HEADER HYDROLASE 13-NOV-21 7VXT TITLE CRYSTAL STRUCTURE OF A SELENOMETHIONINE-LABELED BPSL1038 FROM TITLE 2 BURKHOLDERIA PSEUDOMALLEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: BPSL1038; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA PSEUDOMALLEI K96243; SOURCE 3 ORGANISM_TAXID: 272560; SOURCE 4 STRAIN: K96243; SOURCE 5 GENE: BPSL1038; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS NUCLEASE, CAS2, DSST MOTIF, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SHAIBULLAH,M.MOHD-SHARIF,K.L.HO,M.FIRDAUS-RAIH,S.NATHAN,R.MOHAMED, AUTHOR 2 A.K.TEH,J.WATERMAN,C.L.NG REVDAT 3 15-NOV-23 7VXT 1 REMARK REVDAT 2 20-SEP-23 7VXT 1 TITLE JRNL REVDAT 1 16-AUG-23 7VXT 0 JRNL AUTH S.SHAIBULLAH,N.SHUHAIMI,D.S.KER,N.MOHD-SHARIF,K.L.HO, JRNL AUTH 2 A.H.TEH,J.WATERMAN,T.H.TANG,R.R.WONG,S.NATHAN,R.MOHAMED, JRNL AUTH 3 M.J.NG,S.Y.FUNG,M.A.JONET,M.FIRDAUS-RAIH,C.L.NG JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSES OF BURKHOLDERIA JRNL TITL 2 PSEUDOMALLEI BPSL1038 REVEAL A CAS-2/VAPD NUCLEASE JRNL TITL 3 SUB-FAMILY. JRNL REF COMMUN BIOL V. 6 920 2023 JRNL REFN ESSN 2399-3642 JRNL PMID 37684342 JRNL DOI 10.1038/S42003-023-05265-4 REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18347 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) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1016 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.88 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1276 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1472 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.01000 REMARK 3 B22 (A**2) : -2.39000 REMARK 3 B33 (A**2) : -0.62000 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): 0.110 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.974 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1606 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1494 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2198 ; 2.155 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3443 ; 1.391 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 214 ; 6.011 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;41.489 ;25.128 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 245 ;13.772 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ; 5.269 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 258 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1864 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 379 ; 0.005 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 2 86 B 2 86 4136 0.190 0.050 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 -13 A 87 REMARK 3 ORIGIN FOR THE GROUP (A): 29.2513 10.0401 17.4096 REMARK 3 T TENSOR REMARK 3 T11: 0.0457 T22: 0.0688 REMARK 3 T33: 0.0303 T12: 0.0208 REMARK 3 T13: 0.0172 T23: 0.0384 REMARK 3 L TENSOR REMARK 3 L11: 0.1116 L22: 0.9275 REMARK 3 L33: 0.9319 L12: -0.2714 REMARK 3 L13: 0.0427 L23: -0.1491 REMARK 3 S TENSOR REMARK 3 S11: 0.0068 S12: -0.0347 S13: -0.0106 REMARK 3 S21: -0.0722 S22: -0.0380 S23: -0.0573 REMARK 3 S31: 0.1149 S32: -0.0259 S33: 0.0312 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 87 REMARK 3 ORIGIN FOR THE GROUP (A): 26.5751 21.9692 7.5877 REMARK 3 T TENSOR REMARK 3 T11: 0.0488 T22: 0.0677 REMARK 3 T33: 0.0198 T12: 0.0391 REMARK 3 T13: 0.0068 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.2844 L22: 0.8989 REMARK 3 L33: 0.6565 L12: -0.4498 REMARK 3 L13: -0.1142 L23: 0.0065 REMARK 3 S TENSOR REMARK 3 S11: 0.0572 S12: 0.0149 S13: 0.0285 REMARK 3 S21: -0.1327 S22: -0.0887 S23: -0.0306 REMARK 3 S31: -0.0318 S32: -0.0304 S33: 0.0315 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 7VXT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1300025613. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97972 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19376 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 28.