HEADER HYDROLASE 06-MAY-08 3D1R TITLE STRUCTURE OF E. COLI GLPX WITH ITS SUBSTRATE FRUCTOSE 1,6-BISPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRUCTOSE-1,6-BISPHOSPHATASE CLASS II GLPX; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GLPX; COMPND 5 SYNONYM: D-FRUCTOSE-1,6-BISPHOSPHATE 1-PHOSPHOHYDROLASE CLASS II COMPND 6 GLPX, FBPASE II GLPX; COMPND 7 EC: 3.1.3.11; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: GLPX, B3925, JW3896; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P15-TV-LIC KEYWDS FRUCTOSE-1, 6-BISPHOSPHATASE, 6-BISPHOSPHATE, CARBOHYDRATE KEYWDS 2 METABOLISM, HYDROLASE, MANGANESE, STRUCTURAL GENOMICS, PSI-2, KEYWDS 3 PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL KEYWDS 4 GENOMICS, MCSG EXPDTA X-RAY DIFFRACTION AUTHOR A.SINGER,T.SKARINA,A.DONG,G.BROWN,A.JOACHIMIAK,A.M.EDWARDS, AUTHOR 2 A.F.YAKUNIN,A.SAVCHENKO,MIDWEST CENTER FOR STRUCTURAL GENOMICS AUTHOR 3 (MCSG) REVDAT 6 30-AUG-23 3D1R 1 REMARK REVDAT 5 20-OCT-21 3D1R 1 SEQADV HETSYN REVDAT 4 29-JUL-20 3D1R 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE REVDAT 3 13-JUL-11 3D1R 1 VERSN REVDAT 2 10-FEB-09 3D1R 1 JRNL REVDAT 1 23-DEC-08 3D1R 0 JRNL AUTH G.BROWN,A.SINGER,V.V.LUNIN,M.PROUDFOOT,T.SKARINA,R.FLICK, JRNL AUTH 2 S.KOCHINYAN,R.SANISHVILI,A.JOACHIMIAK,A.M.EDWARDS, JRNL AUTH 3 A.SAVCHENKO,A.F.YAKUNIN JRNL TITL STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE TYPE II JRNL TITL 2 FRUCTOSE-1,6-BISPHOSPHATASE GLPX FROM ESCHERICHIA COLI. JRNL REF J.BIOL.CHEM. V. 284 3784 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19073594 JRNL DOI 10.1074/JBC.M808186200 REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 29726 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1578 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2157 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2368 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 324 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.126 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.631 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2462 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3313 ; 1.627 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 5.900 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;33.188 ;24.184 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 432 ;14.612 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;18.462 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 391 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1802 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1172 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1678 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 296 ; 0.182 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.049 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 33 ; 0.247 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.100 ; 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): 1676 ; 1.090 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2553 ; 1.685 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 