HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 23-DEC-04 1YDH TITLE X-RAY STRUCTURE OF A LYSINE DECARBOXYLASE-LIKE PROTEIN FROM TITLE 2 ARABIDOPSIS THALIANA GENE AT5G11950 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AT5G11950; 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 GENE: AT5G11950; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834(DE3) P(LACI+RARE); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PVP-13 KEYWDS STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, PSI, CENTER FOR KEYWDS 2 EUKARYOTIC STRUCTURAL GENOMICS, CESG, AT5G11950, LYSINE KEYWDS 3 DECARBOXYLASE-LIKE PROTEIN, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR G.E.WESENBERG,G.N.PHILLIPS JR.,E.BITTO,C.A.BINGMAN,S.T.M.ALLARD, AUTHOR 2 CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS (CESG) REVDAT 5 11-OCT-17 1YDH 1 REMARK REVDAT 4 24-FEB-09 1YDH 1 VERSN REVDAT 3 05-DEC-06 1YDH 1 JRNL REVDAT 2 28-NOV-06 1YDH 1 REMARK REVDAT 1 11-JAN-05 1YDH 0 JRNL AUTH W.B.JEON,S.T.M.ALLARD,C.A.BINGMAN,E.BITTO,B.W.HAN, JRNL AUTH 2 G.E.WESENBERG,G.N.PHILLIPS JR. JRNL TITL X-RAY CRYSTAL STRUCTURES OF THE CONSERVED HYPOTHETICAL JRNL TITL 2 PROTEINS FROM ARABIDOPSIS THALIANA GENE LOCI AT5G11950 AND JRNL TITL 3 AT2G37210. JRNL REF PROTEINS V. 65 1051 2006 JRNL REFN ISSN 0887-3585 JRNL PMID 17048257 JRNL DOI 10.1002/PROT.21166 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 25679 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.063 REMARK 3 FREE R VALUE TEST SET COUNT : 1300 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1698 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.1880 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2796 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 319 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.91500 REMARK 3 B22 (A**2) : -0.15800 REMARK 3 B33 (A**2) : -0.58400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.38600 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.180 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.455 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2859 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3839 ; 1.939 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 363 ; 5.547 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;33.733 ;23.729 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 516 ;14.836 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;21.845 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 429 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2111 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1397 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1968 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 271 ; 0.199 ; 0.200 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): 36 ; 0.271 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.170 ; 0.200 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): 1872 ; 1.579 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2860 ; 2.656 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1136 ; 5.121 