HEADER CNMP-BINDING PROTEIN 17-APR-09 3H3Z TITLE CRYSTAL STRUCTURE OF A PUTATIVE CYCLIC NUCLEOTIDE BINDING PROTEIN TITLE 2 (SPOA0323) FROM RUEGERIA POMEROYI DSS-3 AT 2.35 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIC NUCLEOTIDE-BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PUTATIVE CAMP-BINDING REGULATORY PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RUEGERIA POMEROYI DSS-3; SOURCE 3 ORGANISM_TAXID: 246200; SOURCE 4 GENE: SPOA0323, YP_165150.1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS CYCLIC NUCLEOTIDE-BINDING DOMAIN, STRUCTURAL GENOMICS, JOINT CENTER KEYWDS 2 FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, KEYWDS 3 CNMP-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3H3Z 1 REMARK SEQADV REVDAT 4 24-JUL-19 3H3Z 1 REMARK LINK REVDAT 3 25-OCT-17 3H3Z 1 REMARK REVDAT 2 23-MAR-11 3H3Z 1 HEADER TITLE KEYWDS REVDAT 1 05-MAY-09 3H3Z 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE CAMP-BINDING REGULATORY JRNL TITL 2 PROTEIN (YP_165150.1) FROM SILICIBACTER POMEROYI DSS-3 AT JRNL TITL 3 2.35 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 27596 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1409 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1919 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3391 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 98 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.62000 REMARK 3 B22 (A**2) : -0.62000 REMARK 3 B33 (A**2) : 0.94000 REMARK 3 B12 (A**2) : -0.31000 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): 0.267 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.209 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.159 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.698 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3565 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2339 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4863 ; 1.725 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5729 ; 1.055 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 473 ; 3.534 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;32.134 ;23.696 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 578 ;12.223 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.271 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 572 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4043 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 706 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 780 ; 0.214 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2407 ; 0.176 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1737 ; 0.180 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 1811 ; 0.094 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 193 ; 0.163 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.011 ; 0.500 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): 15 ; 0.135 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 35 ; 0.317 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.158 ; 0.500 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): 2437 ; 2.094 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 930 ; 0.685 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3741 ; 3.417 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1322 ; 6.013 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1122 ; 8.009 ;11.