PDB Short entry for 3NO3 HEADER HYDROLASE 24-JUN-10 3NO3 TITLE CRYSTAL STRUCTURE OF A GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE TITLE 2 (BDI_0402) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.89 A TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARABACTEROIDES DISTASONIS; SOURCE 3 ORGANISM_TAXID: 435591; SOURCE 4 STRAIN: ATCC 8503 / DSM 20701 / NCTC 11152; SOURCE 5 GENE: BDI_0402; 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 STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-2, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 2 01-FEB-23 3NO3 1 REMARK SEQADV LINK REVDAT 1 28-JUL-10 3NO3 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A GLYCEROPHOSPHODIESTER JRNL TITL 2 PHOSPHODIESTERASE (BDI_0402) FROM PARABACTEROIDES DISTASONIS JRNL TITL 3 ATCC 8503 AT 1.89 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 21374 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) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1099 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) : 1.89 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1477 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.2320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1909 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 298 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.23000 REMARK 3 B22 (A**2) : 0.59000 REMARK 3 B33 (A**2) : 0.81000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.53000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.028 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2035 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1416 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2758 ; 1.685 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3480 ; 1.475 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 262 ; 6.384 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 100 ;39.177 ;24.800 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 393 ;12.625 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;14.204 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 303 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2262 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 392 ; 0.002 ; 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): 1224 ; 0.710 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 493 ; 0.232 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1993 ; 1.220 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 811 ; 2.498 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 752 ; 3.623 ; 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 258 REMARK 3 ORIGIN FOR THE GROUP (A): -24.5030 23.3060 11.9980 REMARK 3 T TENSOR REMARK 3 T11: 0.0760 T22: 0.1042 REMARK 3 T33: 0.0100 T12: -0.0067 REMARK 3 T13: 0.0114 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 1.2309 L22: 0.6547 REMARK 3 L33: 1.0679 L12: 0.1625 REMARK 3 L13: 0.0070 L23: -0.0329 REMARK 3 S TENSOR REMARK 3 S11: -0.0424 S12: 0.1765 S13: -0.0114 REMARK 3 S21: -0.0671 S22: 0.0315 S23: -0.0784 REMARK 3 S31: 0.0177 S32: 0.2084 S33: 0.0109 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND REMARK 3 RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND REMARK 3 RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS REMARK 3 ASSIGNMENT. 4. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL REMARK 3 S-MET INCORPORATION. 5. MAGNESIUM IONS (MG), GLYCEROL (GOL), AND REMARK 3 FRAGMENTS OF POLYETHYLENE GLYCOL-4000 (PEG) FROM THE REMARK 3 CRYSTALLIZATION SOLUTION HAVE BEEN MODELED INTO THE SOLVENT REMARK 3 STRUCTURE. REMARK 4 REMARK 4 3NO3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000060069. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91837,0.97941,0.97915 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, TOROID REMARK 200 FOCUSING MIRROR 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 : 21375 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 26.955 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.9700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: 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 (%): 48.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2000M MAGNESIUM CHLORIDE, 30.0000% REMARK 280 POLYETHYLENE GLYCOL 4000, 0.1M TRIS PH 8.5, NANODROP, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 68.73000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.43800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.73000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.43800 REMARK 290 SMTRY3 4 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: MONOMERIC 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 MG MG A 302 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 24 CG OD1 ND2 REMARK 470 LYS A 26 NZ REMARK 470 LYS A 101 CE NZ REMARK 470 LYS A 172 CE NZ REMARK 470 LYS A 210 NZ REMARK 470 LYS A 213 CE NZ REMARK 470 LYS A 228 CD CE NZ 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 49 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 152 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 152 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 256 NE - CZ - NH1 ANGL. DEV. = 3.0 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 TYR A 73 142.91 -170.77 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 PEG A 304 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 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 0 O REMARK 620 2 HOH A 454 O 98.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 59 OE2 REMARK 620 2 ASP A 61 OD1 98.7 REMARK 620 3 GLU A 123 OE1 95.3 91.8 REMARK 620 4 GOL A 303 O2 88.1 170.5 94.2 REMARK 620 5 HOH A 305 O 87.6 88.2 177.1 85.4 REMARK 620 6 HOH A 310 O 169.3 88.9 92.0 83.5 85.0 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 396624 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT (22-258) WAS EXPRESSED WITH THE 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 3NO3 A 22 258 UNP A6L916 A6L916_PARD8 22 258 SEQADV 3NO3 GLY A 0 UNP A6L916 EXPRESSION TAG SEQRES 1 A 238 GLY LYS ASP ASN THR LYS VAL ILE ALA HIS ARG GLY TYR SEQRES 2 A 238 TRP LYS THR GLU GLY SER ALA GLN ASN SER ILE ARG SER SEQRES 3 A 238 LEU GLU ARG ALA SER GLU ILE GLY ALA TYR GLY SER GLU SEQRES 4 A 238 PHE ASP VAL HIS LEU THR ALA ASP ASN VAL LEU VAL VAL SEQRES 5 A 238 TYR HIS ASP ASN ASP ILE GLN GLY LYS HIS ILE GLN SER SEQRES 6 A 238 CYS THR TYR ASP GLU LEU LYS ASP LEU GLN LEU SER ASN SEQRES 7 A 238 GLY GLU LYS LEU PRO THR LEU GLU GLN TYR LEU LYS ARG SEQRES 8 A 238 ALA LYS LYS LEU LYS ASN ILE ARG LEU ILE PHE GLU LEU SEQRES 9 A 238 LYS SER HIS ASP THR PRO GLU ARG ASN ARG ASP ALA ALA SEQRES 10 A 238 ARG LEU SER VAL GLN MSE VAL LYS ARG MSE LYS LEU ALA SEQRES 11 A 238 LYS ARG THR ASP TYR ILE SER PHE ASN MSE ASP ALA CYS SEQRES 12 A 238 LYS GLU PHE ILE ARG LEU CYS PRO LYS SER GLU VAL SER SEQRES 13 A 238 TYR LEU ASN GLY GLU LEU SER PRO MSE GLU LEU LYS GLU SEQRES 14 A 238 LEU GLY PHE THR GLY LEU ASP TYR HIS TYR LYS VAL LEU SEQRES 15 A 238 GLN SER HIS PRO ASP TRP VAL LYS ASP CYS LYS VAL LEU SEQRES 16 A 238 GLY MSE THR SER ASN VAL TRP THR VAL ASP ASP PRO LYS SEQRES 17 A 238 LEU MSE