HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 31-MAY-07 2Q46 TITLE ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF GENE PRODUCT TITLE 2 FROM ARABIDOPSIS THALIANA AT5G02240 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN AT5G02240; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 STRAIN: CV. COLUMBIA; SOURCE 6 GENE: AT5G02240, T7H20_290; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: B834(DE3) P(LACI+RARE); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PVP-13 (PQE DERIVATIVE) KEYWDS ENSEMBLE REFINEMENT, REFINEMENT METHODOLOGY DEVELOPMENT, AT5G02240, KEYWDS 2 NADP, STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, PSI, CENTER KEYWDS 3 FOR EUKARYOTIC STRUCTURAL GENOMICS, CESG, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION NUMMDL 8 AUTHOR E.J.LEVIN,D.A.KONDRASHOV,G.E.WESENBERG,G.N.PHILLIPS JR.,CENTER FOR AUTHOR 2 EUKARYOTIC STRUCTURAL GENOMICS (CESG) REVDAT 5 30-AUG-23 2Q46 1 REMARK SEQADV REVDAT 4 10-AUG-11 2Q46 1 REMARK REVDAT 3 24-FEB-09 2Q46 1 VERSN REVDAT 2 02-OCT-07 2Q46 1 JRNL REVDAT 1 19-JUN-07 2Q46 0 JRNL AUTH E.J.LEVIN,D.A.KONDRASHOV,G.E.WESENBERG,G.N.PHILLIPS JRNL TITL ENSEMBLE REFINEMENT OF PROTEIN CRYSTAL STRUCTURES: JRNL TITL 2 VALIDATION AND APPLICATION. JRNL REF STRUCTURE V. 15 1040 2007 JRNL REFN ISSN 0969-2126 JRNL PMID 17850744 JRNL DOI 10.1016/J.STR.2007.06.019 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD USING AMPLITUDES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1092150.750 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 47340 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 SET) : 0.209 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2444 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6964 REMARK 3 BIN R VALUE (WORKING SET) : 0.3580 REMARK 3 BIN FREE R VALUE : 0.4180 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 385 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3816 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.31 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.026 REMARK 3 BOND ANGLES (DEGREES) : 2.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.130 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.420 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.060 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.030 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.630 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 45.73 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NAP_XPLOR_PAR.TXT REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THIS PDB ENTRY IS A RE-REFINEMENT USING AN ENSEMBLE MODEL OF THE REMARK 3 PREVIOUSLY REMARK 3 DEPOSITED SINGLE-CONFORMER STRUCTURE 1XQ6 AND REMARK 3 THE FIRST DATA SET IN THE DEPOSITED STRUCTURE FACTOR FILE REMARK 3 FOR 1XQ6 ALONG WITH THE R-FREE SET DEFINED THEREIN. THE COORDINATES REMARK 3 WERE GENERATED