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 143 5 REMARK 3 1 B 1 B 143 5 REMARK 3 2 A 155 A 223 5 REMARK 3 2 B 155 B 223 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1227 ; 0.240 ; 0.500 REMARK 3 LOOSE POSITIONAL 1 A (A): 1331 ; 0.540 ; 5.000 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1227 ; 1.590 ; 2.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 1331 ; 3.670 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN 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. REMARK 3 4.CHLORIDE IONS FROM CRYSTALLIZATION ARE MODELED IN THE REMARK 3 STRUCTURE. REMARK 4 REMARK 4 3H3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052662. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-09; 12-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SSRL; APS REMARK 200 BEAMLINE : BL9-2; 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946; 0.97967,0.94645 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR; REMARK 200 SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMETER REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, TOROID REMARK 200 FOCUSING MIRROR; ADJUSTABLE REMARK 200 FOCUSING MIRRORS IN K-B GEOMETRY REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD; MARMOSAIC REMARK 200 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27604 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 28.724 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.820 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.60300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2600M (NH4)2SO4, 0.1M CACODYLATE PH REMARK 280 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, TEMPERATURE 277K, REMARK 280 VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 68.52600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.56350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.64567 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 68.52600 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 39.56350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 31.64567 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 68.52600 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 39.56350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.64567 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 79.12701 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 63.29133 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 79.12701 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 63.29133 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 79.12701 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 63.29133 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: THE RESULTS FROM SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE REMARK 300 ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 GLY A 0 REMARK 465 PRO A 227 REMARK 465 ALA A 228 REMARK 465 ASP A 229 REMARK 465 SER A 230 REMARK 465 TRP A 231 REMARK 465 SER A 232 REMARK 465 LYS A 233 REMARK 