HEADER OXIDOREDUCTASE 02-JUN-09 3HOG TITLE METAL-FREE TOMATO CHLOROPLAST SUPEROXIDE DISMUTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [CU-ZN], CHLOROPLASTIC; COMPND 3 CHAIN: A; COMPND 4 EC: 1.15.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SOLANUM LYCOPERSICUM; SOURCE 3 ORGANISM_COMMON: TOMATO; SOURCE 4 ORGANISM_TAXID: 4081; SOURCE 5 GENE: SODCP.2; 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: PAG8H KEYWDS OXIDOREDUCTASE, TOMATO CU, ZN SUPEROXIDE DISMUTASE, ANTIOXIDANT, KEYWDS 2 METAL-BINDING, CHLOROPLAST, DISULFIDE BOND, TRANSIT PEPTIDE EXPDTA X-RAY DIFFRACTION AUTHOR A.GALALELDEEN,A.B.TAYLOR,P.J.HART REVDAT 3 06-SEP-23 3HOG 1 REMARK LINK REVDAT 2 18-JAN-12 3HOG 1 VERSN DBREF SEQRES REMARK REVDAT 2 2 1 KEYWDS REVDAT 1 23-JUN-10 3HOG 0 JRNL AUTH A.GALALELDEEN,A.B.TAYLOR,P.J.HART JRNL TITL BIOPHYSICAL PROPERTIES OF TOMATO CHLOROPLAST SOD JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.4_4) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 3 NUMBER OF REFLECTIONS : 12759 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 650 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 27.5383 - 3.1595 0.84 2410 128 0.1972 0.2387 REMARK 3 2 3.1595 - 2.5083 0.99 2684 142 0.2108 0.2507 REMARK 3 3 2.5083 - 2.1914 0.81 2161 114 0.2033 0.2906 REMARK 3 4 2.1914 - 1.9911 0.97 2559 137 0.1950 0.2226 REMARK 3 5 1.9911 - 1.8500 0.87 2295 129 0.2512 0.3121 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 : 0.36 REMARK 3 B_SOL : 68.21 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.03660 REMARK 3 B22 (A**2) : -2.03660 REMARK 3 B33 (A**2) : 4.07310 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 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 : 0.010 NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: NULL REMARK 4 REMARK 4 3HOG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053385. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : CONFOCAL OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13329 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 FOR THE DATA SET : 30.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.56800 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1AZV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.056 M SODIUM PHOSPHATE, 1.344 M REMARK 280 POTASSIUM PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 35.39200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.41750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.41750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 53.08800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.41750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.41750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.69600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.41750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.41750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 53.08800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.41750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.41750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 17.69600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 35.39200 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: 1850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 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 