HEADER OXIDOREDUCTASE 30-MAR-08 3CP2 TITLE CRYSTAL STRUCTURE OF GIDA FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA URIDINE 5-CARBOXYMETHYLAMINOMETHYL MODIFICATION ENZYME COMPND 3 GIDA; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: GLUCOSE-INHIBITED DIVISION PROTEIN A; COMPND 6 EC: 1.-.-.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 STRAIN: K12; SOURCE 4 GENE: GIDA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET 14B KEYWDS FAD, NAD, OXIDOREDUCTASE, TRNA, CYTOPLASM, FLAVOPROTEIN, TRNA KEYWDS 2 PROCESSING EXPDTA X-RAY DIFFRACTION AUTHOR A.SCRIMA,S.MEYER,W.VERSEES,A.WITTINGHOFER REVDAT 4 13-MAR-24 3CP2 1 REMARK SEQADV REVDAT 3 24-FEB-09 3CP2 1 VERSN REVDAT 2 01-JUL-08 3CP2 1 JRNL REVDAT 1 24-JUN-08 3CP2 0 JRNL AUTH S.MEYER,A.SCRIMA,W.VERSEES,A.WITTINGHOFER JRNL TITL CRYSTAL STRUCTURES OF THE CONSERVED TRNA-MODIFYING ENZYME JRNL TITL 2 GIDA: IMPLICATIONS FOR ITS INTERACTION WITH MNME AND JRNL TITL 3 SUBSTRATE JRNL REF J.MOL.BIOL. V. 380 532 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18565343 JRNL DOI 10.1016/J.JMB.2008.04.072 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17093 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) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.313 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 920 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1199 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4360 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.4890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3790 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 5 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 72.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 88.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.06000 REMARK 3 B22 (A**2) : -1.06000 REMARK 3 B33 (A**2) : 1.58000 REMARK 3 B12 (A**2) : -0.53000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.028 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.437 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.422 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 23.771 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3862 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5233 ; 1.390 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 488 ; 7.077 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 182 ;36.875 ;24.066 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 651 ;20.951 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;17.867 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 587 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2956 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2002 ; 0.247 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2661 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 166 ; 0.152 ; 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): 43 ; 0.191 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.204 ; 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): 2497 ; 0.530 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3910 ; 0.960 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1503 ; 0.939 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1323 ; 1.608 ; 4.500 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 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 REMARK 4 REMARK 4 3CP2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047043. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0438 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18054 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : 0.04400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.60 REMARK 200 R MERGE FOR SHELL (I) : 0.26700 REMARK 200 R SYM FOR SHELL (I) : 0.38800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRI-SODIUM CITRATE PH 5.5, 550MM REMARK 280 AMMONIUMSULFATE, 3% ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 46.10667 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 23.05333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.58000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 11.52667 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 57.63333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 46.10667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 23.05333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 11.52667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 34.58000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 57.63333 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: 3640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.7 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 -23.05333 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 LEU A 159 REMARK 465 ASP A 160 REMARK 465 GLY A 161 REMARK 465 LYS A 162 REMARK 465 ILE A 163 REMARK 465 HIS A 164 REMARK 465 ILE A 165 REMARK 465 GLY A 166 REMARK 465 LEU A 167 REMARK 465 ASP A 168 REMARK 465 ASN A 169 REMARK 465 TYR A 170 REMARK 465 SER A 171 REMARK 465 GLY A 172 REMARK 465 GLY A 173 REMARK 465 ARG A 174 REMARK 465 ALA A 175 REMARK 465 GLY A 176 REMARK 465 ASP A 177 REMARK 465 PRO A 178 REMARK 465 PRO A 179 REMARK 465 SER A 180 REMARK 465 GLU A 249 REMARK 465 LYS A 250 REMARK 465 THR A 251 REMARK 465 HIS A 252 REMARK 465 ASP A 253 REMARK 465 VAL A 254 REMARK 465 ILE A 255 REMARK 465 ARG A 256 REMARK 465 SER A 257 REMARK 465 ASN A 258 REMARK 465 LEU A 259 REMARK 465 ASP A 260 REMARK 465 ARG A 261 REMARK 465 SER A 262 REMARK 465 PRO A 263 REMARK 465 MET A 264 REMARK 465 TYR A 265 REMARK 465 ALA A 266 REMARK 465 GLY A 267 REMARK 465 VAL A 268 REMARK 465 ILE A 269 REMARK 465 GLU A 270 REMARK 465 GLY A 271 REMARK 465 VAL A 272 REMARK 465 GLY A 273 REMARK 465 PRO A 274 REMARK 465 ARG A 275 REMARK 465 TYR A 276 REMARK 465 CYS A 277 REMARK 465 PRO A 278 REMARK 465 SER A 279 REMARK 465 ILE A 280 REMARK 465 GLU A 281 REMARK 465 ASP A 282 REMARK 465 LYS A 283 REMARK 465 VAL A 284 REMARK 465 MET A 285 REMARK 465 ARG A 286 REMARK 465 PHE A 287 REMARK 465 ALA A 288 REMARK 465 ARG A 554 REMARK 465 GLN A 555 REMARK 465 GLN A 556 REMARK 465 ASP A 557 REMARK 465 GLU A 558 REMARK 465 ILE A 559 REMARK 465 GLU A 560 REMARK 465 LYS A 561 REMARK 465 GLN A 562 REMARK 465 LEU A 563 REMARK 465 ARG A 564 REMARK 465 ASN A 565 REMARK 465 GLU A 566 REMARK 465 ASN A 567 REMARK 465 THR A 568 REMARK 465 LEU A 569 REMARK 465 LEU A 570 REMARK 465 PRO A 571 REMARK 465 ALA A 572 REMARK 465 THR A 573 REMARK 465 LEU A 574 REMARK 465 ASP A 575 REMARK 465 TYR A 576 REMARK 465 ARG A 577 REMARK 465 GLN A 578 REMARK 465 VAL A 579 REMARK 465 SER A 580 REMARK 465 GLY A 581 REMARK 465 LEU A 582 REMARK 465 SER A 583 REMARK 465 ASN A 584 REMARK 465 GLU A 585 REMARK 465 VAL A 586 