HEADER METAL BINDING PROTEIN 28-MAY-07 2Z2U TITLE CRYSTAL STRUCTURE OF ARCHAEAL TYW1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0026 PROTEIN MJ0257; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: C41(DE3)CODONPLUS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.SUZUKI,R.ISHITANI,O.NUREKI REVDAT 4 13-MAR-24 2Z2U 1 REMARK REVDAT 3 24-FEB-09 2Z2U 1 VERSN REVDAT 2 15-JAN-08 2Z2U 1 TITLE REVDAT 1 23-OCT-07 2Z2U 0 JRNL AUTH Y.SUZUKI,A.NOMA,T.SUZUKI,M.SENDA,T.SENDA,R.ISHITANI,O.NUREKI JRNL TITL CRYSTAL STRUCTURE OF THE RADICAL SAM ENZYME CATALYZING JRNL TITL 2 TRICYCLIC MODIFIED BASE FORMATION IN TRNA JRNL REF J.MOL.BIOL. V. 372 1204 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17727881 JRNL DOI 10.1016/J.JMB.2007.07.024 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1654039.280 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 11855 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) : 0.220 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1188 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1807 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE : 0.3500 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 181 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2308 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 77 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.65000 REMARK 3 B22 (A**2) : 11.91000 REMARK 3 B33 (A**2) : -8.27000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.76000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.25 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) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.43 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.690 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) : 3.370 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.790 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.150 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.980 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 59.06 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2Z2U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000027450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11855 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 43.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.08400 REMARK 200 FOR SHELL : 18.80 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM POTASSIUM TARTRATE, REMARK 280 20%(W/V) PEG3350, 3%(V/V) PEG400, PH 7.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K 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 30.08950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.32950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.08950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.32950 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: 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 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 CYS A 66 REMARK 465 ILE A 67 REMARK 465 PHE A 68 REMARK 465 CYS A 69 REMARK 465 TRP A 70 REMARK 465 ARG A 71 REMARK 465 VAL A 72 REMARK 465 LEU A 73 REMARK 465 PRO A 74 REMARK 465 ARG A 75 REMARK 465 ASP A 76 REMARK 465 ILE A 77 REMARK 465 GLY A 78 REMARK 465 ILE A 79 REMARK 465 ASP A 80 REMARK 465 ILE A 81 REMARK 465 ARG A 192 REMARK 465 ARG A 193 REMARK 465 ILE A 194 REMARK 465 CYS A 195 REMARK 465 HIS A 254 REMARK 465 VAL A 255 REMARK 465 GLY A 256 REMARK 465 TYR A 257 REMARK 465 