883 ; 2.950 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 758 ; 4.532 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 323 REMARK 3 ORIGIN FOR THE GROUP (A): -6.5762 29.0565 22.5878 REMARK 3 T TENSOR REMARK 3 T11: 0.0095 T22: -0.0378 REMARK 3 T33: -0.0473 T12: -0.0084 REMARK 3 T13: -0.0172 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 0.4151 L22: 1.1142 REMARK 3 L33: 0.1730 L12: 0.0780 REMARK 3 L13: -0.0641 L23: -0.1054 REMARK 3 S TENSOR REMARK 3 S11: -0.0120 S12: -0.0170 S13: -0.0127 REMARK 3 S21: -0.1751 S22: -0.0101 S23: 0.0742 REMARK 3 S31: 0.0195 S32: 0.0100 S33: 0.0221 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 3D1R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047482. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : OSMIC OPTICS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31306 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 40.1000 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) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.10 REMARK 200 R MERGE FOR SHELL (I) : 0.46400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.200 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 CODE 1NI9 PROTEIN ATOMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG400, 0.15M CACL2, 0.1M HEPES PH REMARK 280 7.5, 2.5 % PEG3350, 20MM MGCL2, 10MM FRUCTOSE 1,6 BIS PHOSPHATE, REMARK 280 2MM L-CYSTEINE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 2 2 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 A3771 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3816 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 0 REMARK 465 GLU A 243 REMARK 465 ARG A 313 REMARK 465 LEU A 324 REMARK 465 ASP A 325 REMARK 465 ARG A 326 REMARK 465 LYS A 327 REMARK 465 ASP A 328 REMARK 465 PRO A 329 REMARK 465 GLU A 330 REMARK 465 MET A 331 REMARK 465 GLN A 332 REMARK 465 VAL A 333 REMARK 465 HIS A 334 REMARK 465 ILE A 335 REMARK 465 LEU A 336 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 MET A 1 CG SD CE 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 O HOH A 3519 O HOH A 3750 2.13 REMARK 500 OE2 GLU A 213 O HOH A 3722 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 213 CD GLU A 213 OE1 -0.152 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLU A 213 OE1 - CD - OE2 ANGL. DEV. = -22.5 DEGREES 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 CA A 337 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 33 OD1 REMARK 620 2 GLU A 57 OE1 108.2 REMARK 620 3 GLU A 57 OE2 82.8 51.3 REMARK 620 4 HOH A3538 O 87.5 120.0 75.5 REMARK 620 5 HOH A3544 O 90.7 156.4 148.6 73.5 REMARK 620 6 HOH A3731 O 163.8 70.4 106.8 107.3 87.5 REMARK 620 7 HOH A3829 O 102.7 91.5 141.3 142.2 70.1 61.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A3500 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 85 OD1 REMARK 620 2 ASP A 85 OD2 52.3 REMARK 620 3 GLU A 88 OE1 92.5 84.2 REMARK 620 4 GLU A 213 OE1 128.2 81.7 106.5 REMARK 620 5 HOH A3593 O 81.2 90.7 173.6 76.6 REMARK 620 6 HOH A3722 O 143.1 163.6 98.4 82.1 87.6 REMARK 620 7 HOH A3828 O 75.5 125.8 84.5 151.9 95.3 70.