3 HELIX 17 17 SER B 98 PHE B 110 1 13 HELIX 18 18 ASP B 114 GLN B 116 5 3 HELIX 19 19 ARG B 123 ILE B 127 5 5 HELIX 20 20 ASN B 136 GLU B 141 1 6 HELIX 21 21 ALA B 152 VAL B 156 5 5 HELIX 22 22 GLY B 166 GLU B 178 1 13 SHEET 1 A 6 PHE A 118 PHE A 120 0 SHEET 2 A 6 ASP A 85 THR A 90 1 N ILE A 88 O VAL A 119 SHEET 3 A 6 ARG A 5 ASP A 9 1 N ILE A 6 O TYR A 87 SHEET 4 A 6 TYR A 131 ASP A 134 1 O TYR A 131 N ALA A 7 SHEET 5 A 6 LYS A 146 PHE A 150 1 O ILE A 148 N LEU A 132 SHEET 6 A 6 GLU A 162 VAL A 164 1 O VAL A 164 N MSE A 149 SHEET 1 B 6 PHE B 118 PHE B 120 0 SHEET 2 B 6 ASP B 85 THR B 90 1 N ILE B 88 O VAL B 119 SHEET 3 B 6 ARG B 5 ASP B 9 1 N ILE B 6 O ASP B 85 SHEET 4 B 6 TYR B 131 ASP B 134 1 O TYR B 131 N ALA B 7 SHEET 5 B 6 LYS B 146 PHE B 150 1 O ILE B 148 N LEU B 132 SHEET 6 B 6 GLU B 162 VAL B 164 1 O GLU B 162 N MSE B 149 LINK C ASP A 9 N MSE A 10 1555 1555 1.34 LINK C MSE A 10 N ASP A 11 1555 1555 1.32 LINK C LYS A 34 N MSE A 35 1555 1555 1.33 LINK C MSE A 35 N GLU A 36 1555 1555 1.34 LINK C VAL A 54 N MSE A 55 1555 1555 1.33 LINK C MSE A 55 N ASP A 56 1555 1555 1.33 LINK C VAL A 69 N MSE A 70 1555 1555 1.33 LINK C MSE A 70 N PRO A 71 1555 1555 1.34 LINK C ILE A 148 N MSE A 149 1555 1555 1.33 LINK C MSE A 149 N PHE A 150 1555 1555 1.33 LINK C ASP B 9 N MSE B 10 1555 1555 1.32 LINK C MSE B 10 N ASP B 11 1555 1555 1.34 LINK C LYS B 34 N MSE B 35 1555 1555 1.32 LINK C MSE B 35 N GLU B 36 1555 1555 1.32 LINK C VAL B 54 N MSE B 55 1555 1555 1.33 LINK C MSE B 55 N ASP B 56 1555 1555 1.33 LINK C VAL B 69 N MSE B 70 1555 1555 1.32 LINK C MSE B 70 N PRO B 71 1555 1555 1.36 LINK C ALA B 92 N MSE B 93 1555 1555 1.34 LINK C MSE B 93 N ASP B 94 1555 1555 1.33 LINK C ILE B 148 N MSE B 149 1555 1555 1.33 LINK C MSE B 149 N PHE B 150 1555 1555 1.34 LINK OD2 ASP A 9 MG MG A 300 1555 1555 1.97 LINK O ASP A 11 MG MG A 300 1555 1555 2.12 LINK OD1 ASP A 135 MG MG A 300 1555 1555 2.06 LINK MG MG A 300 O HOH A 374 1555 1555 2.13 LINK MG MG A 300 O HOH A 378 1555 1555 1.98 LINK MG MG A 300 O HOH A 384 1555 1555 1.99 LINK OD2 ASP B 9 MG MG B 300 1555 1555 2.08 LINK O ASP B 11 MG MG B 300 1555 1555 2.07 LINK OD1 ASP B 135 MG MG B 300 1555 1555 2.07 LINK MG MG B 300 O HOH B 383 1555 1555 2.19 LINK MG MG B 300 O HOH B 386 1555 1555 2.12 LINK MG MG B 300 O HOH B 387 1555 1555 2.08 SITE 1 AC1 6 ASP A 9 ASP A 11 ASP A 135 HOH A 374 SITE 2 AC1 6 HOH A 378 HOH A 384 SITE 1 AC2 6 ASP B 9 ASP B 11 ASP B 135 HOH B 383 SITE 2 AC2 6 HOH B 386 HOH B 387 CRYST1 39.310 40.270 55.310 71.93 75.08 83.62 P 1 2 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 0.025439 -0.002843 -0.006217 0.00000 SCALE2 0.000000 0.024987 -0.007662 0.00000 SCALE3 0.000000 0.000000 0.019570 0.00000