186 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 72 REMARK 465 ALA A 73 REMARK 465 PRO A 74 REMARK 465 GLY A 75 REMARK 465 ASP A 76 REMARK 465 GLU A 77 REMARK 465 ILE A 78 REMARK 465 ARG A 79 REMARK 465 GLU A 123 REMARK 465 ASP A 124 REMARK 465 ASP A 125 REMARK 465 LEU A 126 REMARK 465 GLY A 127 REMARK 465 LYS A 128 REMARK 465 GLY A 129 REMARK 465 GLY A 130 REMARK 465 HIS A 131 REMARK 465 GLU A 132 REMARK 465 LEU A 133 REMARK 465 SER A 134 REMARK 465 LEU A 135 REMARK 465 THR A 136 REMARK 465 THR A 137 REMARK 465 GLY A 138 REMARK 465 ASN A 139 REMARK 465 ALA A 140 REMARK 465 GLY A 141 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 THR A 2 -31.04 -23.76 REMARK 500 SER A 13 -169.99 -165.66 REMARK 500 ASP A 25 -116.57 54.75 REMARK 500 GLN A 103 43.61 -141.53 REMARK 500 ARG A 115 -159.51 -101.46 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 K A 155 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 26 O REMARK 620 2 GLY A 27 O 65.1 REMARK 620 3 ASN A 102 O 159.5 133.6 REMARK 620 4 ASN A 102 OD1 107.0 85.2 71.3 REMARK 620 5 HOH A 168 O 124.5 67.7 75.6 96.3 REMARK 620 6 HOH A 172 O 90.2 100.8 93.2 162.6 71.6 REMARK 620 7 HOH A 257 O 75.5 140.6 85.0 104.8 145.1 81.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 155 DBREF 3HOG A 1 154 UNP P14831 SODCP_SOLLC 64 217 SEQRES 1 A 154 ALA THR LYS LYS ALA VAL ALA VAL LEU LYS GLY ASN SER SEQRES 2 A 154 ASN VAL GLU GLY VAL VAL THR LEU SER GLN ASP ASP ASP SEQRES 3 A 154 GLY PRO THR THR VAL ASN VAL ARG ILE THR GLY LEU ALA SEQRES 4 A 154 PRO GLY LEU HIS GLY PHE HIS LEU HIS GLU TYR GLY ASP SEQRES 5 A 154 THR THR ASN GLY CYS MET SER THR GLY ALA HIS PHE ASN SEQRES 6 A 154 PRO ASN LYS LEU THR HIS GLY ALA PRO GLY ASP GLU ILE SEQRES 7 A 154 ARG HIS ALA GLY ASP LEU GLY ASN ILE VAL ALA ASN ALA SEQRES 8 A 154 ASP GLY VAL ALA GLU VAL THR LEU VAL ASP ASN GLN ILE SEQRES 9 A 154 PRO LEU THR GLY PRO ASN SER VAL VAL GLY ARG ALA LEU SEQRES 10 A 154 VAL VAL HIS GLU LEU GLU ASP ASP LEU GLY LYS GLY GLY SEQRES 11 A 154 HIS GLU LEU SER LEU THR THR GLY ASN ALA GLY GLY ARG SEQRES 12 A 154 LEU ALA CYS GLY VAL VAL GLY LEU THR PRO ILE HET K A 155 1 HETNAM K POTASSIUM ION FORMUL 2 K K 1+ FORMUL 3 HOH *163(H2 O) HELIX 1 1 ASN A 55 GLY A 61 5 7 SHEET 1 A 5 ALA A 95 ASP A 101 0 SHEET 2 A 5 THR A 29 THR A 36 -1 N VAL A 31 O LEU A 99 SHEET 3 A 5 GLU A 16 GLN A 23 -1 N GLU A 16 O THR A 36 SHEET 4 A 5 LYS A 3 LYS A 10 -1 N LEU A 9 O GLY A 17 SHEET 5 A 5 GLY A 150 LEU A 151 -1 O GLY A 150 N VAL A 6 SHEET 1 B 4 ILE A 87 ALA A 89 0 SHEET 2 B 4 GLY A 41 HIS A 48 -1 N GLY A 41 O ALA A 89 SHEET 3 B 4 ALA A 116 GLU A 121 -1 O ALA A 116 N HIS A 48 SHEET 4 B 4 ARG A 143 VAL A 148 -1 O ALA A 145 N VAL A 119 SSBOND 1 CYS A 57 CYS A 146 1555 1555 2.06 LINK O ASP A 26 K K A 155 1555 1555 2.94 LINK O GLY A 27 K K A 155 1555 1555 3.03 LINK O ASN A 102 K K A 155 1555 1555 3.17 LINK OD1 ASN A 102 K K A 155 1555 1555 3.49 LINK K K A 155 O HOH A 168 1555 1555 3.10 LINK K K A 155 O HOH A 172 1555 1555 3.21 LINK K K A 155 O HOH A 257 1555 1555 3.35 SITE 1 AC1 4 ASP A 26 GLY A 27 ASN A 102 HOH A 168 CRYST1 66.835 66.835 70.784 90.00 90.00 90.00 P 43 21 2 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 0.014962 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014127 0.00000