HEADER TRANSFERASE 09-MAR-06 2CGL TITLE CRYSTAL STRUCTURE OF L-RHAMNULOSE KINASE FROM ESCHERICHIA COLI IN TITLE 2 COMPLEX WITH L-FRUCTOSE, ADP AND A MODELED ATP GAMMA PHOSPHATE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHAMNULOKINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L-RHAMNULOSE KINASE, RHAMNULOSE KINASE; COMPND 5 EC: 2.7.1.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI BL21(DE3); SOURCE 3 ORGANISM_TAXID: 469008; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: JM105; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PKK223-3 KEYWDS TRANSFERASE, L-RHAMNULOSE KINASE, RHAMNOSE DEGRADATION, HEXOKINASE- KEYWDS 2 HSP70- ACTIN SUPERFAMILY, INDUCED FIT, IN-LINE PHOSPHORYL TRANSFER, KEYWDS 3 KINASE, RHAMNOSE METABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR D.GRUENINGER,G.E.SCHULZ REVDAT 5 29-JUL-20 2CGL 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 24-OCT-18 2CGL 1 SOURCE REMARK REVDAT 3 13-JUL-11 2CGL 1 VERSN REVDAT 2 24-FEB-09 2CGL 1 VERSN REVDAT 1 31-MAY-06 2CGL 0 JRNL AUTH D.GRUENINGER,G.E.SCHULZ JRNL TITL STRUCTURE AND REACTION MECHANISM OF L-RHAMNULOSE KINASE FROM JRNL TITL 2 ESCHERICHIA COLI. JRNL REF J.MOL.BIOL. V. 359 787 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16674975 JRNL DOI 10.1016/J.JMB.2006.04.013 REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 31242 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1644 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) : 1.88 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1738 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1830 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3707 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 192 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) : 24.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41000 REMARK 3 B22 (A**2) : -0.19000 REMARK 3 B33 (A**2) : -0.22000 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): 0.164 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.144 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.812 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3844 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5252 ; 1.529 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 486 ; 5.987 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 184 ;34.825 ;24.402 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 608 ;16.225 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;19.645 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 598 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2952 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1907 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2630 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 237 ; 0.148 ; 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): 100 ; 0.239 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.233 ; 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): 2455 ; 0.970 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3850 ; 1.399 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1583 ; 2.314 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1398 ; 3.402 ; 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 : 2 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 4 A 235 REMARK 3 ORIGIN FOR THE GROUP (A): 69.0750 78.3580 25.5010 REMARK 3 T TENSOR REMARK 3 T11: -0.1025 T22: -0.0382 