REMARK 465 ILE A 587 REMARK 465 ALA A 588 REMARK 465 LYS A 589 REMARK 465 LEU A 590 REMARK 465 ASN A 591 REMARK 465 ASP A 592 REMARK 465 HIS A 593 REMARK 465 LYS A 594 REMARK 465 PRO A 595 REMARK 465 ALA A 596 REMARK 465 SER A 597 REMARK 465 ILE A 598 REMARK 465 GLY A 599 REMARK 465 GLN A 600 REMARK 465 ALA A 601 REMARK 465 SER A 602 REMARK 465 ARG A 603 REMARK 465 ILE A 604 REMARK 465 SER A 605 REMARK 465 GLY A 606 REMARK 465 VAL A 607 REMARK 465 THR A 608 REMARK 465 PRO A 609 REMARK 465 ALA A 610 REMARK 465 ALA A 611 REMARK 465 ILE A 612 REMARK 465 SER A 613 REMARK 465 ILE A 614 REMARK 465 LEU A 615 REMARK 465 LEU A 616 REMARK 465 VAL A 617 REMARK 465 TRP A 618 REMARK 465 LEU A 619 REMARK 465 LYS A 620 REMARK 465 LYS A 621 REMARK 465 GLN A 622 REMARK 465 GLY A 623 REMARK 465 MET A 624 REMARK 465 LEU A 625 REMARK 465 ARG A 626 REMARK 465 ARG A 627 REMARK 465 SER A 628 REMARK 465 ALA A 629 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 ARG A 147 CD NE CZ NH1 NH2 REMARK 470 ARG A 290 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 427 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 549 CG CD OE1 OE2 REMARK 470 TYR A 551 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE A 552 CG1 CG2 CD1 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 PRO A 4 -84.11 -23.60 REMARK 500 ALA A 22 -70.89 -79.41 REMARK 500 MET A 23 -26.95 -37.70 REMARK 500 ALA A 26 -74.91 -55.76 REMARK 500 HIS A 37 -64.16 -17.52 REMARK 500 THR A 41 61.10 -116.21 REMARK 500 CYS A 47 -126.64 -100.44 REMARK 500 ILE A 54 121.40 -38.03 REMARK 500 ASN A 85 39.59 71.14 REMARK 500 SER A 87 -67.79 -26.32 REMARK 500 LYS A 88 -153.77 -80.60 REMARK 500 PRO A 90 -39.07 -28.90 REMARK 500 ASN A 117 -11.67 78.91 REMARK 500 ALA A 124 -172.86 -53.99 REMARK 500 ASN A 132 83.31 33.07 REMARK 500 ASP A 133 -12.63 93.98 REMARK 500 MET A 142 5.65 -65.98 REMARK 500 THR A 154 -124.11 -140.09 REMARK 500 GLU A 189 4.89 -62.04 REMARK 500 PRO A 191 39.90 -59.50 REMARK 500 PRO A 203 -159.12 -62.65 REMARK 500 ASP A 206 95.26 -66.72 REMARK 500 ALA A 207 -19.27 -47.69 REMARK 500 ASP A 221 150.75 -43.27 REMARK 500 THR A 247 -161.12 -66.51 REMARK 500 ARG A 290 46.69 -87.17 REMARK 500 LEU A 316 135.05 -178.17 REMARK 500 ASP A 319 -74.98 -34.67 REMARK 500 PHE A 361 -91.70 -76.78 REMARK 500 ILE A 371 -8.51 -57.76 REMARK 500 LEU A 385 -57.58 -29.79 REMARK 500 ASP A 416 -70.30 -38.27 REMARK 500 THR A 419 -79.74 -77.03 REMARK 500 ARG A 427 -17.48 -46.60 REMARK 500 ARG A 432 -133.16 -92.99 REMARK 500 ARG A 440 170.54 -54.74 REMARK 500 ASN A 443 23.73 -173.62 REMARK 500 VAL A 458 110.16 90.31 REMARK 500 ASP A 459 -153.12 -81.46 REMARK 500 PRO A 487 106.01 -35.92 REMARK 500 SER A 488 92.63 35.23 REMARK 500 ALA A 489 31.26 -85.45 REMARK 500 GLU A 490 15.25 40.80 REMARK 500 THR A 500 -79.52 -62.60 REMARK 500 LEU A 503 -73.07 -59.55 REMARK 500 ARG A 505 -10.96 -175.16 REMARK 500 GLU A 506 91.97 68.31 REMARK 500 ALA A 530 170.02 57.