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.64500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 4.6, 2 M REMARK 280 SODIUM FORMATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.40600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.40600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 42.86300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.94550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.86300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.94550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 23.40600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.86300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.94550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 23.40600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.86300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.94550 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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 GLU A 88 REMARK 465 MSE B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MSE B 1 REMARK 465 GLU B 88 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 HIS A -13 CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 15 O HOH A 201 2.08 REMARK 500 OE1 GLU A 65 O HOH A 202 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 245 O HOH B 207 1556 2.19 REMARK 500 O HOH B 202 O HOH B 263 6555 2.19 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 MSE A 1 CG - SE - CE ANGL. DEV. = 23.4 DEGREES REMARK 500 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 10 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 MSE A 40 CG - SE - CE ANGL. DEV. = -16.0 DEGREES REMARK 500 MSE B 40 CG - SE - CE ANGL. DEV. = -36.1 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 ARG A -3 142.83 -171.70 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 NA A 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 42 O REMARK 620 2 GLU A 65 OE1 121.9 REMARK 620 3 GLU A 65 OE2 118.1 23.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 104 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 58 OH REMARK 620 2 ASP B 50 OD1 33.6 REMARK 620 3 THR B 84 OG1 6.7 32.1 REMARK 620 4 HOH B 258 O 36.0 3.0 34.8 REMARK 620 N 1 2 3 DBREF 7VXT A 1 88 UNP Q63W52 Q63W52_BURPS 1 88 DBREF 7VXT B 1 88 UNP Q63W52 Q63W52_BURPS 1 88 SEQADV 7VXT MSE A -19 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT GLY A -18 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT SER A -17 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT SER A -16 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS A -15 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS A -14 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS A -13 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS A -12 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS A -11 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS A -10 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT SER A -9 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT SER A -8 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT GLY A -7 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT LEU A -6 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT VAL A -5 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT PRO A -4 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT ARG A -3 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT GLY A -2 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT SER A -1 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS A 0 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT MSE B -19 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT GLY B -18 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT SER B -17 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT SER B -16 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS B -15 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS B -14 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS B -13 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS B -12 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS B -11 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS B -10 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT SER B -9 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT SER B -8 