REMARK 3 T33: -0.0419 T12: -0.0207 REMARK 3 T13: -0.0103 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 1.3928 L22: 1.1861 REMARK 3 L33: 2.3183 L12: -0.0472 REMARK 3 L13: -0.4937 L23: -0.2965 REMARK 3 S TENSOR REMARK 3 S11: 0.0554 S12: -0.2811 S13: 0.0903 REMARK 3 S21: 0.0966 S22: -0.0473 S23: -0.1120 REMARK 3 S31: -0.2056 S32: 0.3538 S33: -0.0081 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 240 A 476 REMARK 3 ORIGIN FOR THE GROUP (A): 54.2400 65.5940 13.4310 REMARK 3 T TENSOR REMARK 3 T11: -0.0799 T22: -0.1003 REMARK 3 T33: -0.0019 T12: 0.0119 REMARK 3 T13: -0.0161 T23: 0.0123 REMARK 3 L TENSOR REMARK 3 L11: 0.4324 L22: 1.5689 REMARK 3 L33: 1.5778 L12: 0.0196 REMARK 3 L13: -0.3496 L23: -0.0734 REMARK 3 S TENSOR REMARK 3 S11: -0.0247 S12: 0.0159 S13: 0.0092 REMARK 3 S21: -0.1216 S22: -0.0033 S23: 0.1925 REMARK 3 S31: 0.1730 S32: -0.1318 S33: 0.0281 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. A THEORETICAL GAMMA PHOSPHATE WAS MODELLED IN THE REMARK 3 FINAL STRUCTURE WITH AN OCCUPANCY OF 0.00. THIS WAS NOT USED IN REMARK 3 REFINEMENT. REMARK 4 REMARK 4 2CGL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1290027148. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793, 0.9795, 0.9686 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61818 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 79.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXD, SHELXE, SHARP, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG 8000, 120 MM LICL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.39050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 79.05100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.48300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 79.05100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.39050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.48300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 69 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 70 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ARG 73 TO ALA 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 MSE A 1 REMARK 465 THR A 481 REMARK 465 ARG A 482 REMARK 465 GLN A 483 REMARK 465 THR A 484 REMARK 465 LYS A 485 REMARK 465 GLU A 486 REMARK 465 LEU A 487 REMARK 465 CYS A 488 REMARK 465 ALA A 489 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 O3 PO3 A 1483 O HOH A 2191 1.29 REMARK 500 P PO3 A 1483 O HOH A 2191 1.49 REMARK 500 O1 PO3 A 1483 O HOH A 2191 1.51 REMARK 500 O2 PO3 A 1483 O HOH A 2190 1.55 REMARK 500 O2 PO3 A 1483 O HOH A 2192 2.11 REMARK 500 O1 PO3 A 1483 O HOH A 2190 2.15 REMARK 500 P PO3 A 1483 O HOH A 2190 2.15 REMARK 500 O HOH A 2175 O HOH A 2177 2.17 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 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 CYS A 222 CA - CB - SG ANGL. DEV. = 7.0 DEGREES 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 VAL A 84 -45.62 73.68 REMARK 500 ASP A 190 23.89 47.46 REMARK 500 PRO A 223 -6.76 -44.65 REMARK 500 ASN A 341 53.99 -157.09 REMARK 500 THR A 457 -50.59 -123.