GLU GLU MSE ILE ASP MSE GLY VAL ASP PHE ILE SEQRES 18 A 238 THR THR ASP LEU PRO GLU GLU THR GLN LYS ILE LEU HIS SEQRES 19 A 238 SER ARG ALA GLN MODRES 3NO3 MSE A 143 MET SELENOMETHIONINE MODRES 3NO3 MSE A 147 MET SELENOMETHIONINE MODRES 3NO3 MSE A 160 MET SELENOMETHIONINE MODRES 3NO3 MSE A 185 MET SELENOMETHIONINE MODRES 3NO3 MSE A 217 MET SELENOMETHIONINE MODRES 3NO3 MSE A 230 MET SELENOMETHIONINE MODRES 3NO3 MSE A 233 MET SELENOMETHIONINE MODRES 3NO3 MSE A 236 MET SELENOMETHIONINE HET MSE A 143 8 HET MSE A 147 8 HET MSE A 160 8 HET MSE A 185 8 HET MSE A 217 13 HET MSE A 230 8 HET MSE A 233 8 HET MSE A 236 8 HET MG A 301 1 HET MG A 302 1 HET GOL A 303 6 HET PEG A 304 6 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 MG 2(MG 2+) FORMUL 4 GOL C3 H8 O3 FORMUL 5 PEG C4 H10 O3 FORMUL 6 HOH *298(H2 O) HELIX 1 1 SER A 43 ILE A 53 1 11 HELIX 2 2 GLN A 84 CYS A 86 5 3 HELIX 3 3 THR A 87 LYS A 92 1 6 HELIX 4 4 THR A 104 LEU A 115 1 12 HELIX 5 5 THR A 129 MSE A 147 1 19 HELIX 6 6 LEU A 149 LYS A 151 5 3 HELIX 7 7 ASN A 159 CYS A 170 1 12 HELIX 8 8 SER A 183 LEU A 190 1 8 HELIX 9 9 TYR A 199 HIS A 205 1 7 HELIX 10 10 ASP A 207 LEU A 215 1 9 HELIX 11 11 ASP A 226 GLY A 237 1 12 HELIX 12 12 LEU A 245 ALA A 257 1 13 SHEET 1 A10 LEU A 70 VAL A 72 0 SHEET 2 A10 GLY A 57 LEU A 64 -1 N HIS A 63 O VAL A 71 SHEET 3 A10 ARG A 119 LEU A 124 1 O GLU A 123 N PHE A 60 SHEET 4 A10 THR A 153 SER A 157 1 O ASP A 154 N PHE A 122 SHEET 5 A10 VAL A 175 TYR A 177 1 O SER A 176 N TYR A 155 SHEET 6 A10 GLY A 194 HIS A 198 1 O ASP A 196 N TYR A 177 SHEET 7 A10 THR A 218 TRP A 222 1 O THR A 218 N LEU A 195 SHEET 8 A10 PHE A 240 THR A 243 1 O THR A 242 N VAL A 221 SHEET 9 A10 LYS A 26 ALA A 29 1 N ILE A 28 O ILE A 241 SHEET 10 A10 GLY A 57 LEU A 64 1 O GLY A 57 N ALA A 29 SHEET 1 B 2 ASP A 77 ILE A 78 0 SHEET 2 B 2 LYS A 81 HIS A 82 -1 O LYS A 81 N ILE A 78 LINK C GLN A 142 N MSE A 143 1555 1555 1.32 LINK C MSE A 143 N VAL A 144 1555 1555 1.34 LINK C ARG A 146 N MSE A 147 1555 1555 1.35 LINK C MSE A 147 N LYS A 148 1555 1555 1.33 LINK C ASN A 159 N MSE A 160 1555 1555 1.32 LINK C MSE A 160 N ASP A 161 1555 1555 1.33 LINK C PRO A 184 N MSE A 185 1555 1555 1.33 LINK C MSE A 185 N GLU A 186 1555 1555 1.33 LINK C GLY A 216 N MSE A 217 1555 1555 1.34 LINK C MSE A 217 N THR A 218 1555 1555 1.32 LINK C LEU A 229 N MSE A 230 1555 1555 1.34 LINK C MSE A 230 N GLU A 231 1555 1555 1.33 LINK C GLU A 232 N MSE A 233 1555 1555 1.33 LINK C MSE A 233 N ILE A 234 1555 1555 1.33 LINK C ASP A 235 N MSE A 236 1555 1555 1.33 LINK C MSE A 236 N GLY A 237 1555 1555 1.33 LINK O GLY A 0 MG MG A 302 1555 1555 2.13 LINK OE2 GLU A 59 MG MG A 301 1555 1555 2.11 LINK OD1 ASP A 61 MG MG A 301 1555 1555 2.08 LINK OE1 GLU A 123 MG MG A 301 1555 1555 2.00 LINK MG MG A 301 O2 GOL A 303 1555 1555 2.14 LINK MG MG A 301 O HOH A 305 1555 1555 2.16 LINK MG MG A 301 O HOH A 310 1555 1555 2.14 LINK MG MG A 302 O HOH A 454 1555 1555 1.88 CISPEP 1 TRP A 222 THR A 223 0 -21.69 SITE 1 AC1 6 GLU A 59 ASP A 61 GLU A 123 GOL A 303 SITE 2 AC1 6 HOH A 305 HOH A 310 SITE 1 AC2 2 GLY A 0 HOH A 454 SITE 1 AC3 10 HIS A 30 GLU A 59 GLU A 123 ILE A 156 SITE 2 AC3 10 LEU A 178 MG A 301 HOH A 305 HOH A 310 SITE 3 AC3 10 HOH A 326 HOH A 576 SITE 1 AC4 7 LYS A 145 LYS A 148 LEU A 149 ALA A 150 SITE 2 AC4 7 LYS A 151 HOH A 443 HOH A 594 CRYST1 137.460 40.876 48.328 90.00 99.39 90.00 C 1 2 1 4 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 0.007275 0.000000 0.001203 0.00000 SCALE2 0.000000 0.024464 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020973 0.00000