BY AN AUTOMATED PROTOCOL FROM AN INITIAL MODEL REMARK 3 CONSISTING REMARK 3 OF 8 IDENTICAL COPIES OF THE PROTEIN AND NON-WATER REMARK 3 HETERO-ATOMS ASSIGNED FRACTIONAL OCCUPANCIES ADDING UP TO ONE, AND REMARK 3 A REMARK 3 SINGLE COPY OF THE SOLVENT MOLECULES. REFINEMENT WAS CARRIED OUT REMARK 3 WITH REMARK 3 ALL THE CONFORMERS PRESENT SIMULTANEOUSLY AND WITH THE POTENTIAL REMARK 3 ENERGY REMARK 3 TERMS CORRESPONDING TO INTERACTIONS BETWEEN THE DIFFERENT REMARK 3 CONFORMERS REMARK 3 EXCLUDED. THE HELIX AND SHEET RECORDS WERE CALCULATED USING REMARK 3 COORDINATES REMARK 3 FROM THE FIRST CONFORMER ONLY. THE STRUCTURE VISUALIZATION PROGRAM REMARK 3 PYMOL IS WELL-SUITED FOR DIRECTLY VIEWING THE ENSEMBLE MODEL REMARK 3 PRESENTED IN THIS PDB FILE. REMARK 4 REMARK 4 2Q46 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043126. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RE-REFINEMENT USING REMARK 200 ENSEMBLE MODEL REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: PDB ENTRY 1XQ6 REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 1XQ6. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.89950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 2 VAL B 20 CB VAL B 20 CG1 0.130 REMARK 500 5 ALA A 174 CA ALA A 174 CB 0.127 REMARK 500 5 CYS A 212 CB CYS A 212 SG -0.192 REMARK 500 5 VAL B 20 CB VAL B 20 CG1 0.172 REMARK 500 6 VAL B 20 CB VAL B 20 CG1 0.142 REMARK 500 6 PHE B 53 CE1 PHE B 53 CZ 0.119 REMARK 500 7 VAL A 20 CB VAL A 20 CG2 0.155 REMARK 500 7 PHE B 53 CE1 PHE B 53 CZ 0.116 REMARK 500 7 ALA B 215 CA ALA B 215 CB 0.144 REMARK 500 8 MET A 134 CG MET A 134 SD 0.205 REMARK 500 8 PHE B 53 CE1 PHE B 53 CZ 0.117 REMARK 500 8 ALA B 123 CA ALA B 123 CB 0.146 REMARK 500 8 ALA B 215 CA ALA B 215 CB 0.130 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 1 GLY A 93 N - CA - C ANGL. DEV. = -16.3 DEGREES REMARK 500 1 ARG A 156 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 ASP B 241 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 ARG A 156 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 ARG A 173 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 ASP A 193 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 CYS A 212 CA - CB - SG ANGL. DEV. = 9.8 DEGREES REMARK 500 3 ALA A 2 N - CA - C ANGL. DEV. = -16.2 DEGREES REMARK 500 3 GLY A 93 N - CA - C ANGL. DEV. = -15.8 DEGREES REMARK 500 3 ARG A 156 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 ASP B 241 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 4 ALA A 2 N - CA - C ANGL. DEV. = -16.7 DEGREES REMARK 500 4 GLY A 93 N - CA - C ANGL. DEV. = -15.6 DEGREES REMARK 500 5 GLY A 93 N - CA - C ANGL. DEV. = -15.7 DEGREES REMARK 500 5 ARG A 156 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 5 ARG A 156 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 5 CYS A 212 CA - CB - SG ANGL. DEV. = 8.5 DEGREES REMARK 