HEADER HYDROLASE 03-APR-00 1C81 TITLE MICHAELIS COMPLEX OF FRUCTOSE-2,6-BISPHOSPHATASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRUCTOSE-2,6-BISPHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.3.46; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 ORGAN: LIVER; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3 KEYWDS ROSSMANN FOLD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.LEE,T.W.OLSON,R.W.MCCLARD,J.F.WITTE,S.C.MCFARLAN,L.J.BANASZAK, AUTHOR 2 D.G.LEVITT,A.J.LANGE REVDAT 6 13-MAR-24 1C81 1 COMPND SOURCE REVDAT 5 21-DEC-22 1C81 1 SEQADV HETSYN REVDAT 4 29-JUL-20 1C81 1 COMPND REMARK HETNAM SITE REVDAT 3 12-NOV-14 1C81 1 KEYWDS REVDAT 2 24-FEB-09 1C81 1 VERSN REVDAT 1 10-JUN-03 1C81 0 JRNL AUTH Y.-H.LEE,T.W.OLSON,R.W.MCCLARD,J.F.WITTE,S.C.MCFARLAN, JRNL AUTH 2 L.J.BANASZAK,D.G.LEVITT,A.J.LANGE JRNL TITL REACTION MECHANISM OF FRUCTOSE-2,6-BISPHOSPHATASE SUGGESTED JRNL TITL 2 BY THE CRYSTAL STRUCTURES OF A PSEUDO-MICHAELIS COMPLEX AND JRNL TITL 3 METABOLITE COMPLEXES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.H.LEE,T.W.OLSON,C.M.OGATA,D.G.LEVITT,L.J.BANASZAK, REMARK 1 AUTH 2 A.J.LANGE REMARK 1 TITL CRYSTAL STRUCTURE OF A TRAPPED PHOSPHOENZYME DURING A REMARK 1 TITL 2 CATALYTIC REACTION REMARK 1 REF NAT.STRUCT.BIOL. V. 4 615 1997 REMARK 1 REFN ISSN 1072-8368 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 79.1 REMARK 3 NUMBER OF REFLECTIONS : 5551 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 622 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 : 1555 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 249 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.10 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) : 0.020 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 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: WEIGHTED MATRIX LEAST SQUARES PROCEDURE REMARK 4 REMARK 4 1C81 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-00. REMARK 100 THE DEPOSITION ID IS D_1000001450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9875 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6173 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 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: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM CHLORIDE, HEPES, PH REMARK 280 7.25, EVAPORATION, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 25.80000 REMARK 290 SMTRY3 2 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: DIMERIC 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 -1.000000 0.000000 0.000000 -84.99646 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 25.80000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 49.05624 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 338 O HOH A 493 0.97 REMARK 500 CE2 TYR A 338 O HOH A 649 0.99 REMARK 500 CD2 TYR A 338 O HOH A 656 1.34 REMARK 500 CZ TYR A 338 O HOH A 649 1.35 REMARK 500 O HOH A 678 O HOH A 686 1.63 REMARK 500 CG TYR A 338 O HOH A 656 1.73 REMARK 500 CE2 TYR A 338 O HOH A 656 1.86 REMARK 500 CD2 TYR A 338 O HOH A 649 1.86 REMARK 500 O HOH A 475 O HOH A 476 1.90 REMARK 500 O HOH A 586 O HOH A 609 1.94 REMARK 500 OD1 ASP A 353 O HOH A 639 2.06 REMARK 500 O HOH A 623 O HOH A 662 2.07 REMARK 