HEADER TOXIN 25-SEP-09 3K0Y TITLE CRYSTAL STRUCTURE OF PUTATIVE TOXIN RELATED PROTEIN (YP_001303978.1) TITLE 2 FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 2.16 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE TOXIN RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARABACTEROIDES DISTASONIS ATCC 8503; SOURCE 3 ORGANISM_TAXID: 435591; SOURCE 4 STRAIN: ATCC 8503 / DSM 20701 / NCTC 11152; SOURCE 5 GENE: BDI_2637; 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 TOXIN RELATED PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, KEYWDS 3 UNKNOWN FUNCTION, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3K0Y 1 REMARK SEQADV REVDAT 4 17-JUL-19 3K0Y 1 REMARK LINK REVDAT 3 25-OCT-17 3K0Y 1 REMARK REVDAT 2 13-JUL-11 3K0Y 1 VERSN REVDAT 1 06-OCT-09 3K0Y 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE TOXIN RELATED PROTEIN JRNL TITL 2 (YP_001303978.1) FROM PARABACTEROIDES DISTASONIS ATCC 8503 JRNL TITL 3 AT 2.16 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0053 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) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 16861 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 853 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) : 2.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.22 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1160 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1580 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 56 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 52.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.48000 REMARK 3 B22 (A**2) : -1.48000 REMARK 3 B33 (A**2) : 2.21000 REMARK 3 B12 (A**2) : -0.74000 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): 0.189 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.167 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.129 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.948 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1656 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1073 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2256 ; 1.596 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2627 ; 0.850 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 199 ; 6.504 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;39.016 ;25.366 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 250 ;15.148 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;17.405 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 243 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1840 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 323 ; 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): 992 ; 0.922 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 399 ; 0.210 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1606 ; 1.678 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 664 ; 2.241 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 648 ; 3.529 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 34 A 87 REMARK 3 RESIDUE RANGE : A 97 A 234 REMARK 3 RESIDUE RANGE : A 248 A 253 REMARK 3 ORIGIN FOR THE GROUP (A): 51.4500 19.0650 5.9700 REMARK 3 T TENSOR REMARK 3 T11: 0.1886 T22: 0.1817 REMARK 3 T33: 0.0666 T12: -0.0875 REMARK 3 T13: -0.0951 T23: 0.0382 REMARK 3 L TENSOR REMARK 3 L11: 2.3937 L22: 3.7006 REMARK 3 L33: 1.3899 L12: 1.5787 REMARK 3 L13: 0.8588 L23: -0.0071 REMARK 3 S TENSOR REMARK 3 S11: 0.1345 S12: 0.0720 S13: -0.0036 REMARK 3 S21: 0.0284 S22: -0.1037 S23: -0.1479 REMARK 3 S31: 0.1042 S32: 0.0812 S33: -0.0309 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 : 1.40 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 RECORDS CONTAIN 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 FOR THE REDUCED REMARK 3 SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. PEG-400 REMARK 3 (2PE) FRAGMENTS FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. REMARK 4 REMARK 4 3K0Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-09; 23-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 5.79 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SSRL; SSRL REMARK 200 BEAMLINE : BL9-2; BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97911; 0.97835,0.97876 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR; REMARK 200 SINGLE CRYSTAL SI(111) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, TOROID REMARK 200 FOCUSING MIRROR; FLAT MIRROR REMARK 200 (VERTICAL FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD; MARMOSAIC REMARK 200 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16892 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.160 REMARK 200 RESOLUTION RANGE LOW (A) : 39.559 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.68800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE STRUCTURE WAS PHASED BY MAD METHOD AT 2.46 A REMARK 200 RESOLUTION AND REFINED AT 2.16 A RESOLUTION AGAINST A DATASET REMARK 200 COLLECTED FROM A DIFFERENT CRYSTAL. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5.0000% POLYETHYLENE GLYCOL 3000, REMARK 280 44.0000% POLYETHYLENE GLYCOL 400, 0.1M MES PH 5.79, VAPOR REMARK 280 DIFFUSION,SITTING DROP,NANODROP, TEMPERATURE 277K, VAPOR REMARK 280 DIFFUSION, SITTING DROP 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 34.18867 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 68.37733 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 68.37733 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 34.18867 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: ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE REMARK 300 ASSIGNMENT OF A MONOMER 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ASP A 26 REMARK 465 ASP A 27 REMARK 465 ASN A 28 REMARK 465 SER A 29 REMARK 465 TYR A 30 REMARK 465 SER A 31 REMARK 465 LEU A 32 REMARK 465 GLY A 33 REMARK 465 SER A 88 REMARK 465 THR A 89 REMARK 465 GLN A 90 REMARK 465 SER A 91 REMARK 465 ASN A 92 REMARK 465 LEU A 93 REMARK 465 GLY A 94 REMARK 465 GLY A 95 REMARK 465 PHE A 96 REMARK 465 GLU A 235 REMARK 465 ASP A 236 REMARK 465 THR A 237 REMARK 465 SER A 238 REMARK 465 GLN A 239 REMARK 465 GLY A 240 REMARK 465 TYR A 241 REMARK 465 THR A 242 REMARK 465 ASN A 243 REMARK 465 ASP A 244 REMARK 465 SER A 245 REMARK 465 ILE A 246 REMARK 465 SER A 247 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 LYS A 115 CG CD CE NZ REMARK 470 GLU A 168 CG CD OE1 OE2 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 192 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 192 NE - CZ - NH2 ANGL. DEV. = -3.2 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 45 -44.89 -137.82 REMARK 500 ASN A 47 -115.74 48.43 REMARK 500 TYR A 67 75.76 -117.34 REMARK 500 ALA A 86 134.31 -171.47 REMARK 500 ASN A 135 -6.86 98.28 REMARK 500 ASP A 166 84.82 -151.93 REMARK 500 ASP A 170 59.18 -153.97 REMARK 500 TYR A 181 -124.76 50.34 REMARK 500 GLN A 185 74.19 -104.00 REMARK 500 LYS A 204 -128.06 70.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 2PE A 500 REMARK 610 2PE A 501 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2PE A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2PE A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 394722 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT (RESIDUE 26-253) WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3K0Y A 26 253 UNP A6LF92 A6LF92_PARD8 26 253 SEQADV 3K0Y GLY A 0 UNP A6LF92 EXPRESSION TAG SEQRES 1 A 229 GLY ASP ASP ASN SER TYR SER LEU GLY ASP ILE TRP ILE SEQRES 2 A 229 ALA VAL ALA THR VAL VAL PRO GLU GLY ASN ASN VAL TYR SEQRES 3 A 229 TYR LEU ARG LEU ASP ASP GLY ASP LYS LEU TRP PRO ALA SEQRES 4 A 229 ALA THR ASN TYR PRO ASN TYR GLN PRO LYS PRO ASN GLN SEQRES 5 A 229 ARG ALA LEU VAL ASN PHE THR ILE LEU ALA ASP SER THR SEQRES 6 A 229 GLN SER ASN LEU GLY GLY PHE SER HIS TYR ILE LYS VAL SEQRES 7 A 229 ASN ALA ILE HIS ASN ILE LEU THR LYS SER ILE ALA LYS SEQRES 8 A 229 ASN GLU GLY ALA ALA ASN ASP SER ILE TYR GLY THR ASP SEQRES 9 A 229 PRO VAL SER ILE TYR ASN ASN ASN MSE TRP ILE GLY ASP SEQRES 10 A 229 GLY TYR LEU ASN ILE TYR PHE GLU THR LEU TRP GLY GLY SEQRES 11 A 229 LYS THR ALA HIS PHE ILE ASN LEU ILE GLN PRO ASP ALA SEQRES 12 A 229 GLU ASN ASP PRO TYR THR LEU GLU PHE ARG HIS ASN ALA SEQRES 13 A 229 TYR ASP ASP PRO GLN TYR THR ILE GLY ALA GLY ARG VAL SEQRES 14 A 229 ALA PHE ASN LEU SER SER LEU PRO ASP THR LYS GLY GLU SEQRES 15 A 229 THR VAL ASP LEU VAL VAL ASN TYR TRP THR SER GLU GLY SEQRES 16 A 229 LYS GLN ALA TYR LYS LEU LYS TYR ASN SER ASP LYS THR SEQRES 17 A 229 LYS MSE GLU ASP THR SER GLN GLY TYR THR ASN ASP SER SEQRES 18 A 229 ILE SER ASN ILE THR ASP MSE LYS MODRES 3K0Y MSE A 137 MET SELENOMETHIONINE MODRES 3K0Y MSE A 234 MET SELENOMETHIONINE MODRES 3K0Y MSE A 252 MET SELENOMETHIONINE HET MSE A 137 8 HET MSE A 234 8 HET MSE A 252 8 HET 2PE A 500 10 HET 2PE A 501 13 HETNAM MSE SELENOMETHIONINE HETNAM 2PE NONAETHYLENE GLYCOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 2PE 2(C18 H38 O10) FORMUL 4 HOH *56(H2 O) HELIX 1 1 GLU A 117 ALA A 119 5 3 HELIX 2 2 ALA A 120 GLY A 126 1 7 SHEET 1 A 9 MSE A 137 GLY A 140 0 SHEET 2 A 9 TYR A 143 TRP A 152 -1 O ASN A 145 N TRP A 138 SHEET 3 A 9 THR A 187 ASN A 196 -1 O THR A 187 N TRP A 152 SHEET 4 A 9 HIS A 98 SER A 112 1 N LYS A 111 O ASN A 196 SHEET 5 A 9 GLN A 76 ALA A 86 -1 N LEU A 79 O HIS A 106 SHEET 6 A 9 ILE A 35 GLY A 46 -1 N ALA A 38 O VAL A 80 SHEET 7 A 9 VAL A 49 LEU A 54 -1 O TYR A 51 N VAL A 43 SHEET 8 A 9 LYS A 59 THR A 65 -1 O LEU A 60 N LEU A 52 SHEET 9 A 9 HIS A 98 SER A 112 1 O HIS A 98 N TRP A 61 SHEET 1 B 4 PHE A 159 ILE A 163 0 SHEET 2 B 4 THR A 173 ASN A 179 -1 O ARG A 177 N ASN A 161 SHEET 3 B 4 VAL A 208 THR A 216 1 O VAL A 211 N LEU A 174 SHEET 4 B 4 GLY A 219 TYR A 227 -1 O LEU A 225 N LEU A 210 LINK C ASN A 136 N MSE A 137 1555 1555 1.33 LINK C MSE A 137 N TRP A 138 1555 1555 1.33 LINK C LYS A 233 N MSE A 234 1555 1555 1.33 LINK C ASP A 251 N MSE A 252 1555 1555 1.35 LINK C MSE A 252 N LYS A 253 1555 1555 1.31 SITE 1 AC1 2 ASN A 135 TRP A 138 SITE 1 AC2 4 ASN A 136 TRP A 138 TYR A 147 ARG A 192 CRYST1 71.722 71.722 102.566 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 0.013943 0.008050 0.000000 0.00000 SCALE2 0.000000 0.016100 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009750 0.00000