500 6 ARG A 156 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 6 ARG A 156 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 6 ASP B 118 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 7 GLY A 93 N - CA - C ANGL. DEV. = -16.0 DEGREES REMARK 500 8 GLY A 93 N - CA - C ANGL. DEV. = -15.8 DEGREES REMARK 500 8 ARG A 156 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 8 ARG A 156 NE - CZ - NH2 ANGL. DEV. = -3.1 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 1 PRO A 85 5.96 -62.10 REMARK 500 1 THR A 90 -14.72 -46.15 REMARK 500 1 TRP A 110 -91.07 -89.41 REMARK 500 1 THR A 200 63.59 -117.35 REMARK 500 1 LYS A 240 -42.14 -137.37 REMARK 500 1 LYS B 25 -94.14 -81.38 REMARK 500 1 TRP B 110 -77.52 -101.40 REMARK 500 1 VAL B 203 137.47 -170.35 REMARK 500 1 PRO B 232 156.89 -49.76 REMARK 500 1 GLU B 233 38.83 -80.15 REMARK 500 1 SER B 236 -146.25 36.37 REMARK 500 2 TRP A 110 -70.95 -93.53 REMARK 500 2 ALA A 174 -91.39 -55.94 REMARK 500 2 ASP A 179 65.19 -105.09 REMARK 500 2 SER A 236 -146.21 -163.38 REMARK 500 2 LYS B 25 -85.29 -76.07 REMARK 500 2 LYS B 82 -89.27 -127.61 REMARK 500 2 MET B 83 109.31 157.33 REMARK 500 2 PRO B 85 11.87 -62.14 REMARK 500 2 TRP B 110 -74.18 -90.36 REMARK 500 2 ASN B 148 42.82 38.02 REMARK 500 2 ASP B 179 44.53 -83.75 REMARK 500 2 ASP B 193 7.77 52.20 REMARK 500 2 THR B 198 -165.75 -102.82 REMARK 500 2 PRO B 232 157.01 -48.91 REMARK 500 2 SER B 236 -131.52 54.49 REMARK 500 3 LYS A 30 -36.12 -134.75 REMARK 500 3 GLN A 41 -70.13 -54.96 REMARK 500 3 ALA A 50 -8.54 -52.06 REMARK 500 3 ILE A 57 -8.05 -52.74 REMARK 500 3 ALA A 60 10.93 -67.61 REMARK 500 3 LEU A 73 104.81 -169.77 REMARK 500 3 PRO A 85 42.30 -62.74 REMARK 500 3 THR A 90 -9.30 -52.58 REMARK 500 3 TRP A 110 -86.13 -87.88 REMARK 500 3 ASP A 193 34.32 72.72 REMARK 500 3 THR A 200 59.70 -118.07 REMARK 500 3 LYS B 25 -89.14 -85.84 REMARK 500 3 PRO B 85 29.10 -63.00 REMARK 500 3 ASP B 88 76.20 -118.19 REMARK 500 3 TRP B 110 -88.56 -97.29 REMARK 500 3 ASP B 179 31.42 -99.62 REMARK 500 3 ASP B 193 8.19 55.48 REMARK 500 3 ASP B 199 72.14 -118.53 REMARK 500 3 THR B 200 45.47 -159.28 REMARK 500 3 PRO B 232 156.33 -49.32 REMARK 500 3 GLU B 233 37.52 -74.36 REMARK 500 3 SER B 236 -135.64 37.34 REMARK 500 4 SER A 28 1.45 -63.52 REMARK 500 4 GLN A 41 -80.70 -48.76 REMARK 500 REMARK 500 THIS ENTRY HAS 117 RAMACHANDRAN OUTLIERS. 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 NAP A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP B 801 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GO.23662 RELATED DB: TARGETDB REMARK 900 RELATED ID: 1XQ6 RELATED DB: PDB REMARK 900 ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET. DBREF 2Q46 A 2 253 UNP Q94EG6 Y5224_ARATH 2 253 DBREF 2Q46 B 2 253 UNP Q94EG6 Y5224_ARATH 2 253 SEQADV 2Q46 SER A 1 UNP Q94EG6 EXPRESSION TAG SEQADV 2Q46 SER B 1 UNP Q94EG6 EXPRESSION TAG SEQRES 