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT GLY B -7 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT LEU B -6 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT VAL B -5 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT PRO B -4 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT ARG B -3 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT GLY B -2 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT SER B -1 UNP Q63W52 EXPRESSION TAG SEQADV 7VXT HIS B 0 UNP Q63W52 EXPRESSION TAG SEQRES 1 A 108 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 108 LEU VAL PRO ARG GLY SER HIS MSE ALA GLY ASN LEU VAL SEQRES 3 A 108 ILE VAL CYS ARG ASP GLN ASP ALA ASP ALA PHE ASP GLN SEQRES 4 A 108 LEU MSE GLN GLU TYR GLY SER PHE GLN THR ARG LEU SER SEQRES 5 A 108 SER THR ALA TRP TYR LEU ASN MSE ASN ILE VAL PRO GLU SEQRES 6 A 108 THR LEU GLN GLU ASP ILE LEU GLU ARG VAL GLY LYS TYR SEQRES 7 A 108 THR THR LEU TYR ILE PHE GLU ALA THR SER VAL THR TYR SEQRES 8 A 108 ASN THR ILE ASP SER ASN ALA ALA GLU THR LEU SER THR SEQRES 9 A 108 LEU PHE GLY GLU SEQRES 1 B 108 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 108 LEU VAL PRO ARG GLY SER HIS MSE ALA GLY ASN LEU VAL SEQRES 3 B 108 ILE VAL CYS ARG ASP GLN ASP ALA ASP ALA PHE ASP GLN SEQRES 4 B 108 LEU MSE GLN GLU TYR GLY SER PHE GLN THR ARG LEU SER SEQRES 5 B 108 SER THR ALA TRP TYR LEU ASN MSE ASN ILE VAL PRO GLU SEQRES 6 B 108 THR LEU GLN GLU ASP ILE LEU GLU ARG VAL GLY LYS TYR SEQRES 7 B 108 THR THR LEU TYR ILE PHE GLU ALA THR SER VAL THR TYR SEQRES 8 B 108 ASN THR ILE ASP SER ASN ALA ALA GLU THR LEU SER THR SEQRES 9 B 108 LEU PHE GLY GLU MODRES 7VXT MSE A 1 MET MODIFIED RESIDUE MODRES 7VXT MSE A 21 MET MODIFIED RESIDUE MODRES 7VXT MSE A 40 MET MODIFIED RESIDUE MODRES 7VXT MSE B 21 MET MODIFIED RESIDUE MODRES 7VXT MSE B 40 MET MODIFIED RESIDUE HET MSE A 1 13 HET MSE A 21 8 HET MSE A 40 13 HET MSE B 21 8 HET MSE B 40 13 HET BME A 101 4 HET BME A 102 4 HET NA A 103 1 HET BME B 101 4 HET BME B 102 4 HET BME B 103 4 HET NA B 104 1 HETNAM MSE SELENOMETHIONINE HETNAM BME BETA-MERCAPTOETHANOL HETNAM NA SODIUM ION FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 3 BME 5(C2 H6 O S) FORMUL 5 NA 2(NA 1+) FORMUL 10 HOH *158(H2 O) HELIX 1 AA1 ASP A 13 GLN A 22 1 10 HELIX 2 AA2 GLU A 23 SER A 26 5 4 HELIX 3 AA3 VAL A 43 GLY A 56 1 14 HELIX 4 AA4 ASP A 75 GLY A 87 1 13 HELIX 5 AA5 ASP B 13 GLN B 22 1 10 HELIX 6 AA6 GLU B 23 SER B 26 5 4 HELIX 7 AA7 VAL B 43 GLY B 56 1 14 HELIX 8 AA8 ASP B 75 PHE B 86 1 12 SHEET 1 AA1 5 HIS A -11 SER A -8 0 SHEET 2 AA1 5 LEU A 61 ASN A 72 -1 O TYR A 71 N HIS A -10 SHEET 3 AA1 5 ASN A 4 CYS A 9 -1 N VAL A 6 O PHE A 64 SHEET 4 AA1 5 ALA A 35 ASN A 39 -1 O LEU A 38 N LEU A 5 SHEET 5 AA1 5 GLN A 28 SER A 32 -1 N LEU A 31 O ALA A 35 SHEET 1 AA2 6 HIS A -11 SER A -8 0 SHEET 2 AA2 6 LEU A 61 ASN A 72 -1 O TYR A 71 N HIS A -10 SHEET 3 AA2 6 LEU B 61 ASN B 72 -1 O THR B 70 N ILE A 63 SHEET 4 AA2 6 ASN B 4 CYS B 9 -1 N ASN B 4 O ALA B 66 SHEET 5 AA2 6 ALA B 35 ASN B 39 -1 O LEU B 38 N LEU B 5 SHEET 6 AA2 6 GLN B 28 SER B 32 -1 N THR B 29 O TYR B 37 LINK C HIS A 0 N MSE A 1 1555 1555 1.34 LINK C MSE A 1 N ALA A 2 1555 1555 1.33 LINK C LEU A 20 N MSE A 21 1555 1555 1.33 LINK C MSE A 21 N GLN A 22 1555 1555 1.33 LINK C ASN A 39 N MSE A 40 1555 1555 1.31 LINK C MSE A 40 N ASN A 41 1555 1555 1.34 LINK C LEU B 20 N MSE B 21 1555 1555 1.34 LINK C MSE B 21 N GLN B 22 1555 1555 1.33 LINK C ASN B 39 N MSE B 40 1555 1555 1.32 LINK C MSE B 40 N ASN B 41 1555 1555 1.34 LINK O ILE A 42 NA NA A 103 1555 1555 2.69 LINK OH TYR A 58 NA NA B 104 1555 1556 2.65 LINK OE1AGLU A 65 NA NA A 103 1555 1555 3.11 LINK OE2BGLU A 65 NA NA A 103 1555 1555 2.16 LINK OD1 ASP B 50 NA NA B 104 1555 1555 2.48 LINK OG1 THR B 84 NA NA B 104 1555 6555 2.82 LINK NA NA B 104 O HOH B 258 1555 1555 3.13 CRYST1 85.726 115.891 46.812 90.00 90.00 90.00 C 2 2 21 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 0.011665 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008629 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021362 0.00000