HEADER HYDROLASE 14-MAR-08 3CJY TITLE CRYSTAL STRUCTURE OF PUTATIVE THIOESTERASE (YP_496845.1) FROM TITLE 2 NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 AT 1.70 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE THIOESTERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOVOSPHINGOBIUM AROMATICIVORANS; SOURCE 3 ORGANISM_TAXID: 279238; SOURCE 4 STRAIN: DSM 12444; SOURCE 5 GENE: YP_496845.1, SARO_1571; 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 YP_496845.1, PUTATIVE THIOESTERASE, STRUCTURAL GENOMICS, JOINT CENTER KEYWDS 2 FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 01-FEB-23 3CJY 1 REMARK SEQADV REVDAT 5 24-JUL-19 3CJY 1 REMARK LINK REVDAT 4 25-OCT-17 3CJY 1 REMARK REVDAT 3 13-JUL-11 3CJY 1 VERSN REVDAT 2 24-FEB-09 3CJY 1 VERSN REVDAT 1 01-APR-08 3CJY 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE THIOESTERASE (YP_496845.1) JRNL TITL 2 FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 AT 1.70 A JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0067 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28130 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1414 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1946 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1823 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 193 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 17.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.31000 REMARK 3 B22 (A**2) : -0.68000 REMARK 3 B33 (A**2) : -0.63000 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): 0.102 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.099 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.029 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1974 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1335 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2690 ; 1.730 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3251 ; 1.186 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 267 ; 4.256 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 72 ;34.239 ;23.194 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 275 ;11.943 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;14.416 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 300 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2260 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 391 ; 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): 1298 ; 0.941 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 530 ; 0.254 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2072 ; 1.605 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 676 ; 2.406 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 617 ; 3.722 ; 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 4 A 258 REMARK 3 ORIGIN FOR THE GROUP (A): -12.1263 -44.1296 3.7875 REMARK 3 T TENSOR REMARK 3 T11: -0.0170 T22: -0.0315 REMARK 3 T33: -0.0352 T12: 0.0149 REMARK 3 T13: 0.0100 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.7355 L22: 0.8839 REMARK 3 L33: 0.4209 L12: 0.0484 REMARK 3 L13: 0.2721 L23: -0.1065 REMARK 3 S TENSOR REMARK 3 S11: 0.0035 S12: -0.0359 S13: 0.0877 REMARK 3 S21: 0.0477 S22: -0.0166 S23: 0.0710 REMARK 3 S31: -0.0879 S32: -0.0519 S33: 0.0131 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 SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY REMARK 3 OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 REMARK 3 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. REMARK 3 3. GLYCEROL, PEG AND CALCIUM WERE MODELED BASED REMARK 3 ON PURIFICATION, CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS. REMARK 3 4. THERE IS UNMODELED DENSITY BETWEEN AMINO ACIDS ASP139 AND REMARK 3 ASN141. REMARK 4 REMARK 4 3CJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000046867. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.19 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, 0.97932, 0.97914 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28153 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 29.161 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.63600 REMARK 200 R SYM FOR SHELL (I) : 0.63600 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: SHELX, SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NANODROP, 0.19M CALCIUM CHLORIDE, REMARK 280 19.6% PEG 400, 5.0% GLYCEROL, 0.1M HEPES PH 7.19, VAPOR REMARK 280 DIFFUSION, SITTING 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 37.48350 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 37.48350 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 30.02650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.87750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.02650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.87750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.48350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.02650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 55.87750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 37.48350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.02650 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 55.87750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.5 KCAL/MOL 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -111.75500 REMARK 350 BIOMT3 2 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 HOH A 415 LIES ON A SPECIAL POSITION. 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 THR A 2 REMARK 465 GLU A 3 REMARK 465 GLY A 199 REMARK 465 GLY A 200 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 15 CD NE CZ NH1 NH2 REMARK 470 ARG A 83 CB CG CD NE CZ NH1 NH2 REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 ARG A 143 CZ NH1 NH2 REMARK 470 GLU A 157 CG CD OE1 OE2 REMARK 470 LYS A 257 CG CD CE NZ 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 446 O HOH A 446 4545 2.17 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 ASP A 13 N - CA - C ANGL. DEV. = -18.6 DEGREES REMARK 500 LEU A 85 CA - CB - CG ANGL. DEV. = 15.5 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 ALA A 14 -35.63 80.25 REMARK 500 GLN A 80 144.24 -172.69 REMARK 500 MSE A 108 110.75 -168.35 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 CA A 259 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 ASP A 13 OD2 53.3 REMARK 620 3 THR A 50 O 99.4 99.8 REMARK 620 4 HOH A 459 O 118.8 65.6 87.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 266 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 371292 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 REMARK 999 LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE. DBREF 3CJY A 1 258 UNP Q2G812 Q2G812_NOVAD 1 258 SEQADV 3CJY GLY A 0 UNP Q2G812 EXPRESSION TAG SEQRES 1 A 259 GLY MSE THR GLU ALA PHE PRO ALA LEU VAL ARG GLN ASP SEQRES 2 A 259 ASP ALA ARG TYR ALA ILE THR VAL GLY PRO ASP LEU ALA SEQRES 3 A 259 VAL GLY PRO PRO GLY HIS ALA TYR LEU PHE GLY GLY ALA SEQRES 4 A 259 SER MSE ALA LEU ALA LEU ASP VAL ALA ALA GLU THR VAL SEQRES 5 A 259 GLY ARG PRO VAL VAL GLN GLY SER LEU GLN PHE VAL SER SEQRES 6 A 259 PHE THR PRO LEU GLY SER VAL LEU ASP LEU THR VAL GLU SEQRES 7 A 259 VAL LEU GLN SER GLY ARG THR LEU ALA GLN ALA ARG VAL SEQRES 8 A 259 ALA GLY THR VAL ASP GLY ARG LEU VAL PHE HIS SER GLY SEQRES 9 A 259 ILE SER LEU GLY MSE ARG GLU GLY PHE SER ALA ARG GLN SEQRES 10 A 259 TRP ALA LEU ALA PRO PRO VAL PRO GLN PRO ASP ASN CYS SEQRES 11 A 259 PRO PRO CYS THR THR LEU PRO ALA GLN ASP ASP ASN ALA SEQRES 12 A 259 ARG TYR LEU GLU GLY ILE GLU VAL ARG GLU ALA GLY GLY SEQRES 13 A 259 PRO GLU VAL PRO SER GLY ARG THR ARG LEU TRP LEU ARG SEQRES 14 A 259 ARG LYS ASP GLY ALA PRO LEU