1 A 253 SER ALA ASN LEU PRO THR VAL LEU VAL THR GLY ALA SER SEQRES 2 A 253 GLY ARG THR GLY GLN ILE VAL TYR LYS LYS LEU LYS GLU SEQRES 3 A 253 GLY SER ASP LYS PHE VAL ALA LYS GLY LEU VAL ARG SER SEQRES 4 A 253 ALA GLN GLY LYS GLU LYS ILE GLY GLY GLU ALA ASP VAL SEQRES 5 A 253 PHE ILE GLY ASP ILE THR ASP ALA ASP SER ILE ASN PRO SEQRES 6 A 253 ALA PHE GLN GLY ILE ASP ALA LEU VAL ILE LEU THR SER SEQRES 7 A 253 ALA VAL PRO LYS MET LYS PRO GLY PHE ASP PRO THR LYS SEQRES 8 A 253 GLY GLY ARG PRO GLU PHE ILE PHE GLU ASP GLY GLN TYR SEQRES 9 A 253 PRO GLU GLN VAL ASP TRP ILE GLY GLN LYS ASN GLN ILE SEQRES 10 A 253 ASP ALA ALA LYS VAL ALA GLY VAL LYS HIS ILE VAL VAL SEQRES 11 A 253 VAL GLY SER MET GLY GLY THR ASN PRO ASP HIS PRO LEU SEQRES 12 A 253 ASN LYS LEU GLY ASN GLY ASN ILE LEU VAL TRP LYS ARG SEQRES 13 A 253 LYS ALA GLU GLN TYR LEU ALA ASP SER GLY THR PRO TYR SEQRES 14 A 253 THR ILE ILE ARG ALA GLY GLY LEU LEU ASP LYS GLU GLY SEQRES 15 A 253 GLY VAL ARG GLU LEU LEU VAL GLY LYS ASP ASP GLU LEU SEQRES 16 A 253 LEU GLN THR ASP THR LYS THR VAL PRO ARG ALA ASP VAL SEQRES 17 A 253 ALA GLU VAL CYS ILE GLN ALA LEU LEU PHE GLU GLU ALA SEQRES 18 A 253 LYS ASN LYS ALA PHE ASP LEU GLY SER LYS PRO GLU GLY SEQRES 19 A 253 THR SER THR PRO THR LYS ASP PHE LYS ALA LEU PHE SER SEQRES 20 A 253 GLN VAL THR SER ARG PHE SEQRES 1 B 253 SER ALA ASN LEU PRO THR VAL LEU VAL THR GLY ALA SER SEQRES 2 B 253 GLY ARG THR GLY GLN ILE VAL TYR LYS LYS LEU LYS GLU SEQRES 3 B 253 GLY SER ASP LYS PHE VAL ALA LYS GLY LEU VAL ARG SER SEQRES 4 B 253 ALA GLN GLY LYS GLU LYS ILE GLY GLY GLU ALA ASP VAL SEQRES 5 B 253 PHE ILE GLY ASP ILE THR ASP ALA ASP SER ILE ASN PRO SEQRES 6 B 253 ALA PHE GLN GLY ILE ASP ALA LEU VAL ILE LEU THR SER SEQRES 7 B 253 ALA VAL PRO LYS MET LYS PRO GLY PHE ASP PRO THR LYS SEQRES 8 B 253 GLY GLY ARG PRO GLU PHE ILE PHE GLU ASP GLY GLN TYR SEQRES 9 B 253 PRO GLU GLN VAL ASP TRP ILE GLY GLN LYS ASN GLN ILE SEQRES 10 B 253 ASP ALA ALA LYS VAL ALA GLY VAL LYS HIS ILE VAL VAL SEQRES 11 B 253 VAL GLY SER MET GLY GLY THR ASN PRO ASP HIS PRO LEU SEQRES 12 B 253 ASN LYS LEU GLY ASN GLY ASN ILE LEU VAL TRP LYS ARG SEQRES 13 B 253 LYS ALA GLU GLN TYR LEU ALA ASP SER GLY THR PRO TYR SEQRES 14 B 253 THR ILE ILE ARG ALA GLY GLY LEU LEU ASP LYS GLU GLY SEQRES 15 B 253 GLY VAL ARG GLU LEU LEU VAL GLY LYS ASP ASP GLU LEU SEQRES 16 B 253 LEU GLN THR ASP THR LYS THR VAL PRO ARG ALA ASP VAL SEQRES 17 B 253 ALA GLU VAL CYS ILE GLN ALA LEU LEU PHE GLU GLU ALA SEQRES 18 B 253 LYS ASN LYS ALA PHE ASP LEU GLY SER LYS PRO GLU GLY SEQRES 19 B 253 THR SER THR PRO THR LYS ASP PHE LYS ALA LEU PHE SER SEQRES 20 B 253 GLN VAL THR SER ARG PHE HET NAP A 800 48 HET NAP B 801 48 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 NAP 2(C21 H28 N7 O17 P3) FORMUL 5 HOH *400(H2 O) HELIX 1 1 THR A 16 GLY A 27 1 12 HELIX 2 2 SER A 39 ILE A 46 1 8 HELIX 3 3 ASP A 59 