465 SER A 234 REMARK 465 GLY B 0 REMARK 465 MSE B 1 REMARK 465 ALA B 2 REMARK 465 PRO B 227 REMARK 465 ALA B 228 REMARK 465 ASP B 229 REMARK 465 SER B 234 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 ARG A 38 CZ NH1 NH2 REMARK 470 LYS A 48 CD CE NZ REMARK 470 ARG A 79 NH1 NH2 REMARK 470 LYS A 147 CD CE NZ REMARK 470 GLU A 161 CD OE1 OE2 REMARK 470 ASP A 164 CG OD1 OD2 REMARK 470 ASP A 166 OD1 OD2 REMARK 470 THR A 167 OG1 CG2 REMARK 470 CYS A 170 SG REMARK 470 LYS A 178 NZ REMARK 470 LYS A 188 CG CD CE NZ REMARK 470 GLU A 190 CG CD OE1 OE2 REMARK 470 SER A 197 OG REMARK 470 VAL A 206 CG1 CG2 REMARK 470 LYS A 207 CG CD CE NZ REMARK 470 ARG A 208 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 210 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 213 CG1 CG2 CD1 REMARK 470 GLU A 214 CG CD OE1 OE2 REMARK 470 ALA A 217 CB REMARK 470 ARG A 220 NE CZ NH1 NH2 REMARK 470 GLU A 224 OE1 OE2 REMARK 470 SER A 225 OG REMARK 470 ASP A 226 CG OD1 OD2 REMARK 470 ARG B 38 CZ NH1 NH2 REMARK 470 LYS B 48 CD CE NZ REMARK 470 ARG B 64 NE CZ NH1 NH2 REMARK 470 ARG B 79 NH1 NH2 REMARK 470 ASP B 164 CG OD1 OD2 REMARK 470 GLU B 171 CD OE1 OE2 REMARK 470 LYS B 178 NZ REMARK 470 LYS B 188 CG CD CE NZ REMARK 470 GLU B 190 OE1 OE2 REMARK 470 ARG B 194 NE CZ NH1 NH2 REMARK 470 LYS B 200 CE NZ REMARK 470 VAL B 204 CG1 CG2 REMARK 470 LYS B 207 CD CE NZ REMARK 470 ARG B 208 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 210 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 214 CG CD OE1 OE2 REMARK 470 ARG B 220 NE CZ NH1 NH2 REMARK 470 SER B 225 OG REMARK 470 ASP B 226 CG OD1 OD2 REMARK 470 SER B 230 OG REMARK 470 LYS B 233 CG 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 CYS A 104 CB CYS A 104 SG -0.142 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 ARG A 17 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 CYS B 104 CA - CB - SG ANGL. DEV. = 10.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 46 -6.45 76.97 REMARK 500 ARG A 79 121.76 -33.62 REMARK 500 ASP A 164 -37.77 81.74 REMARK 500 GLU A 224 47.60 -98.05 REMARK 500 GLU B 46 -7.01 71.22 REMARK 500 ARG B 79 122.19 -31.93 REMARK 500 SER B 225 152.36 -45.65 REMARK 500 REMARK 500 REMARK: NULL 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 235 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 235 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 391453 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3H3Z A 1 234 UNP Q5LKQ8 Q5LKQ8_SILPO 1 234 DBREF 3H3Z B 1 234 UNP Q5LKQ8 Q5LKQ8_SILPO 1 234 SEQADV 3H3Z GLY A 0 UNP Q5LKQ8 EXPRESSION TAG SEQADV 3H3Z GLY B 0 UNP Q5LKQ8 EXPRESSION TAG SEQRES 1 A 235 GLY MSE ALA HIS GLU ALA GLN LYS ALA ILE ALA ARG ASN SEQRES 2 A 235 SER LEU LEU ILE ARG SER LEU PRO GLU GLN HIS VAL ASP SEQRES 3 A 235 ALA LEU LEU SER GLN ALA VAL TRP ARG SER TYR ASP ARG SEQRES 4 A 235 GLY GLU THR LEU PHE LEU GLN GLU GLU LYS ALA GLN ALA SEQRES 5 A 235 ILE HIS VAL VAL ILE ASP GLY TRP VAL LYS LEU PHE ARG SEQRES 6 A 235 MSE THR PRO THR GLY SER GLU ALA VAL VAL SER VAL PHE SEQRES 7 A 235 THR ARG GLY GLU SER PHE GLY GLU ALA VAL ALA LEU ARG SEQRES 8 A 235 ASN THR PRO TYR PRO VAL SER ALA GLU ALA VAL THR PRO SEQRES 