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A3504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 194 O REMARK 620 2 SER A 200 O 139.7 REMARK 620 3 VAL A 202 O 93.6 99.4 REMARK 620 4 HOH A3730 O 111.6 105.3 94.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A3502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 FBP A3499 O5P REMARK 620 2 HOH A3675 O 84.1 REMARK 620 3 HOH A3759 O 89.5 166.5 REMARK 620 4 HOH A3761 O 91.5 89.4 78.9 REMARK 620 5 HOH A3762 O 167.6 108.1 79.0 91.0 REMARK 620 6 HOH A3763 O 87.7 104.0 87.5 166.4 87.0 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NI9 RELATED DB: PDB REMARK 900 2.0 A STRUCTURE OF APO-GLPX REMARK 900 RELATED ID: APC5007 RELATED DB: TARGETDB DBREF 3D1R A 1 336 UNP P0A9C9 GLPX_ECOLI 1 336 SEQADV 3D1R GLY A 0 UNP P0A9C9 EXPRESSION TAG SEQADV 3D1R ALA A 61 UNP P0A9C9 ASP 61 ENGINEERED MUTATION SEQRES 1 A 337 GLY MET ARG ARG GLU LEU ALA ILE GLU PHE SER ARG VAL SEQRES 2 A 337 THR GLU SER ALA ALA LEU ALA GLY TYR LYS TRP LEU GLY SEQRES 3 A 337 ARG GLY ASP LYS ASN THR ALA ASP GLY ALA ALA VAL ASN SEQRES 4 A 337 ALA MET ARG ILE MET LEU ASN GLN VAL ASN ILE ASP GLY SEQRES 5 A 337 THR ILE VAL ILE GLY GLU GLY GLU ILE ALA GLU ALA PRO SEQRES 6 A 337 MET LEU TYR ILE GLY GLU LYS VAL GLY THR GLY ARG GLY SEQRES 7 A 337 ASP ALA VAL ASP ILE ALA VAL ASP PRO ILE GLU GLY THR SEQRES 8 A 337 ARG MET THR ALA MET GLY GLN ALA ASN ALA LEU ALA VAL SEQRES 9 A 337 LEU ALA VAL GLY ASP LYS GLY CYS PHE LEU ASN ALA PRO SEQRES 10 A 337 ASP MET TYR MET GLU LYS LEU ILE VAL GLY PRO GLY ALA SEQRES 11 A 337 LYS GLY THR ILE ASP LEU ASN LEU PRO LEU ALA ASP ASN SEQRES 12 A 337 LEU ARG ASN VAL ALA ALA ALA LEU GLY LYS PRO LEU SER SEQRES 13 A 337 GLU LEU THR VAL THR ILE LEU ALA LYS PRO ARG HIS ASP SEQRES 14 A 337 ALA VAL ILE ALA GLU MET GLN GLN LEU GLY VAL ARG VAL SEQRES 15 A 337 PHE ALA ILE PRO ASP GLY ASP VAL ALA ALA SER ILE LEU SEQRES 16 A 337 THR CYS MET PRO ASP SER GLU VAL ASP VAL LEU TYR GLY SEQRES 17 A 337 ILE GLY GLY ALA PRO GLU GLY VAL VAL SER ALA ALA VAL SEQRES 18 A 337 ILE ARG ALA LEU ASP GLY ASP MET ASN GLY ARG LEU LEU SEQRES 19 A 337 ALA ARG HIS ASP VAL LYS GLY ASP ASN GLU GLU ASN ARG SEQRES 20 A 337 ARG ILE GLY GLU GLN GLU LEU ALA ARG CYS LYS ALA MET SEQRES 21 A 337 GLY ILE GLU ALA GLY LYS VAL LEU ARG LEU GLY ASP MET SEQRES 22 A 337 ALA ARG SER ASP ASN VAL ILE PHE SER ALA THR GLY ILE SEQRES 23 A 337 THR LYS GLY ASP LEU LEU GLU GLY ILE SER ARG LYS GLY SEQRES 24 A 337 ASN ILE ALA THR THR GLU THR LEU LEU ILE ARG GLY LYS SEQRES 25 A 337 SER ARG THR ILE ARG ARG ILE GLN SER ILE HIS TYR LEU SEQRES 26 A 337 ASP ARG LYS ASP PRO GLU MET GLN VAL HIS ILE LEU HET FBP A3499 20 HET CA A3500 1 HET MG A3502 1 HET CL A3503 1 HET CA A 337 1 HET MG A3504 1 HETNAM FBP 1,6-DI-O-PHOSPHONO-BETA-D-FRUCTOFURANOSE HETNAM CA CALCIUM ION HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETSYN FBP BETA-FRUCTOSE-1,6-DIPHOSPHATE; FRUCTOSE-1,6- HETSYN 2 FBP BISPHOSPHATE; 1,6-DI-O-PHOSPHONO-BETA-D-FRUCTOSE; 1,6- HETSYN 3 FBP DI-O-PHOSPHONO-D-FRUCTOSE; 1,6-DI-O-PHOSPHONO-FRUCTOSE FORMUL 