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 503 SER A 504 -139.26 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 SO4 A 630 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CP8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GIDA FROM CHLOROBIUM TEPIDUM DBREF 3CP2 A 1 629 UNP P0A6U3 GIDA_ECOLI 1 629 SEQADV 3CP2 MET A -19 UNP P0A6U3 INITIATING METHIONINE SEQADV 3CP2 GLY A -18 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 SER A -17 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 SER A -16 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 HIS A -15 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 HIS A -14 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 HIS A -13 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 HIS A -12 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 HIS A -11 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 HIS A -10 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 SER A -9 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 SER A -8 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 GLY A -7 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 LEU A -6 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 VAL A -5 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 PRO A -4 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 ARG A -3 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 GLY A -2 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 SER A -1 UNP P0A6U3 EXPRESSION TAG SEQADV 3CP2 HIS A 0 UNP P0A6U3 EXPRESSION TAG SEQRES 1 A 649 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 649 LEU VAL PRO ARG GLY SER HIS MET PHE TYR PRO ASP PRO SEQRES 3 A 649 PHE ASP VAL ILE ILE ILE GLY GLY GLY HIS ALA GLY THR SEQRES 4 A 649 GLU ALA ALA MET ALA ALA ALA ARG MET GLY GLN GLN THR SEQRES 5 A 649 LEU LEU LEU THR HIS ASN ILE ASP THR LEU GLY GLN MET SEQRES 6 A 649 SER CYS ASN PRO ALA ILE GLY GLY ILE GLY LYS GLY HIS SEQRES 7 A 649 LEU VAL LYS GLU VAL ASP ALA LEU GLY GLY LEU MET ALA SEQRES 8 A 649 LYS ALA ILE ASP GLN ALA GLY ILE GLN PHE ARG ILE LEU SEQRES 9 A 649 ASN ALA SER LYS GLY PRO ALA VAL ARG ALA THR ARG ALA SEQRES 10 A 649 GLN ALA ASP ARG VAL LEU TYR ARG GLN ALA VAL ARG THR SEQRES 11 A 649 ALA LEU GLU ASN GLN PRO ASN LEU MET ILE PHE GLN GLN SEQRES 12 A 649 ALA VAL GLU ASP LEU ILE VAL GLU ASN ASP ARG VAL VAL SEQRES 13 A 649 GLY ALA VAL THR GLN MET GLY LEU LYS PHE ARG ALA LYS SEQRES 14 A 649 ALA VAL VAL LEU THR VAL GLY THR PHE LEU ASP GLY LYS SEQRES 15 A 649 ILE HIS ILE GLY LEU ASP ASN TYR SER GLY GLY ARG ALA SEQRES 16 A 649 GLY ASP PRO PRO SER ILE PRO LEU SER ARG ARG LEU ARG SEQRES 17 A 649 GLU LEU PRO LEU ARG VAL GLY ARG LEU LYS THR GLY THR SEQRES 18 A 649 PRO PRO ARG ILE ASP ALA ARG THR ILE ASP PHE SER VAL SEQRES 19 A 649 LEU ALA GLN GLN HIS GLY ASP ASN PRO MET PRO VAL PHE SEQRES 20 A 649 SER PHE MET GLY ASN ALA SER GLN HIS PRO GLN GLN VAL SEQRES 21 A 649 PRO CYS TYR ILE THR HIS THR ASN GLU LYS THR HIS ASP SEQRES 22 A 649 VAL ILE ARG SER ASN LEU ASP ARG SER PRO MET TYR ALA SEQRES 23 A 649 GLY VAL ILE GLU GLY VAL GLY PRO ARG TYR CYS PRO SER SEQRES 24 A 649 ILE GLU ASP LYS VAL MET ARG PHE ALA ASP ARG ASN GLN SEQRES 25 A 649 HIS GLN ILE PHE LEU GLU PRO GLU GLY LEU THR SER ASN SEQRES 26 A 649 GLU ILE TYR PRO ASN GLY ILE SER THR SER LEU PRO PHE SEQRES 27 A 649 ASP VAL GLN MET GLN ILE VAL ARG SER MET GLN GLY MET SEQRES 28 A 649 GLU ASN ALA LYS ILE VAL ARG PRO GLY TYR ALA ILE GLU SEQRES 29 A 649 TYR ASP PHE PHE ASP PRO ARG ASP LEU LYS PRO THR LEU SEQRES 30 A 649 GLU SER LYS PHE ILE GLN GLY LEU PHE PHE ALA GLY GLN SEQRES 31 A 649 ILE ASN GLY THR THR GLY TYR GLU GLU ALA ALA ALA GLN SEQRES 32 A 649 GLY LEU LEU ALA GLY LEU ASN ALA ALA ARG LEU SER ALA SEQRES 33 A 649 ASP LYS GLU