9 A 235 CYS GLU VAL MSE HIS ILE PRO SER PRO VAL PHE VAL SER SEQRES 10 A 235 LEU MSE ARG ARG ASP PRO GLU ILE CYS ILE SER ILE LEU SEQRES 11 A 235 ALA THR THR PHE GLY HIS LEU HIS SER LEU VAL ALA GLN SEQRES 12 A 235 LEU GLU GLN LEU LYS ALA GLN THR GLY ALA GLN ARG VAL SEQRES 13 A 235 ALA GLU PHE LEU LEU GLU LEU CYS ASP CYS ASP THR GLY SEQRES 14 A 235 ALA CYS GLU VAL THR LEU PRO TYR ASP LYS MSE LEU ILE SEQRES 15 A 235 ALA GLY ARG LEU GLY MSE LYS PRO GLU SER LEU SER ARG SEQRES 16 A 235 ALA PHE SER ARG LEU LYS ALA ALA GLY VAL THR VAL LYS SEQRES 17 A 235 ARG ASN HIS ALA GLU ILE GLU ASP ILE ALA LEU LEU ARG SEQRES 18 A 235 ASP TYR ALA GLU SER ASP PRO ALA ASP SER TRP SER LYS SEQRES 19 A 235 SER SEQRES 1 B 235 GLY MSE ALA HIS GLU ALA GLN LYS ALA ILE ALA ARG ASN SEQRES 2 B 235 SER LEU LEU ILE ARG SER LEU PRO GLU GLN HIS VAL ASP SEQRES 3 B 235 ALA LEU LEU SER GLN ALA VAL TRP ARG SER TYR ASP ARG SEQRES 4 B 235 GLY GLU THR LEU PHE LEU GLN GLU GLU LYS ALA GLN ALA SEQRES 5 B 235 ILE HIS VAL VAL ILE ASP GLY TRP VAL LYS LEU PHE ARG SEQRES 6 B 235 MSE THR PRO THR GLY SER GLU ALA VAL VAL SER VAL PHE SEQRES 7 B 235 THR ARG GLY GLU SER PHE GLY GLU ALA VAL ALA LEU ARG SEQRES 8 B 235 ASN THR PRO TYR PRO VAL SER ALA GLU ALA VAL THR PRO SEQRES 9 B 235 CYS GLU VAL MSE HIS ILE PRO SER PRO VAL PHE VAL SER SEQRES 10 B 235 LEU MSE ARG ARG ASP PRO GLU ILE CYS ILE SER ILE LEU SEQRES 11 B 235 ALA THR THR PHE GLY HIS LEU HIS SER LEU VAL ALA GLN SEQRES 12 B 235 LEU GLU GLN LEU LYS ALA GLN THR GLY ALA GLN ARG VAL SEQRES 13 B 235 ALA GLU PHE LEU LEU GLU LEU CYS ASP CYS ASP THR GLY SEQRES 14 B 235 ALA CYS GLU VAL THR LEU PRO TYR ASP LYS MSE LEU ILE SEQRES 15 B 235 ALA GLY ARG LEU GLY MSE LYS PRO GLU SER LEU SER ARG SEQRES 16 B 235 ALA PHE SER ARG LEU LYS ALA ALA GLY VAL THR VAL LYS SEQRES 17 B 235 ARG ASN HIS ALA GLU ILE GLU ASP ILE ALA LEU LEU ARG SEQRES 18 B 235 ASP TYR ALA GLU SER ASP PRO ALA ASP SER TRP SER LYS SEQRES 19 B 235 SER MODRES 3H3Z MSE A 1 MET SELENOMETHIONINE MODRES 3H3Z MSE A 65 MET SELENOMETHIONINE MODRES 3H3Z MSE A 107 MET SELENOMETHIONINE MODRES 3H3Z MSE A 118 MET SELENOMETHIONINE MODRES 3H3Z MSE A 179 MET SELENOMETHIONINE MODRES 3H3Z MSE A 187 MET SELENOMETHIONINE MODRES 3H3Z MSE B 65 MET SELENOMETHIONINE MODRES 3H3Z MSE B 107 MET SELENOMETHIONINE MODRES 3H3Z MSE B 118 MET SELENOMETHIONINE MODRES 3H3Z MSE B 179 MET SELENOMETHIONINE MODRES 3H3Z MSE B 187 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 65 8 HET MSE A 107 8 HET MSE A 118 8 HET MSE A 179 16 HET MSE A 187 8 HET MSE B 65 8 HET MSE B 107 8 HET MSE B 118 8 HET MSE B 179 8 HET MSE B 187 8 HET CL A 235 1 HET CL B 235 1 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *98(H2 O) HELIX 1 1 HIS A 3 ARG A 11 1 9 HELIX 2 2 SER A 13 SER A 18 1 6 HELIX 3 3 PRO A 20 SER A 29 1 10 HELIX 4 4 GLY A 84 ASN A 91 1 8 HELIX 5 5 SER A 111 ASP A 121 1 11 HELIX 6 6 ASP A 121 LEU A 146 1 26 HELIX 7 7 THR A 150 LEU A 162 1 13 HELIX 8 8 LYS A 178 GLY A 186 1 9 HELIX 9 9 LYS A 188 ALA A 201 1 14 HELIX 10 10 ASP A 215 GLU A 224 1 10 HELIX 11 11 HIS B 3 ARG B 11 1 9 HELIX 12 12 SER B 13 SER B 18 1 6 HELIX 13 13 HIS B 23 SER B 29 1 7 HELIX 14 14 GLY B 84 ASN B 91 1 8 HELIX 15 