2 FBP C6 H14 O12 P2 FORMUL 3 CA 2(CA 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 CL CL 1- FORMUL 8 HOH *324(H2 O) HELIX 1 1 ARG A 2 GLU A 4 5 3 HELIX 2 2 LEU A 5 LYS A 22 1 18 HELIX 3 3 ASP A 28 ASN A 45 1 18 HELIX 4 4 GLY A 89 MET A 95 1 7 HELIX 5 5 PRO A 127 LYS A 130 5 4 HELIX 6 6 PRO A 138 GLY A 151 1 14 HELIX 7 7 PRO A 153 GLU A 156 5 4 HELIX 8 8 LYS A 164 ARG A 166 5 3 HELIX 9 9 HIS A 167 GLY A 178 1 12 HELIX 10 10 GLY A 187 LEU A 194 1 8 HELIX 11 11 THR A 195 MET A 197 5 3 HELIX 12 12 ALA A 211 LEU A 224 1 14 HELIX 13 13 ALA A 234 GLY A 240 1 7 HELIX 14 14 GLU A 244 MET A 259 1 16 HELIX 15 15 LEU A 269 ALA A 273 1 5 SHEET 1 A 7 LYS A 71 VAL A 72 0 SHEET 2 A 7 ASP A 50 ILE A 55 -1 N GLY A 51 O VAL A 72 SHEET 3 A 7 ALA A 79 GLU A 88 1 O ILE A 82 N VAL A 54 SHEET 4 A 7 LEU A 101 ASP A 108 -1 O LEU A 101 N GLU A 88 SHEET 5 A 7 VAL A 278 GLY A 284 -1 O SER A 281 N LEU A 104 SHEET 6 A 7 ILE A 300 ARG A 309 -1 O LEU A 306 N ALA A 282 SHEET 7 A 7 SER A 295 LYS A 297 -1 N LYS A 297 O ILE A 300 SHEET 1 B 7 LYS A 71 VAL A 72 0 SHEET 2 B 7 ASP A 50 ILE A 55 -1 N GLY A 51 O VAL A 72 SHEET 3 B 7 ALA A 79 GLU A 88 1 O ILE A 82 N VAL A 54 SHEET 4 B 7 LEU A 101 ASP A 108 -1 O LEU A 101 N GLU A 88 SHEET 5 B 7 VAL A 278 GLY A 284 -1 O SER A 281 N LEU A 104 SHEET 6 B 7 ILE A 300 ARG A 309 -1 O LEU A 306 N ALA A 282 SHEET 7 B 7 ILE A 315 HIS A 322 -1 O HIS A 322 N ALA A 301 SHEET 1 C 6 ARG A 180 ILE A 184 0 SHEET 2 C 6 THR A 158 LEU A 162 1 N VAL A 159 O ARG A 180 SHEET 3 C 6 VAL A 204 GLY A 210 1 O VAL A 204 N THR A 160 SHEET 4 C 6 TYR A 119 VAL A 125 -1 N ILE A 124 O LEU A 205 SHEET 5 C 6 ASP A 227 LEU A 233 -1 O ARG A 231 N GLU A 121 SHEET 6 C 6 VAL A 266 ARG A 268 -1 O LEU A 267 N GLY A 230 LINK OD1 ASP A 33 CA CA A 337 1555 1555 2.40 LINK OE1 GLU A 57 CA CA A 337 1555 1555 2.47 LINK OE2 GLU A 57 CA CA A 337 1555 1555 2.54 LINK OD1 ASP A 85 CA CA A3500 1555 1555 2.50 LINK OD2 ASP A 85 CA CA A3500 1555 1555 2.40 LINK OE1 GLU A 88 CA CA A3500 1555 1555 2.36 LINK O LEU A 194 MG MG A3504 1555 1555 2.26 LINK O SER A 200 MG MG A3504 1555 1555 2.24 LINK O VAL A 202 MG MG A3504 1555 1555 2.23 LINK OE1 GLU A 213 CA CA A3500 1555 1555 2.82 LINK CA CA A 337 O HOH A3538 1555 1555 2.34 LINK CA CA A 337 O HOH A3544 1555 1555 2.39 LINK CA CA A 337 O HOH A3731 1555 1555 2.43 LINK CA CA A 337 O HOH A3829 1555 1555 2.54 LINK O5P FBP A3499 MG MG A3502 1555 1555 2.15 LINK CA CA A3500 O HOH A3593 1555 1555 2.33 LINK CA CA A3500 O HOH A3722 1555 1555 2.35 LINK CA CA A3500 O HOH A3828 1555 1555 2.54 LINK MG MG A3502 O HOH A3675 1555 1555 2.19 LINK MG MG A3502 O HOH A3759 1555 1555 2.18 LINK MG MG A3502 O HOH A3761 1555 1555 2.17 LINK MG MG A3502 O HOH A3762 1555 1555 2.16 LINK MG MG A3502 O HOH A3763 1555 1555 2.16 LINK MG MG A3504 O HOH A3730 1555 1555 2.17 CISPEP 1 MET A 1 ARG A 2 0 -3.79 CRYST1 91.296 91.296 84.913 90.00 90.00 90.00 P 4 2 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 0.010953 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010953 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011777 0.00000