HEADER HYDROLASE 11-MAY-06 2GZR TITLE ENTEROBACTIN AND SALMOCHELIN HYDROLASE IROE COMPND MOL_ID: 1; COMPND 2 MOLECULE: IROE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: IROE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SERINE HYDROLASE, CATALYTIC DYAD, ENTEROBACTIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.A.LARSEN,C.T.WALSH REVDAT 4 15-NOV-23 2GZR 1 REMARK REVDAT 3 30-AUG-23 2GZR 1 SEQADV LINK REVDAT 2 24-FEB-09 2GZR 1 VERSN REVDAT 1 05-SEP-06 2GZR 0 JRNL AUTH N.A.LARSEN,H.LIN,R.WEI,M.A.FISCHBACH,C.T.WALSH JRNL TITL STRUCTURAL CHARACTERIZATION OF ENTEROBACTIN HYDROLASE IROE. JRNL REF BIOCHEMISTRY V. 45 10184 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16922493 JRNL DOI 10.1021/BI060950I REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 16903 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 815 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1895 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GZR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037749. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97960 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18258 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 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: MOLREP REMARK 200 STARTING MODEL: 2GZS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6-10% PEG 3350, 100 MM HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 SER A 140 REMARK 465 ARG A 141 REMARK 465 LYS A 142 REMARK 465 THR A 143 REMARK 465 ASP A 144 REMARK 465 LEU A 145 REMARK 465 HIS A 146 REMARK 465 SER A 147 REMARK 465 GLY A 148 REMARK 465 ARG A 149 REMARK 465 PHE A 150 REMARK 465 SER A 151 REMARK 465 THR A 247 REMARK 465 GLN A 248 REMARK 465 GLY A 249 REMARK 465 ASP A 250 REMARK 465 ASN A 251 REMARK 465 ARG A 252 REMARK 465 GLU A 253 REMARK 465 THR A 254 REMARK 465 HIS A 255 REMARK 465 ALA A 256 REMARK 465 VAL A 257 REMARK 465 ASN A 306 REMARK 465 ALA A 307 REMARK 465 ASN A 308 REMARK 465 TYR A 309 REMARK 465 THR A 310 REMARK 465 ALA A 311 REMARK 465 GLY A 312 REMARK 465 CYS A 313 REMARK 465 HIS A 314 REMARK 465 GLU A 315 REMARK 465 LEU A 316 REMARK 465 SER A 317 REMARK 465 HIS A 318 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 LYS A 46 -75.54 -53.17 REMARK 500 LYS A 109 -125.20 -118.96 REMARK 500 ARG A 167 -57.57 -128.31 REMARK 500 SER A 189 -114.20 63.65 REMARK 500 ARG A 217 64.30 -156.83 REMARK 500 VAL A 229 150.37 -43.47 REMARK 500 LEU A 232 -76.95 -54.65 REMARK 500 SER A 245 -49.56 63.00 REMARK 500 ASN A 284 11.93 58.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GZS RELATED DB: PDB DBREF 2GZR A 41 318 UNP Q6KD95 Q6KD95_ECOLI 41 318 SEQADV 2GZR MSE A 88 UNP Q6KD95 MET 88 MODIFIED RESIDUE SEQADV 2GZR MSE A 95 UNP Q6KD95 MET 95 MODIFIED RESIDUE SEQADV 2GZR MSE A 242 UNP Q6KD95 MET 242 MODIFIED RESIDUE SEQADV 2GZR MSE A 290 UNP Q6KD95 MET 290 MODIFIED RESIDUE SEQRES 1 A 278 PRO ASN ILE ALA ASP LYS GLY SER VAL PHE TYR HIS PHE SEQRES 2 A 278 SER ALA THR SER PHE ASP SER VAL ASP GLY