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 979 ; 6.985 ; 8.000 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS, SELENIUM C COEFFICIENT FOR STRUCTURE FACTOR REMARK 3 CALCULATION SET TO -9.0000, MOLPROBITY USED TO ASSIST IN FINAL REMARK 3 MODEL BUILDING REMARK 4 REMARK 4 1YDH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97940 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR: WATER COOLED REMARK 200 OPTICS : SAGITALLY FOCUSING 2ND CRYSTAL, REMARK 200 ROSENBAUM-ROCK VERTICAL FOCUSING REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : APS-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25771 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.152 REMARK 200 RESOLUTION RANGE LOW (A) : 35.451 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.38400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2660 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.38400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.401 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE 2.06, RESOLVE 2.06 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: UNMODELED DENSITY BETWEEN ASP 94A AND ILE 133B IS POSSIBLY REMARK 200 DUE TO AN L-LYSINE MOLECULE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML PROTEIN, 13% MPEG 2K, 0.28 M REMARK 280 POTASSIUM NITRATE, 0.1 M MOPS, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K, PH 7.00 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 60.79450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.21350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.79450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.21350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 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 850 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 SER A 1 REMARK 465 GLU A 2 REMARK 465 ASP A 3 REMARK 465 ASN A 4 REMARK 465 PRO A 189 REMARK 465 SER A 190 REMARK 465 HIS A 191 REMARK 465 MSE A 192 REMARK 465 HIS A 193 REMARK 465 VAL A 194 REMARK 465 ALA A 195 REMARK 465 SER A 196 REMARK 465 HIS A 197 REMARK 465 GLU A 198 REMARK 465 SER A 199 REMARK 465 TRP A 200 REMARK 465 LYS A 201 REMARK 465 VAL A 202 REMARK 465 GLU A 203 REMARK 465 GLU A 204 REMARK 465 LEU A 205 REMARK 465 GLY A 206 REMARK 465 ASP A 207 REMARK 465 TYR A 208 REMARK 465 PRO A 209 REMARK 465 GLY A 210 REMARK 465 GLN A 211 REMARK 465 GLU A 212 REMARK 465 ASN A 213 REMARK 465 LYS A 214 REMARK 465 PRO A 215 REMARK 465 GLN A 216 REMARK 465 SER B 1 REMARK 465 GLU B 2 REMARK 465 ASP B 3 REMARK 465 ASN B 4 REMARK 465 GLN B 5 REMARK 465 ARG B 6 REMARK 465 SER B 7 REMARK 465 PRO B 189 REMARK 465 SER B 190 REMARK 465 HIS B 191 REMARK 465 MSE B 192 REMARK 465 HIS B 193 REMARK 465 VAL B 194 REMARK 465 ALA B 195 REMARK 465 SER B 196 REMARK 465 HIS B 197 REMARK 465 GLU B 198 REMARK 465 SER B 199 REMARK 465 TRP B 200 REMARK 465 LYS B 201 REMARK 465 VAL B 202 REMARK 465 GLU B 203 REMARK 465 GLU B 204 REMARK 465 LEU B 205 REMARK 465 GLY B 206 REMARK 465 ASP B 207 REMARK 465 TYR B 208 REMARK 465 PRO B 209 REMARK 465 GLY B 210 REMARK 465 GLN B 211 REMARK 465 GLU B 212 REMARK 465 ASN