500 CZ TYR A 338 O HOH A 493 2.11 REMARK 500 CG ASP A 353 O HOH A 639 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N GLY A 267 O HOH A 621 2456 1.81 REMARK 500 C ARG A 266 O HOH A 621 2456 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 260 129.44 -39.27 REMARK 500 SER A 297 73.28 43.13 REMARK 500 SER A 303 -165.16 -115.96 REMARK 500 GLU A 313 -7.25 -54.91 REMARK 500 ARG A 383 21.91 -140.09 REMARK 500 GLU A 385 -99.83 -96.05 REMARK 500 CYS A 391 -132.63 -124.21 REMARK 500 ASP A 405 79.92 34.99 REMARK 500 PRO A 412 1.27 -64.76 REMARK 500 HIS A 419 18.70 55.96 REMARK 500 ALA A 428 -36.30 -33.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TIP RELATED DB: PDB REMARK 900 REACTION MECHANISM OF FRUCTOSE-2,6-BISPHOSPHATASE REMARK 900 RELATED ID: 1C7Z RELATED DB: PDB REMARK 900 FRUCTOSE-2,6-BISPHOSPHATASE COMPLEXED WITH G3P AND PI REMARK 900 RELATED ID: 1C80 RELATED DB: PDB REMARK 900 FRUCTOSE-2,6-BISPHOSPHATASE COMPLEXED WITH GTP AND PI DBREF 1C81 A 251 440 UNP P07953 F261_RAT 251 440 SEQADV 1C81 MET A 250 UNP P07953 INITIATING METHIONINE SEQRES 1 A 191 MET ARG SER ILE TYR LEU CYS ARG HIS GLY GLU SER GLU SEQRES 2 A 191 LEU ASN LEU ARG GLY ARG ILE GLY GLY ASP SER GLY LEU SEQRES 3 A 191 SER ALA ARG GLY LYS GLN TYR ALA TYR ALA LEU ALA ASN SEQRES 4 A 191 PHE ILE ARG SER GLN GLY ILE SER SER LEU LYS VAL TRP SEQRES 5 A 191 THR SER HIS MET LYS ARG THR ILE GLN THR ALA GLU ALA SEQRES 6 A 191 LEU GLY VAL PRO TYR GLU GLN TRP LYS ALA LEU ASN GLU SEQRES 7 A 191 ILE ASP ALA GLY VAL CYS GLU GLU MET THR TYR GLU GLU SEQRES 8 A 191 ILE GLN GLU HIS TYR PRO GLU GLU PHE ALA LEU ARG ASP SEQRES 9 A 191 GLN ASP LYS TYR ARG TYR ARG TYR PRO LYS GLY GLU SER SEQRES 10 A 191 TYR GLU ASP LEU VAL GLN ARG LEU GLU PRO VAL ILE MET SEQRES 11 A 191 GLU LEU GLU ARG GLN GLU ASN VAL LEU VAL ILE CYS HIS SEQRES 12 A 191 GLN ALA VAL MET ARG CYS LEU LEU ALA TYR PHE LEU ASP SEQRES 13 A 191 LYS SER SER ASP GLU LEU PRO TYR LEU LYS CYS PRO LEU SEQRES 14 A 191 HIS THR VAL LEU LYS LEU THR PRO VAL ALA TYR GLY CYS SEQRES 15 A 191 ARG VAL GLU SER ILE TYR LEU ASN VAL HET FDQ A 441 18 HETNAM FDQ 2,5-ANHYDRO-1-DEOXY-1-PHOSPHONO-6-O-PHOSPHONO-D- HETNAM 2 FDQ GLUCITOL HETSYN FDQ D-GLUCO-2,5-ANHYDRO-1-DEOXY-1-PHOSPHONOHEXITOL-6- HETSYN 2 FDQ PHOSPHATE FORMUL 2 FDQ C6 H14 O10 P2 FORMUL 3 HOH *249(H2 O) HELIX 1 1 SER A 261 ARG A 266 1 6 HELIX 2 2 SER A 276 GLY A 294 1 19 HELIX 3 3 MET A 305 GLU A 313 1 9 HELIX 4 4 LYS A 323 ASN A 326 5 4 HELIX 5 5 ALA A 330 GLU A 334 5 5 HELIX 6 6 THR A 337 TYR A 345 1 9 HELIX 7 7 TYR A 345 ASP A 355 1 11 HELIX 8 8 SER A 366 GLU A 382 1 17 HELIX 9 9 HIS A 392 LEU A 404 1 13 HELIX 10 10 GLU A 410 LEU A 414 5 5 SHEET 1 A 6 TYR A 319 GLN A 321 0 SHEET 2 A 6 LYS A 299 THR A 302 1 O VAL A 300 N GLU A 320 SHEET 3 A 6 VAL A 387 CYS A 391 1 N LEU A 388 O LYS A 299 SHEET 4 A 6 ILE A 253 ARG A 257 1 N TYR A 254 O VAL A 387 SHEET 5 A 6 THR A 420 THR A 425 -1 O THR A 420 N ARG A 257 SHEET 6 A 6 ARG A 432 TYR A 437 -1 O ARG A 432 N THR A 425 CRYST1 80.100 51.600 49.300 90.00 95.70 90.00 P 1 21 1 2 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 0.012484 0.000000 0.001246 0.00000 SCALE2 0.000000 0.019380 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020385 0.00000