THR ARG HIS SEQRES 3 A 278 TYR ARG VAL TRP THR ALA VAL PRO ASN THR THR ALA PRO SEQRES 4 A 278 ALA SER GLY TYR PRO ILE LEU TYR MSE LEU ASP GLY ASN SEQRES 5 A 278 ALA VAL MSE ASP ARG LEU ASP ASP GLU LEU LEU LYS GLN SEQRES 6 A 278 LEU SER GLU LYS THR PRO PRO VAL ILE VAL ALA VAL GLY SEQRES 7 A 278 TYR GLN THR ASN LEU PRO PHE ASP LEU ASN SER ARG ALA SEQRES 8 A 278 TYR ASP TYR THR PRO ALA ALA GLU SER ARG LYS THR ASP SEQRES 9 A 278 LEU HIS SER GLY ARG PHE SER ARG LYS SER GLY GLY SER SEQRES 10 A 278 ASN ASN PHE ARG GLN LEU LEU GLU THR ARG ILE ALA PRO SEQRES 11 A 278 LYS VAL GLU GLN GLY LEU ASN ILE ASP ARG GLN ARG ARG SEQRES 12 A 278 GLY LEU TRP GLY HIS SER TYR GLY GLY LEU PHE VAL LEU SEQRES 13 A 278 ASP SER TRP LEU SER SER SER TYR PHE ARG SER TYR TYR SEQRES 14 A 278 SER ALA SER PRO SER LEU GLY ARG GLY TYR ASP ALA LEU SEQRES 15 A 278 LEU SER ARG VAL THR ALA VAL GLU PRO LEU GLN PHE CYS SEQRES 16 A 278 THR LYS HIS LEU ALA ILE MSE GLU GLY SER ALA THR GLN SEQRES 17 A 278 GLY ASP ASN ARG GLU THR HIS ALA VAL GLY VAL LEU SER SEQRES 18 A 278 LYS ILE HIS THR THR LEU THR ILE LEU LYS ASP LYS GLY SEQRES 19 A 278 VAL ASN ALA VAL PHE TRP ASP PHE PRO ASN LEU GLY HIS SEQRES 20 A 278 GLY PRO MSE PHE ASN ALA SER PHE ARG GLN ALA LEU LEU SEQRES 21 A 278 ASP ILE SER GLY GLU ASN ALA ASN TYR THR ALA GLY CYS SEQRES 22 A 278 HIS GLU LEU SER HIS MODRES 2GZR MSE A 88 MET SELENOMETHIONINE MODRES 2GZR MSE A 95 MET SELENOMETHIONINE MODRES 2GZR MSE A 242 MET SELENOMETHIONINE MODRES 2GZR MSE A 290 MET SELENOMETHIONINE HET MSE A 88 8 HET MSE A 95 8 HET MSE A 242 8 HET MSE A 290 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) HELIX 1 1 PRO A 41 GLY A 47 1 7 HELIX 2 2 ASP A 90 LEU A 98 1 9 HELIX 3 3 ASP A 99 GLU A 108 1 10 HELIX 4 4 ASP A 126 TYR A 134 1 9 HELIX 5 5 GLY A 156 ARG A 167 1 12 HELIX 6 6 ARG A 167 GLU A 173 1 7 HELIX 7 7 SER A 189 SER A 202 1 14 HELIX 8 8 TYR A 219 ALA A 228 1 10 HELIX 9 9 PRO A 231 CYS A 235 5 5 HELIX 10 10 GLY A 258 LYS A 273 1 16 HELIX 11 11 GLY A 286 SER A 303 1 18 SHEET 1 A 8 TYR A 51 ASP A 59 0 SHEET 2 A 8 HIS A 66 PRO A 74 -1 O TYR A 67 N PHE A 58 SHEET 3 A 8 VAL A 113 TYR A 119 -1 O ILE A 114 N ALA A 72 SHEET 4 A 8 TYR A 83 MSE A 88 1 N MSE A 88 O VAL A 115 SHEET 5 A 8 ILE A 178 HIS A 188 1 O GLY A 184 N TYR A 87 SHEET 6 A 8 SER A 207 ALA A 211 1 O TYR A 209 N LEU A 185 SHEET 7 A 8 HIS A 238 GLU A 243 1 O MSE A 242 N SER A 210 SHEET 8 A 8 ASN A 276 ASP A 281 1 O VAL A 278 N LEU A 239 LINK C TYR A 87 N MSE A 88 1555 1555 1.32 LINK C MSE A 88 N LEU A 89 1555 1555 1.33 LINK C VAL A 94 N MSE A 95 1555 1555 1.33 LINK C MSE A 95 N ASP A 96 1555 1555 1.33 LINK C ILE A 241 N MSE A 242 1555 1555 1.33 LINK C MSE A 242 N GLU A 243 1555 1555 1.33 LINK C PRO A 289 N MSE A 290 1555 1555 1.33 LINK C MSE A 290 N PHE A 291 1555 1555 1.34 CRYST1 36.220 36.980 44.208 111.47 89.69 102.99 P 1 1 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 0.027609 0.006369 0.002411 0.00000 SCALE2 0.000000 0.027752 0.011204 0.00000 SCALE3 0.000000 0.000000 0.024395 0.00000