B 213 REMARK 465 LYS B 214 REMARK 465 PRO B 215 REMARK 465 GLN B 216 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 855 O HOH B 857 1.96 REMARK 500 O HOH A 759 O HOH A 834 2.15 REMARK 500 O HOH B 731 O HOH B 845 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 MSE A 77 SE MSE A 77 CE -0.393 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 8 NE - CZ - NH1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 8 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 LEU A 66 CA - CB - CG ANGL. DEV. = -15.7 DEGREES REMARK 500 ARG B 60 NE - CZ - NH1 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG B 60 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 98 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 LEU B 140 CA - CB - CG ANGL. DEV. = 27.1 DEGREES REMARK 500 LEU B 140 CB - CG - CD1 ANGL. DEV. = -22.0 DEGREES 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 NO3 A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 703 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2A33 RELATED DB: PDB REMARK 900 60 PERCENT SEQUENCE IDENTITY, SAME FOLD REMARK 900 RELATED ID: GO.19912 RELATED DB: TARGETDB DBREF 1YDH A 1 216 UNP Q84MC2 Y5195_ARATH 1 216 DBREF 1YDH B 1 216 UNP Q84MC2 Y5195_ARATH 1 216 SEQADV 1YDH SER A 1 UNP Q84MC2 MET 1 CLONING ARTIFACT SEQADV 1YDH MSE A 54 UNP Q84MC2 MET 54 MODIFIED RESIDUE SEQADV 1YDH MSE A 77 UNP Q84MC2 MET 77 MODIFIED RESIDUE SEQADV 1YDH MSE A 95 UNP Q84MC2 MET 95 MODIFIED RESIDUE SEQADV 1YDH MSE A 102 UNP Q84MC2 MET 102 MODIFIED RESIDUE SEQADV 1YDH MSE A 119 UNP Q84MC2 MET 119 MODIFIED RESIDUE SEQADV 1YDH MSE A 125 UNP Q84MC2 MET 125 MODIFIED RESIDUE SEQADV 1YDH MSE A 181 UNP Q84MC2 MET 181 MODIFIED RESIDUE SEQADV 1YDH MSE A 184 UNP Q84MC2 MET 184 MODIFIED RESIDUE SEQADV 1YDH MSE A 192 UNP Q84MC2 MET 192 MODIFIED RESIDUE SEQADV 1YDH SER B 1 UNP Q84MC2 MET 1 CLONING ARTIFACT SEQADV 1YDH MSE B 54 UNP Q84MC2 MET 54 MODIFIED RESIDUE SEQADV 1YDH MSE B 77 UNP Q84MC2 MET 77 MODIFIED RESIDUE SEQADV 1YDH MSE B 95 UNP Q84MC2 MET 95 MODIFIED RESIDUE SEQADV 1YDH MSE B 102 UNP Q84MC2 MET 102 MODIFIED RESIDUE SEQADV 1YDH MSE B 119 UNP Q84MC2 MET 119 MODIFIED RESIDUE SEQADV 1YDH MSE B 125 UNP Q84MC2 MET 125 MODIFIED RESIDUE SEQADV 1YDH MSE B 181 UNP Q84MC2 MET 181 MODIFIED RESIDUE SEQADV 1YDH MSE B 184 UNP Q84MC2 MET 184 MODIFIED RESIDUE SEQADV 1YDH MSE B 192 UNP Q84MC2 MET 192 MODIFIED RESIDUE SEQRES 1 A 216 SER GLU ASP ASN GLN ARG SER ARG PHE ARG LYS ILE CYS SEQRES 2 A 216 VAL PHE CYS GLY SER HIS SER GLY HIS ARG GLU VAL PHE SEQRES 3 A 216 SER ASP ALA ALA ILE GLU LEU GLY ASN GLU LEU VAL LYS SEQRES 4 A 216 ARG LYS ILE ASP LEU VAL TYR GLY GLY GLY SER VAL GLY SEQRES 5 A 216 LEU MSE GLY LEU ILE SER ARG ARG VAL TYR GLU GLY GLY SEQRES 6 A 216 LEU HIS VAL LEU GLY ILE ILE PRO LYS ALA LEU MSE PRO SEQRES 7 A 216 ILE GLU ILE SER GLY GLU THR VAL GLY ASP VAL ARG VAL SEQRES 8 A 216 VAL ALA ASP MSE HIS GLU ARG LYS ALA ALA MSE ALA GLN SEQRES 9 A 216 GLU ALA GLU ALA PHE ILE ALA LEU PRO GLY GLY TYR GLY SEQRES 10 A 216 THR MSE GLU GLU LEU LEU GLU MSE ILE THR TRP SER GLN SEQRES 11 A 216 LEU GLY ILE