GLN A 68 1 10 HELIX 4 4 TYR A 104 ASP A 109 1 6 HELIX 5 5 TRP A 110 GLY A 124 1 15 HELIX 6 6 HIS A 141 GLY A 149 5 9 HELIX 7 7 ASN A 150 SER A 165 1 16 HELIX 8 8 ASP A 193 THR A 198 5 6 HELIX 9 9 ARG A 205 LEU A 216 1 12 HELIX 10 10 LEU A 217 LYS A 222 5 6 HELIX 11 11 ASP A 241 SER A 247 1 7 HELIX 12 12 GLY B 14 LYS B 25 1 12 HELIX 13 13 SER B 39 ILE B 46 1 8 HELIX 14 14 ASP B 59 ASN B 64 1 6 HELIX 15 15 PRO B 65 GLN B 68 5 4 HELIX 16 16 ASP B 88 GLY B 92 5 5 HELIX 17 17 TYR B 104 ASP B 109 1 6 HELIX 18 18 TRP B 110 GLY B 124 1 15 HELIX 19 19 HIS B 141 GLY B 149 5 9 HELIX 20 20 ASN B 150 SER B 165 1 16 HELIX 21 21 ASP B 193 THR B 198 5 6 HELIX 22 22 ARG B 205 PHE B 218 1 14 HELIX 23 23 GLU B 219 LYS B 222 5 4 HELIX 24 24 ASP B 241 GLN B 248 1 8 SHEET 1 A 8 VAL A 52 ILE A 54 0 SHEET 2 A 8 VAL A 32 VAL A 37 1 N GLY A 35 O PHE A 53 SHEET 3 A 8 THR A 6 THR A 10 1 N VAL A 7 O VAL A 32 SHEET 4 A 8 ALA A 72 ILE A 75 1 O ALA A 72 N LEU A 8 SHEET 5 A 8 HIS A 127 SER A 133 1 O VAL A 129 N ILE A 75 SHEET 6 A 8 TYR A 169 ALA A 174 1 O ILE A 172 N GLY A 132 SHEET 7 A 8 LYS A 224 SER A 230 1 O PHE A 226 N ARG A 173 SHEET 8 A 8 LEU A 187 GLY A 190 -1 N LEU A 188 O GLY A 229 SHEET 1 B 2 LYS A 82 MET A 83 0 SHEET 2 B 2 PHE A 97 ILE A 98 -1 O ILE A 98 N LYS A 82 SHEET 1 C 2 GLY A 176 LEU A 178 0 SHEET 2 C 2 THR A 202 PRO A 204 1 O VAL A 203 N GLY A 176 SHEET 1 D 8 VAL B 52 ILE B 54 0 SHEET 2 D 8 VAL B 32 VAL B 37 1 N GLY B 35 O PHE B 53 SHEET 3 D 8 THR B 6 THR B 10 1 N VAL B 7 O VAL B 32 SHEET 4 D 8 ALA B 72 ILE B 75 1 O ALA B 72 N LEU B 8 SHEET 5 D 8 HIS B 127 SER B 133 1 O VAL B 129 N ILE B 75 SHEET 6 D 8 TYR B 169 ALA B 174 1 O ILE B 172 N GLY B 132 SHEET 7 D 8 LYS B 224 SER B 230 1 O PHE B 226 N ARG B 173 SHEET 8 D 8 LEU B 187 GLY B 190 -1 N LEU B 188 O GLY B 229 SHEET 1 E 2 LYS B 82 MET B 83 0 SHEET 2 E 2 PHE B 97 ILE B 98 -1 O ILE B 98 N LYS B 82 SHEET 1 F 2 GLY B 176 LEU B 178 0 SHEET 2 F 2 THR B 202 PRO B 204 1 O VAL B 203 N LEU B 178 SITE 1 AC1 23 SER A 13 GLY A 14 ARG A 15 THR A 16 SITE 2 AC1 23 ARG A 38 ASP A 56 ILE A 57 LEU A 76 SITE 3 AC1 23 THR A 77 SER A 78 GLN A 103 VAL A 131 SITE 4 AC1 23 GLY A 132 SER A 133 LYS A 155 ALA A 174 SITE 5 AC1 23 GLY A 175 LEU A 177 ARG A 205 HOH A 943 SITE 6 AC1 23 HOH A 957 HOH A 958 HOH A 959 SITE 1 AC2 27 GLY B 11 SER B 13 GLY B 14 ARG B 15 SITE 2 AC2 27 THR B 16 ARG B 38 ASP B 56 ILE B 57 SITE 3 AC2 27 THR B 58 LEU B 76 THR B 77 SER B 78 SITE 4 AC2 27 GLN B 103 VAL B 108 VAL B 131 GLY B 132 SITE 5 AC2 27 SER B 133 LYS B 155 GLY B 175 LEU B 177 SITE 6 AC2 27 ARG B 205 HOH B 832 HOH B 927 HOH B 934 SITE 7 AC2 27 HOH B 952 HOH B 955 HOH B 956 CRYST1 46.750 69.799 83.828 90.00 96.01 90.00 P 1 21 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 0.021390 0.000000 0.002252 0.00000 SCALE2 0.000000 0.014327 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011995 0.00000 MODEL 1