15 SER B 111 ASP B 121 1 11 HELIX 16 16 ASP B 121 GLN B 145 1 25 HELIX 17 17 THR B 150 ASP B 164 1 15 HELIX 18 18 LYS B 178 LEU B 185 1 8 HELIX 19 19 LYS B 188 LEU B 199 1 12 HELIX 20 20 LYS B 200 ALA B 202 5 3 HELIX 21 21 ASP B 215 SER B 225 1 11 SHEET 1 A 4 VAL A 32 TYR A 36 0 SHEET 2 A 4 CYS A 104 PRO A 110 -1 O HIS A 108 N VAL A 32 SHEET 3 A 4 ALA A 51 ASP A 57 -1 N VAL A 54 O MSE A 107 SHEET 4 A 4 GLU A 81 PHE A 83 -1 O PHE A 83 N HIS A 53 SHEET 1 B 4 THR A 41 PHE A 43 0 SHEET 2 B 4 SER A 97 ALA A 100 -1 O ALA A 98 N LEU A 42 SHEET 3 B 4 TRP A 59 MSE A 65 -1 N PHE A 63 O SER A 97 SHEET 4 B 4 GLU A 71 THR A 78 -1 O PHE A 77 N VAL A 60 SHEET 1 C 3 CYS A 170 THR A 173 0 SHEET 2 C 3 HIS A 210 ILE A 213 -1 O ILE A 213 N CYS A 170 SHEET 3 C 3 VAL A 204 VAL A 206 -1 N THR A 205 O GLU A 212 SHEET 1 D 4 VAL B 32 TYR B 36 0 SHEET 2 D 4 CYS B 104 PRO B 110 -1 O HIS B 108 N VAL B 32 SHEET 3 D 4 ALA B 51 ASP B 57 -1 N ILE B 52 O ILE B 109 SHEET 4 D 4 SER B 82 PHE B 83 -1 O PHE B 83 N HIS B 53 SHEET 1 E 4 THR B 41 PHE B 43 0 SHEET 2 E 4 SER B 97 ALA B 100 -1 O ALA B 98 N LEU B 42 SHEET 3 E 4 TRP B 59 MSE B 65 -1 N PHE B 63 O SER B 97 SHEET 4 E 4 GLU B 71 THR B 78 -1 O SER B 75 N LEU B 62 SHEET 1 F 3 CYS B 170 THR B 173 0 SHEET 2 F 3 HIS B 210 ILE B 213 -1 O ILE B 213 N CYS B 170 SHEET 3 F 3 VAL B 204 VAL B 206 -1 N THR B 205 O GLU B 212 SSBOND 1 CYS A 125 CYS B 125 1555 1555 2.58 SSBOND 2 CYS B 163 CYS B 170 1555 1555 2.08 LINK C MSE A 1 N ALA A 2 1555 1555 1.33 LINK C ARG A 64 N MSE A 65 1555 1555 1.32 LINK C MSE A 65 N THR A 66 1555 1555 1.32 LINK C VAL A 106 N MSE A 107 1555 1555 1.33 LINK C MSE A 107 N HIS A 108 1555 1555 1.33 LINK C LEU A 117 N MSE A 118 1555 1555 1.32 LINK C MSE A 118 N ARG A 119 1555 1555 1.34 LINK C LYS A 178 N AMSE A 179 1555 1555 1.33 LINK C LYS A 178 N BMSE A 179 1555 1555 1.34 LINK C AMSE A 179 N LEU A 180 1555 1555 1.33 LINK C BMSE A 179 N LEU A 180 1555 1555 1.34 LINK C GLY A 186 N MSE A 187 1555 1555 1.32 LINK C MSE A 187 N LYS A 188 1555 1555 1.33 LINK C ARG B 64 N MSE B 65 1555 1555 1.33 LINK C MSE B 65 N THR B 66 1555 1555 1.34 LINK C VAL B 106 N MSE B 107 1555 1555 1.33 LINK C MSE B 107 N HIS B 108 1555 1555 1.32 LINK C LEU B 117 N MSE B 118 1555 1555 1.33 LINK C MSE B 118 N ARG B 119 1555 1555 1.32 LINK C LYS B 178 N MSE B 179 1555 1555 1.33 LINK C MSE B 179 N LEU B 180 1555 1555 1.34 LINK C GLY B 186 N MSE B 187 1555 1555 1.33 LINK C MSE B 187 N LYS B 188 1555 1555 1.33 SITE 1 AC1 2 ARG A 38 PRO A 103 SITE 1 AC2 1 ARG B 34 CRYST1 137.052 137.052 94.937 90.00 90.00 120.00 H 3 18 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 0.007297 0.004213 0.000000 0.00000 SCALE2 0.000000 0.008425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010533 0.00000 HETATM 1 N MSE A 1 2.228 97.480 13.356 1.00 84.36 N HETATM 2 CA MSE A 1 1.693 96.085 13.651 1.00 86.63 C HETATM 3 C MSE A 1 2.396 94.948 12.878 1.00 87.78 C HETATM 4 O MSE A 1 2.206 93.761 13.194 1.00 89.91 O HETATM 5 CB MSE A 1 0.179 95.977 13.395 1.00 85.76 C HETATM 6 CG MSE A 1 -0.703 96.574 14.484 1.00 86.31 C HETATM 7 SE MSE A 1 -2.582 96.034 14.166 0.75 82.21 SE HETATM 8 CE MSE A 1 -2.994 97.009 12.374 1.00 79.91 C