HIS LYS LYS THR VAL GLY LEU LEU ASN VAL SEQRES 12 A 216 ASP GLY TYR TYR ASN ASN LEU LEU ALA LEU PHE ASP THR SEQRES 13 A 216 GLY VAL GLU GLU GLY PHE ILE LYS PRO GLY ALA ARG ASN SEQRES 14 A 216 ILE VAL VAL SER ALA PRO THR ALA LYS GLU LEU MSE GLU SEQRES 15 A 216 LYS MSE GLU GLU TYR THR PRO SER HIS MSE HIS VAL ALA SEQRES 16 A 216 SER HIS GLU SER TRP LYS VAL GLU GLU LEU GLY ASP TYR SEQRES 17 A 216 PRO GLY GLN GLU ASN LYS PRO GLN SEQRES 1 B 216 SER GLU ASP ASN GLN ARG SER ARG PHE ARG LYS ILE CYS SEQRES 2 B 216 VAL PHE CYS GLY SER HIS SER GLY HIS ARG GLU VAL PHE SEQRES 3 B 216 SER ASP ALA ALA ILE GLU LEU GLY ASN GLU LEU VAL LYS SEQRES 4 B 216 ARG LYS ILE ASP LEU VAL TYR GLY GLY GLY SER VAL GLY SEQRES 5 B 216 LEU MSE GLY LEU ILE SER ARG ARG VAL TYR GLU GLY GLY SEQRES 6 B 216 LEU HIS VAL LEU GLY ILE ILE PRO LYS ALA LEU MSE PRO SEQRES 7 B 216 ILE GLU ILE SER GLY GLU THR VAL GLY ASP VAL ARG VAL SEQRES 8 B 216 VAL ALA ASP MSE HIS GLU ARG LYS ALA ALA MSE ALA GLN SEQRES 9 B 216 GLU ALA GLU ALA PHE ILE ALA LEU PRO GLY GLY TYR GLY SEQRES 10 B 216 THR MSE GLU GLU LEU LEU GLU MSE ILE THR TRP SER GLN SEQRES 11 B 216 LEU GLY ILE HIS LYS LYS THR VAL GLY LEU LEU ASN VAL SEQRES 12 B 216 ASP GLY TYR TYR ASN ASN LEU LEU ALA LEU PHE ASP THR SEQRES 13 B 216 GLY VAL GLU GLU GLY PHE ILE LYS PRO GLY ALA ARG ASN SEQRES 14 B 216 ILE VAL VAL SER ALA PRO THR ALA LYS GLU LEU MSE GLU SEQRES 15 B 216 LYS MSE GLU GLU TYR THR PRO SER HIS MSE HIS VAL ALA SEQRES 16 B 216 SER HIS GLU SER TRP LYS VAL GLU GLU LEU GLY ASP TYR SEQRES 17 B 216 PRO GLY GLN GLU ASN LYS PRO GLN MODRES 1YDH MSE A 54 MET SELENOMETHIONINE MODRES 1YDH MSE A 77 MET SELENOMETHIONINE MODRES 1YDH MSE A 95 MET SELENOMETHIONINE MODRES 1YDH MSE A 102 MET SELENOMETHIONINE MODRES 1YDH MSE A 119 MET SELENOMETHIONINE MODRES 1YDH MSE A 125 MET SELENOMETHIONINE MODRES 1YDH MSE A 181 MET SELENOMETHIONINE MODRES 1YDH MSE A 184 MET SELENOMETHIONINE MODRES 1YDH MSE B 54 MET SELENOMETHIONINE MODRES 1YDH MSE B 77 MET SELENOMETHIONINE MODRES 1YDH MSE B 95 MET SELENOMETHIONINE MODRES 1YDH MSE B 102 MET SELENOMETHIONINE MODRES 1YDH MSE B 119 MET SELENOMETHIONINE MODRES 1YDH MSE B 125 MET SELENOMETHIONINE MODRES 1YDH MSE B 181 MET SELENOMETHIONINE MODRES 1YDH MSE B 184 MET SELENOMETHIONINE HET MSE A 54 8 HET MSE A 77 8 HET MSE A 95 8 HET MSE A 102 8 HET MSE A 119 8 HET MSE A 125 8 HET MSE A 181 8 HET MSE A 184 8 HET MSE B 54 8 HET MSE B 77 8 HET MSE B 95 8 HET MSE B 102 8 HET MSE B 119 8 HET MSE B 125 8 HET MSE B 181 8 HET MSE B 184 8 HET NO3 A 600 4 HET EDO A 701 4 HET EDO A 703 4 HET EDO B 700 4 HET EDO B 702 4 HETNAM MSE SELENOMETHIONINE HETNAM NO3 NITRATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 16(C5 H11 N O2 SE) FORMUL 3 NO3 N O3 1- FORMUL 4 EDO 4(C2 H6 O2) FORMUL 8 HOH *319(H2 O) HELIX 1 1 ARG A 23 ARG A 40 1 18 HELIX 2 2 VAL A 51 GLY A 64 1 14 HELIX 3 3 LEU A 76 ILE A 81 1 6 HELIX 4 4 ASP A 94 ALA A 106 1 13 HELIX 5 5 GLY A 115 LEU A 131 1 17 HELIX 6 6 VAL A 143 TYR A 146 5 4 HELIX 7 7 TYR A 147 GLU A 160 1 14 HELIX 8 8 LYS A 164 ASN A 169 1 6 HELIX 9 9 THR A 176 TYR A 187 1 12 HELIX 10 10 GLU B 24 