ASP ALA ALA SER LEU ALA SEQRES 15 A 259 MSE PHE ALA ASP PHE LEU PRO ILE ALA LEU GLY ARG ALA SEQRES 16 A 259 THR GLY CYS SER GLY GLY GLY ASN SER LEU ASP ASN SER SEQRES 17 A 259 LEU ARG ILE THR GLY ALA ALA ALA PRO GLY TRP CYS LEU SEQRES 18 A 259 CYS ASP MSE ILE ILE PRO SER SER ALA SER GLY PHE ALA SEQRES 19 A 259 GLN GLY GLN VAL THR LEU TRP ASP GLN SER GLY ARG LEU SEQRES 20 A 259 LEU ALA THR GLY ALA GLN SER LEU LEU LEU LYS GLY MODRES 3CJY MSE A 40 MET SELENOMETHIONINE MODRES 3CJY MSE A 108 MET SELENOMETHIONINE MODRES 3CJY MSE A 182 MET SELENOMETHIONINE MODRES 3CJY MSE A 223 MET SELENOMETHIONINE HET MSE A 40 13 HET MSE A 108 8 HET MSE A 182 8 HET MSE A 223 8 HET CA A 259 1 HET PGE A 260 10 HET GOL A 261 6 HET GOL A 262 6 HET GOL A 263 6 HET GOL A 264 6 HET PEG A 265 7 HET PEG A 266 7 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION HETNAM PGE TRIETHYLENE GLYCOL HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 CA CA 2+ FORMUL 3 PGE C6 H14 O4 FORMUL 4 GOL 4(C3 H8 O3) FORMUL 8 PEG 2(C4 H10 O3) FORMUL 10 HOH *193(H2 O) HELIX 1 1 GLY A 21 ASP A 23 5 3 HELIX 2 2 PHE A 35 GLY A 52 1 18 HELIX 3 3 GLN A 125 CYS A 129 5 5 HELIX 4 4 TYR A 144 GLU A 146 5 3 HELIX 5 5 ASP A 176 ASP A 185 1 10 HELIX 6 6 PHE A 186 GLY A 196 1 11 SHEET 1 A12 VAL A 9 ASP A 12 0 SHEET 2 A12 ARG A 15 THR A 19 -1 O ARG A 15 N GLN A 11 SHEET 3 A12 VAL A 71 SER A 81 -1 O LEU A 72 N ILE A 18 SHEET 4 A12 ALA A 86 VAL A 94 -1 O THR A 93 N ASP A 73 SHEET 5 A12 ARG A 97 LEU A 106 -1 O LEU A 106 N ALA A 86 SHEET 6 A12 VAL A 55 PHE A 62 -1 N VAL A 56 O SER A 105 SHEET 7 A12 ASP A 205 ILE A 210 -1 O ASN A 206 N LEU A 60 SHEET 8 A12 LEU A 246 LEU A 255 -1 O THR A 249 N ARG A 209 SHEET 9 A12 PHE A 232 TRP A 240 -1 N LEU A 239 O ALA A 248 SHEET 10 A12 CYS A 219 ALA A 229 -1 N ASP A 222 O THR A 238 SHEET 11 A12 ARG A 162 ARG A 169 -1 N LEU A 165 O CYS A 221 SHEET 12 A12 ILE A 148 GLU A 152 -1 N GLU A 149 O ARG A 168 SHEET 1 B 9 VAL A 9 ASP A 12 0 SHEET 2 B 9 ARG A 15 THR A 19 -1 O ARG A 15 N GLN A 11 SHEET 3 B 9 VAL A 71 SER A 81 -1 O LEU A 72 N ILE A 18 SHEET 4 B 9 ALA A 86 VAL A 94 -1 O THR A 93 N ASP A 73 SHEET 5 B 9 ARG A 97 LEU A 106 -1 O LEU A 106 N ALA A 86 SHEET 6 B 9 VAL A 55 PHE A 62 -1 N VAL A 56 O SER A 105 SHEET 7 B 9 ASP A 205 ILE A 210 -1 O ASN A 206 N LEU A 60 SHEET 8 B 9 LEU A 246 LEU A 255 -1 O THR A 249 N ARG A 209 SHEET 9 B 9 ASN A 202 SER A 203 -1 N ASN A 202 O LEU A 255 SHEET 1 C 2 ALA A 25 VAL A 26 0 SHEET 2 C 2 TYR A 33 LEU A 34 -1 O TYR A 33 N VAL A 26 LINK C SER A 39 N MSE A 40 1555 1555 1.32 LINK C MSE A 40 N ALA A 41 1555 1555 1.32 LINK C GLY A 107 N MSE A 108 1555 1555 1.32 LINK C MSE A 108 N ARG A 109 1555 1555 1.32 LINK C ALA A 181 N MSE A 182 1555 1555 1.33 LINK C MSE A 182 N PHE A 183 1555 1555 1.34 LINK C ASP A 222 N MSE A 223 1555 1555 1.33 LINK C MSE A 223 N ILE A 224 1555 1555 1.33 LINK OD1 ASP A 13 CA CA A 259 1555 1555 2.34 LINK OD2 ASP A 13 CA CA A 259 1555 1555 2.53 LINK O THR A 50 CA CA A 259 1555 1555 2.33 LINK CA CA A 259 O HOH A 459 1555 1555 2.30 SITE 1 AC1 3 ASP A 13 THR A 50 HOH A 459 SITE 1 AC2 3 GLN A 116 ARG A 245 HOH A 325 SITE 1 AC3 7 ARG A 162 ASP A 222 GLN A 236 THR A 238 SITE 2 AC3 7 HOH A 283 HOH A 323 HOH A 329 SITE 1 AC4 5 ARG A 162 THR A 238 HOH A 302 HOH A 323 SITE 2 AC4 5 HOH A 343 SITE 1 AC5 7 ALA A 120 PRO A 121 ASP A 241 GLN A 242 SITE 2 AC5 7 SER A 243 GLY A 244 HOH A 453 SITE 1 AC6 4 PHE A 112 GLN A 116 TRP A 117 ALA A 118 SITE 1 AC7 6 PHE A 112 SER A 113 ARG A 115 THR A 195 SITE 2 AC7 6 HOH A 338 HOH A 384 SITE 1 AC8 2 GLY A 111 GLY A 258 CRYST1 60.053 111.755 74.967 90.00 90.00 90.00 C 2 2 21 8 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 0.016652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008948 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013339 0.00000