GLY TRP ALA PRO ALA ARG SER GLN ALA TYR SEQRES 34 A 649 LEU GLY VAL LEU VAL ASP ASP LEU CYS THR LEU GLY THR SEQRES 35 A 649 LYS GLU PRO TYR ARG MET PHE THR SER ARG ALA GLU TYR SEQRES 36 A 649 ARG LEU MET LEU ARG GLU ASP ASN ALA ASP LEU ARG LEU SEQRES 37 A 649 THR GLU ILE GLY ARG GLU LEU GLY LEU VAL ASP ASP GLU SEQRES 38 A 649 ARG TRP ALA ARG PHE ASN GLU LYS LEU GLU ASN ILE GLU SEQRES 39 A 649 ARG GLU ARG GLN ARG LEU LYS SER THR TRP VAL THR PRO SEQRES 40 A 649 SER ALA GLU ALA ALA ALA GLU VAL ASN ALA HIS LEU THR SEQRES 41 A 649 ALA PRO LEU SER ARG GLU ALA SER GLY GLU ASP LEU LEU SEQRES 42 A 649 ARG ARG PRO GLU MET THR TYR GLU LYS LEU THR THR LEU SEQRES 43 A 649 THR PRO PHE ALA PRO ALA LEU THR ASP GLU GLN ALA ALA SEQRES 44 A 649 GLU GLN VAL GLU ILE GLN VAL LYS TYR GLU GLY TYR ILE SEQRES 45 A 649 ALA ARG GLN GLN ASP GLU ILE GLU LYS GLN LEU ARG ASN SEQRES 46 A 649 GLU ASN THR LEU LEU PRO ALA THR LEU ASP TYR ARG GLN SEQRES 47 A 649 VAL SER GLY LEU SER ASN GLU VAL ILE ALA LYS LEU ASN SEQRES 48 A 649 ASP HIS LYS PRO ALA SER ILE GLY GLN ALA SER ARG ILE SEQRES 49 A 649 SER GLY VAL THR PRO ALA ALA ILE SER ILE LEU LEU VAL SEQRES 50 A 649 TRP LEU LYS LYS GLN GLY MET LEU ARG ARG SER ALA HET SO4 A 630 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *5(H2 O) HELIX 1 1 HIS A 16 MET A 28 1 13 HELIX 2 2 GLY A 55 LEU A 66 1 12 HELIX 3 3 LEU A 69 ALA A 77 1 9 HELIX 4 4 ASP A 100 ASN A 114 1 15 HELIX 5 5 ILE A 181 GLU A 189 1 9 HELIX 6 6 ARG A 208 ILE A 210 5 3 HELIX 7 7 ASN A 232 HIS A 236 5 5 HELIX 8 8 PRO A 317 SER A 327 1 11 HELIX 9 9 ASP A 349 LEU A 353 5 5 HELIX 10 10 GLY A 369 GLY A 373 5 5 HELIX 11 11 GLY A 376 ALA A 396 1 21 HELIX 12 12 ALA A 408 LEU A 420 1 13 HELIX 13 13 PRO A 425 PHE A 429 5 5 HELIX 14 14 ALA A 433 LEU A 439 1 7 HELIX 15 15 ASN A 443 GLU A 454 1 12 HELIX 16 16 ASP A 459 THR A 483 1 25 HELIX 17 17 ALA A 491 ASN A 496 1 6 HELIX 18 18 GLY A 509 ARG A 514 1 6 HELIX 19 19 THR A 519 LEU A 526 1 8 HELIX 20 20 THR A 527 ALA A 530 5 4 HELIX 21 21 ASP A 535 TYR A 548 1 14 SHEET 1 A 5 LEU A 118 PHE A 121 0 SHEET 2 A 5 THR A 32 LEU A 35 1 N THR A 32 O MET A 119 SHEET 3 A 5 VAL A 9 ILE A 12 1 N VAL A 9 O LEU A 33 SHEET 4 A 5 ALA A 150 LEU A 153 1 O VAL A 152 N ILE A 12 SHEET 5 A 5 LEU A 365 PHE A 367 1 O PHE A 366 N LEU A 153 SHEET 1 B 3 ALA A 50 GLY A 52 0 SHEET 2 B 3 ALA A 94 ALA A 99 -1 O ALA A 97 N ILE A 51 SHEET 3 B 3 GLY A 78 LEU A 84 -1 N LEU A 84 O ALA A 94 SHEET 1 C 3 ASP A 127 GLU A 131 0 SHEET 2 C 3 ARG A 134 VAL A 139 -1 O GLY A 137 N ILE A 129 SHEET 3 C 3 LYS A 145 ARG A 147 -1 O PHE A 146 N ALA A 138 SHEET 1 D 2 LEU A 197 THR A 201 0 SHEET 2 D 2 TYR A 341 TYR A 345 -1 O ILE A 343 N THR A 199 SHEET 1 E 5 ILE A 205 ASP A 206 0 SHEET 2 E 5 GLU A 306 PRO A 309 -1 O ILE A 307 N ILE A 205 SHEET 3 E 5 ILE A 295 PRO A 299 -1 N GLU A 298 O TYR A 308 SHEET 4 E 5 CYS A 242 THR A 245 -1 N THR A 245 O ILE A 295 SHEET 5 E 5 ALA A 216 GLN A 218 -1 N GLN A 218 O CYS A 242 SHEET 1 F 2 TRP A 484 VAL A 485 0 SHEET 2 F 2 ALA A 507 SER A 508 -1 O ALA A 507 N VAL A 485 CISPEP 1 ASN A 222 PRO A 223 0 7.52 SITE 1 AC1 3 HIS A 16 ALA A 17 GLN A 370 CRYST1 197.600 197.600 69.160 90.00 90.00 120.00 P 65 2 2 12 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 0.005061 0.002922 0.000000 0.00000 SCALE2 0.000000 0.005844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014459 0.00000