ARG B 40 1 17 HELIX 11 11 VAL B 51 GLY B 64 1 14 HELIX 12 12 LEU B 76 ILE B 81 1 6 HELIX 13 13 ASP B 94 ALA B 106 1 13 HELIX 14 14 GLY B 115 LEU B 131 1 17 HELIX 15 15 VAL B 143 TYR B 146 5 4 HELIX 16 16 TYR B 147 GLU B 160 1 14 HELIX 17 17 LYS B 164 ASN B 169 1 6 HELIX 18 18 THR B 176 TYR B 187 1 12 SHEET 1 A 7 ASP A 88 VAL A 92 0 SHEET 2 A 7 VAL A 68 PRO A 73 1 N GLY A 70 O ARG A 90 SHEET 3 A 7 ASP A 43 TYR A 46 1 N LEU A 44 O LEU A 69 SHEET 4 A 7 LYS A 11 PHE A 15 1 N VAL A 14 O VAL A 45 SHEET 5 A 7 ALA A 108 ALA A 111 1 O ALA A 108 N CYS A 13 SHEET 6 A 7 THR A 137 LEU A 141 1 O GLY A 139 N PHE A 109 SHEET 7 A 7 VAL A 171 ALA A 174 1 O VAL A 172 N VAL A 138 SHEET 1 B 7 ASP B 88 VAL B 92 0 SHEET 2 B 7 VAL B 68 PRO B 73 1 N GLY B 70 O ASP B 88 SHEET 3 B 7 ASP B 43 TYR B 46 1 N TYR B 46 O LEU B 69 SHEET 4 B 7 LYS B 11 PHE B 15 1 N ILE B 12 O ASP B 43 SHEET 5 B 7 ALA B 108 ALA B 111 1 O ILE B 110 N PHE B 15 SHEET 6 B 7 THR B 137 LEU B 141 1 O THR B 137 N PHE B 109 SHEET 7 B 7 VAL B 171 ALA B 174 1 O VAL B 172 N VAL B 138 LINK C LEU A 53 N MSE A 54 1555 1555 1.34 LINK C MSE A 54 N GLY A 55 1555 1555 1.34 LINK C LEU A 76 N MSE A 77 1555 1555 1.33 LINK C MSE A 77 N PRO A 78 1555 1555 1.37 LINK C ASP A 94 N MSE A 95 1555 1555 1.33 LINK C MSE A 95 N HIS A 96 1555 1555 1.32 LINK C ALA A 101 N MSE A 102 1555 1555 1.33 LINK C MSE A 102 N ALA A 103 1555 1555 1.34 LINK C THR A 118 N MSE A 119 1555 1555 1.33 LINK C MSE A 119 N GLU A 120 1555 1555 1.33 LINK C GLU A 124 N MSE A 125 1555 1555 1.33 LINK C MSE A 125 N ILE A 126 1555 1555 1.33 LINK C LEU A 180 N MSE A 181 1555 1555 1.33 LINK C MSE A 181 N GLU A 182 1555 1555 1.33 LINK C LYS A 183 N MSE A 184 1555 1555 1.33 LINK C MSE A 184 N GLU A 185 1555 1555 1.33 LINK C LEU B 53 N MSE B 54 1555 1555 1.34 LINK C MSE B 54 N GLY B 55 1555 1555 1.33 LINK C LEU B 76 N MSE B 77 1555 1555 1.33 LINK C MSE B 77 N PRO B 78 1555 1555 1.36 LINK C ASP B 94 N MSE B 95 1555 1555 1.34 LINK C MSE B 95 N HIS B 96 1555 1555 1.34 LINK C ALA B 101 N MSE B 102 1555 1555 1.32 LINK C MSE B 102 N ALA B 103 1555 1555 1.35 LINK C THR B 118 N MSE B 119 1555 1555 1.34 LINK C MSE B 119 N GLU B 120 1555 1555 1.33 LINK C GLU B 124 N MSE B 125 1555 1555 1.34 LINK C MSE B 125 N ILE B 126 1555 1555 1.34 LINK C LEU B 180 N MSE B 181 1555 1555 1.33 LINK C MSE B 181 N GLU B 182 1555 1555 1.33 LINK C LYS B 183 N MSE B 184 1555 1555 1.33 LINK C MSE B 184 N GLU B 185 1555 1555 1.33 SITE 1 AC1 5 GLU A 84 HOH A 825 VAL B 89 ARG B 90 SITE 2 AC1 5 HOH B 813 SITE 1 AC2 4 ARG B 168 VAL B 171 SER B 173 HOH B 734 SITE 1 AC3 9 TYR A 62 THR A 85 GLY A 87 HOH A 742 SITE 2 AC3 9 HOH A 757 HOH A 782 GLY B 87 ASP B 88 SITE 3 AC3 9 HOH B 815 SITE 1 AC4 4 GLY A 161 HIS B 19 SER B 20 GLY B 21 SITE 1 AC5 9 GLY A 17 SER A 18 HIS A 19 GLY A 114 SITE 2 AC5 9 GLY A 115 THR A 118 HOH A 709 HOH A 717 SITE 3 AC5 9 PHE B 162 CRYST1 121.589 80.427 50.709 90.00 102.97 90.00 C 1 2 1 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 0.008200 0.000000 0.001900 0.00000 SCALE2 0.000000 0.012400 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020200 0.00000