HEADER PROTEIN BINDING 24-AUG-12 4GQV TITLE CRYSTAL STRUCTURE OF CBS-PAIR PROTEIN, CBSX1 FROM ARABIDOPSIS THALIANA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CBS DOMAIN-CONTAINING PROTEIN CBSX1, CHLOROPLASTIC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CBS DOMAIN-CONTAINING PROTEIN 2, ATCDCP2, PROTEIN LOSS OF COMPND 5 THE TIMING OF ET AND JA BIOSYNTHESIS 2, ATLEJ2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: AP22.61, AT4G36910, C7A10.450, CBSX1, CDCP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-GST KEYWDS CBS DOMAIN, THIOREDOXIN, CHLOROPLAST, PLANT, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR B.-C.JEONG,S.H.PARK,K.S.YOO,J.S.SHIN,H.K.SONG REVDAT 3 20-MAR-24 4GQV 1 SEQADV REVDAT 2 03-SEP-14 4GQV 1 JRNL REVDAT 1 16-JAN-13 4GQV 0 JRNL AUTH B.C.JEONG,S.H.PARK,K.S.YOO,J.S.SHIN,H.K.SONG JRNL TITL CRYSTAL STRUCTURE OF THE SINGLE CYSTATHIONINE BETA-SYNTHASE JRNL TITL 2 DOMAIN-CONTAINING PROTEIN CBSX1 FROM ARABIDOPSIS THALIANA JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 430 265 2013 JRNL REFN ISSN 0006-291X JRNL PMID 23159611 JRNL DOI 10.1016/J.BBRC.2012.10.139 REMARK 2 REMARK 2 RESOLUTION. 2.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 11556 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.255 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.310 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1158 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 31.5297 - 4.7796 0.98 1286 142 0.2637 0.3254 REMARK 3 2 4.7796 - 3.7957 1.00 1303 146 0.2244 0.2632 REMARK 3 3 3.7957 - 3.3165 1.00 1298 135 0.2236 0.2670 REMARK 3 4 3.3165 - 3.0136 1.00 1321 164 0.2549 0.3316 REMARK 3 5 3.0136 - 2.7977 1.00 1289 138 0.2656 0.3796 REMARK 3 6 2.7977 - 2.6328 1.00 1326 132 0.2777 0.3831 REMARK 3 7 2.6328 - 2.5010 1.00 1282 144 0.2767 0.3327 REMARK 3 8 2.5010 - 2.3922 0.98 1293 157 0.2811 0.3956 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 957 REMARK 3 ANGLE : 1.190 1299 REMARK 3 CHIRALITY : 0.070 165 REMARK 3 PLANARITY : 0.004 161 REMARK 3 DIHEDRAL : 18.180 359 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 4GQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074524. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97923 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL SI(111) LIQUID REMARK 200 -NITROGEN-COOLED REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11556 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.392 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 60.8000 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM PHOPHATE-ACETATE PH 4.2, 200MM REMARK 280 NACL, 20%(W/W) PEG 8000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.53167 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.06333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.06333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.53167 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: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 27.53167 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 71 REMARK 465 SER A 72 REMARK 465 GLY A 73 REMARK 465 SER A 134 REMARK 465 ILE A 135 REMARK 465 SER A 136 REMARK 465 GLY A 137 REMARK 465 SER A 138 REMARK 465 GLY A 139 REMARK 465 ARG A 140 REMARK 465 THR A 141 REMARK 465 GLU A 142 REMARK 465 ASN A 143 REMARK 465 SER A 144 REMARK 465 MET A 145 REMARK 465 PHE A 146 REMARK 465 PRO A 147 REMARK 465 GLU A 148 REMARK 465 VAL A 149 REMARK 465 ASP A 150 REMARK 465 SER A 151 REMARK 465 THR A 152 REMARK 465 TRP A 153 REMARK 465 LYS A 154 REMARK 465 THR A 155 REMARK 465 PHE A 156 REMARK 465 ASN A 157 REMARK 465 ALA A 158 REMARK 465 VAL A 159 REMARK 465 GLN A 160 REMARK 465 LYS A 161 REMARK 465 LEU A 162 REMARK 465 LEU A 163 REMARK 465 SER A 164 REMARK 465 LYS A 165 REMARK 465 THR A 166 REMARK 465 ASN A 167 REMARK 465 ARG A 230 REMARK 465 SER A 231 REMARK 465 GLY A 232 REMARK 465 ASP A 233 REMARK 465 ARG A 234 REMARK 465 ASN A 235 REMARK 465 ALA A 236 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 ASP A 133 CG OD1 OD2 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 131 66.00 33.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GQW RELATED DB: PDB DBREF 4GQV A 72 236 UNP O23193 CBSX1_ARATH 72 236 SEQADV 4GQV GLY A 71 UNP O23193 EXPRESSION TAG SEQRES 1 A 166 GLY SER GLY VAL TYR THR VAL GLY GLU PHE MET THR LYS SEQRES 2 A 166 LYS GLU ASP LEU HIS VAL VAL LYS PRO THR THR THR VAL SEQRES 3 A 166 ASP GLU ALA LEU GLU LEU LEU VAL GLU ASN ARG ILE THR SEQRES 4 A 166 GLY PHE PRO VAL ILE ASP GLU ASP TRP LYS LEU VAL GLY SEQRES 5 A 166 LEU VAL SER ASP TYR ASP LEU LEU ALA LEU ASP SER ILE SEQRES 6 A 166 SER GLY SER GLY ARG THR GLU ASN SER MET PHE PRO GLU SEQRES 7 A 166 VAL ASP SER THR TRP LYS THR PHE ASN ALA VAL GLN LYS SEQRES 8 A 166 LEU LEU SER LYS THR ASN GLY LYS LEU VAL GLY ASP LEU SEQRES 9 A 166 MET THR PRO ALA PRO LEU VAL VAL GLU GLU LYS THR ASN SEQRES 10 A 166 LEU GLU ASP ALA ALA LYS ILE LEU LEU GLU THR LYS TYR SEQRES 11 A 166 ARG ARG LEU PRO VAL VAL ASP SER ASP GLY LYS LEU VAL SEQRES 12 A 166 GLY ILE ILE THR ARG GLY ASN VAL VAL ARG ALA ALA LEU SEQRES 13 A 166 GLN ILE LYS ARG SER GLY ASP ARG ASN ALA FORMUL 2 HOH *34(H2 O) HELIX 1 1 THR A 76 MET A 81 1 6 HELIX 2 2 GLU A 85 LEU A 87 5 3 HELIX 3 3 THR A 95 ARG A 107 1 13 HELIX 4 4 ASP A 126 LEU A 130 1 5 HELIX 5 5 LEU A 170 MET A 175 1 6 HELIX 6 6 ASN A 187 THR A 198 1 12 HELIX 7 7 THR A 217 GLN A 227 1 11 SHEET 1 A 3 THR A 82 LYS A 83 0 SHEET 2 A 3 LEU A 212 ILE A 215 -1 O ILE A 215 N THR A 82 SHEET 3 A 3 PRO A 204 VAL A 206 -1 N VAL A 205 O GLY A 214 SHEET 1 B 3 GLY A 110 ILE A 114 0 SHEET 2 B 3 LEU A 120 SER A 125 -1 O GLY A 122 N VAL A 113 SHEET 3 B 3 THR A 176 PRO A 177 -1 O THR A 176 N LEU A 123 CRYST1 56.361 56.361 82.595 90.00 90.00 120.00 P 31 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017743 0.010244 0.000000 0.00000 SCALE2 0.000000 0.020488 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012107 0.00000