SER A 258 REMARK 465 GLN A 259 REMARK 465 LYS A 260 REMARK 465 ARG A 261 REMARK 465 LEU A 262 REMARK 465 LYS A 263 REMARK 465 LYS A 264 REMARK 465 GLU A 265 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 GLU A 4 -18.23 -48.48 REMARK 500 GLN A 63 -82.75 -64.26 REMARK 500 SER A 134 15.25 -152.66 REMARK 500 ASP A 231 63.82 -63.90 REMARK 500 LEU A 233 -8.96 -59.38 REMARK 500 REMARK 500 REMARK: NULL DBREF 2Z2U A 1 311 UNP Q57705 Y257_METJA 1 311 SEQRES 1 A 311 MET ILE PRO GLU GLU ILE TYR LYS ILE LEU ARG LYS GLN SEQRES 2 A 311 ARG TYR GLN ILE ASP GLY HIS THR ALA VAL LYS LEU CYS SEQRES 3 A 311 GLY TRP VAL ARG LYS LYS MET LEU GLU ASP LYS ASN CYS SEQRES 4 A 311 TYR LYS SER LYS PHE TYR GLY ILE GLU THR HIS ARG CYS SEQRES 5 A 311 ILE GLN CYS THR PRO SER VAL ILE TRP CYS GLN GLN ASN SEQRES 6 A 311 CYS ILE PHE CYS TRP ARG VAL LEU PRO ARG ASP ILE GLY SEQRES 7 A 311 ILE ASP ILE SER GLN ILE LYS GLU PRO LYS TRP GLU GLU SEQRES 8 A 311 PRO GLU VAL VAL TYR GLU LYS ILE LEU ALA MET HIS LYS SEQRES 9 A 311 ARG ILE ILE MET GLY TYR ALA GLY VAL LEU ASP ARG VAL SEQRES 10 A 311 GLY GLU LYS LYS PHE LYS GLU ALA LEU GLU PRO LYS HIS SEQRES 11 A 311 VAL ALA ILE SER LEU SER GLY GLU PRO THR LEU TYR PRO SEQRES 12 A 311 TYR LEU ASP GLU LEU ILE LYS ILE PHE HIS LYS ASN GLY SEQRES 13 A 311 PHE THR THR PHE VAL VAL SER ASN GLY ILE LEU THR ASP SEQRES 14 A 311 VAL ILE GLU LYS ILE GLU PRO THR GLN LEU TYR ILE SER SEQRES 15 A 311 LEU ASP ALA TYR ASP LEU ASP SER TYR ARG ARG ILE CYS SEQRES 16 A 311 GLY GLY LYS LYS GLU TYR TRP GLU SER ILE LEU ASN THR SEQRES 17 A 311 LEU ASP ILE LEU LYS GLU LYS LYS ARG THR CYS ILE ARG SEQRES 18 A 311 THR THR LEU ILE ARG GLY TYR ASN ASP ASP ILE LEU LYS SEQRES 19 A 311 PHE VAL GLU LEU TYR GLU ARG ALA ASP VAL HIS PHE ILE SEQRES 20 A 311 GLU LEU LYS SER TYR MET HIS VAL GLY TYR SER GLN LYS SEQRES 21 A 311 ARG LEU LYS LYS GLU ASP MET LEU GLN HIS ASP GLU ILE SEQRES 22 A 311 LEU LYS LEU ALA LYS MET LEU ASP GLU ASN SER SER TYR SEQRES 23 A 311 LYS LEU ILE ASP ASP SER GLU ASP SER ARG VAL ALA LEU SEQRES 24 A 311 LEU GLN ASN GLU ASN ARG LYS ILE ASN PRO LYS LEU FORMUL 2 HOH *77(H2 O) HELIX 1 1 PRO A 3 LYS A 12 1 10 HELIX 2 2 TRP A 28 LEU A 34 1 7 HELIX 3 3 CYS A 39 GLY A 46 1 8 HELIX 4 4 GLU A 48 HIS A 50 5 3 HELIX 5 5 GLU A 91 GLY A 109 1 19 HELIX 6 6 TYR A 110 GLY A 112 5 3 HELIX 7 7 VAL A 113 GLY A 118 1 6 HELIX 8 8 GLY A 118 LEU A 126 1 9 HELIX 9 9 GLU A 138 TYR A 142 5 5 HELIX 10 10 TYR A 144 ASN A 155 1 12 HELIX 11 11 LEU A 167 ILE A 174 1 8 HELIX 12 12 LYS A 198 LYS A 213 1 16 HELIX 13 13 ASP A 231 LYS A 234 5 4 HELIX 14 14 PHE A 235 ASP A 243 1 9 HELIX 15 15 GLN A 269 GLU A 282 1 14 SHEET 1 A10 GLN A 16 ASP A 18 0 SHEET 2 A10 THR A 21 LYS A 24 -1 O VAL A 23 N GLN A 16 SHEET 3 A10 CYS A 52 THR A 56 -1 O THR A 56 N ALA A 22 SHEET 4 A10 HIS A 130 ILE A 133 1 O ALA A 132 N ILE A 53 SHEET 5 A10 THR A 158 SER A 163 1 O PHE A 160 N ILE A 133 SHEET 6 A10 GLN A 178 SER A 182 1 O TYR A 180 N VAL A 161 SHEET 7 A10 THR A 218 LEU A 224 1 O ARG A 221 N ILE A 181 SHEET 8 A10 PHE A 246 SER A 251 1 O LYS A 250 N THR A 222 SHEET 9 A10 VAL A 297 ASN A 302 -1 O LEU A 300 N ILE A 247 SHEET 10 A10 TYR A 286 SER A 292 -1 N LYS A 287 O GLN A 301 CRYST1 60.179 68.659 75.252 90.00 95.75 90.00 C 1 2 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 0.016617 0.000000 0.001673 0.00000 SCALE2 0.000000 0.014565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013356 0.00000