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 PO3 A 1483 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CGJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF L-RHAMNULOSE KINASE FROM ESCHERICHIA COLI IN REMARK 900 COMPLEX WITH L- FRUCTOSE AND ADP. REMARK 900 RELATED ID: 2CGK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF L-RHAMNULOSE KINASE FROM ESCHERICHIA COLI IN REMARK 900 AN OPEN UNCOMPLEXED CONFORMATION. REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE DISCREPANCIES ARE BECAUSE THE DATABASE REMARK 999 SEQUENCE IS FROM E.COLI STRAIN O157-H7. THE GENE WHICH WAS REMARK 999 USED FOR PROTEIN EXPRESSION AND STRUCTURE DETERMINATION REMARK 999 WAS ISOLATED FROM E.COLI BL21 (DE3). DBREF 2CGL A 1 489 UNP Q8X899 RHAB_ECO57 1 489 SEQADV 2CGL ALA A 69 UNP Q8X899 GLU 69 ENGINEERED MUTATION SEQADV 2CGL ALA A 70 UNP Q8X899 GLU 70 ENGINEERED MUTATION SEQADV 2CGL ALA A 73 UNP Q8X899 ARG 73 ENGINEERED MUTATION SEQADV 2CGL ALA A 320 UNP Q8X899 SER 320 CONFLICT SEQADV 2CGL ASP A 343 UNP Q8X899 GLU 343 CONFLICT SEQADV 2CGL GLU A 344 UNP Q8X899 THR 344 CONFLICT SEQADV 2CGL MSE A 356 UNP Q8X899 THR 356 CONFLICT SEQADV 2CGL LEU A 477 UNP Q8X899 ARG 477 CONFLICT SEQRES 1 A 489 MSE THR PHE ARG ASN CYS VAL ALA VAL ASP LEU GLY ALA SEQRES 2 A 489 SER SER GLY ARG VAL MSE LEU ALA ARG TYR GLU ARG GLU SEQRES 3 A 489 CYS ARG SER LEU THR LEU ARG GLU ILE HIS ARG PHE ASN SEQRES 4 A 489 ASN GLY LEU HIS SER GLN ASN GLY TYR VAL THR TRP ASP SEQRES 5 A 489 VAL ASP SER LEU GLU SER ALA ILE ARG LEU GLY LEU ASN SEQRES 6 A 489 LYS VAL CYS ALA ALA GLY ILE ALA ILE ASP SER ILE GLY SEQRES 7 A 489 ILE ASP THR TRP GLY VAL ASP PHE VAL LEU LEU ASP GLN SEQRES 8 A 489 GLN GLY GLN ARG VAL GLY LEU PRO VAL ALA TYR ARG ASP SEQRES 9 A 489 SER ARG THR ASN GLY LEU MSE ALA GLN ALA GLN GLN GLN SEQRES 10 A 489 LEU GLY LYS ARG ASP ILE TYR GLN ARG SER GLY ILE GLN SEQRES 11 A 489 PHE LEU PRO PHE ASN THR LEU TYR GLN LEU ARG ALA LEU SEQRES 12 A 489 THR GLU GLN GLN PRO GLU LEU ILE PRO HIS ILE ALA HIS SEQRES 13 A 489 ALA LEU LEU MSE PRO ASP TYR PHE SER TYR ARG LEU THR SEQRES 14 A 489 GLY LYS MSE ASN TRP GLU TYR THR ASN ALA THR THR THR SEQRES 15 A 489 GLN LEU VAL ASN ILE ASN SER ASP ASP TRP ASP GLU SER SEQRES 16 A 489 LEU LEU ALA TRP SER GLY ALA ASN LYS ALA TRP PHE GLY SEQRES 17 A 489 ARG PRO THR HIS PRO GLY ASN VAL ILE GLY HIS TRP ILE SEQRES 18 A 489 CYS PRO GLN GLY ASN GLU ILE PRO VAL VAL ALA VAL ALA SEQRES 19 A 489 SER HIS ASP THR ALA SER ALA VAL ILE ALA SER PRO LEU SEQRES 20 A 489 ASN GLY SER ARG ALA ALA TYR LEU SER SER GLY THR TRP SEQRES 21 A 489 SER LEU MSE GLY PHE GLU SER GLN THR PRO PHE THR ASN SEQRES 22 A 489 ASP THR ALA LEU ALA ALA ASN ILE THR ASN GLU GLY GLY SEQRES 23 A 489 ALA GLU GLY ARG TYR ARG VAL LEU LYS ASN ILE MSE GLY SEQRES 24 A 489 LEU TRP LEU LEU GLN ARG VAL LEU GLN GLU ARG GLN ILE SEQRES 25 A 489 ASN ASP LEU PRO ALA LEU ILE ALA ALA THR GLN ALA LEU SEQRES 26 A 489 PRO ALA CYS ARG PHE ILE ILE ASN PRO ASN ASP ASP ARG SEQRES 27 A 489 PHE ILE ASN PRO ASP GLU MSE CYS SER GLU ILE GLN ALA SEQRES 28 A 489 ALA CYS ARG GLU MSE ALA GLN PRO ILE PRO GLU SER ASP SEQRES 29 A 489 ALA GLU LEU ALA ARG CYS ILE PHE ASP SER LEU ALA LEU SEQRES 30 A 489 LEU TYR ALA ASP VAL LEU HIS GLU LEU ALA GLN LEU ARG SEQRES 31 A 489 GLY GLU ASP PHE SER GLN LEU HIS ILE VAL GLY GLY GLY SEQRES 32 A 489 CYS GLN ASN THR LEU LEU ASN GLN LEU CYS ALA ASP ALA SEQRES 33 A 489 CYS GLY ILE ARG VAL ILE ALA GLY PRO VAL GLU ALA SER SEQRES 34 A 489 THR LEU GLY ASN ILE GLY ILE GLN LEU MSE THR LEU ASP SEQRES 35 A 489 GLU LEU ASN ASN VAL ASP ASP PHE ARG GLN VAL VAL SER SEQRES 36 A 489 THR THR ALA ASN LEU THR THR PHE THR PRO ASN PRO ASP SEQRES 37 A 489 SER GLU ILE ALA HIS TYR VAL ALA LEU ILE HIS SER THR SEQRES 38 A 489 ARG GLN THR LYS GLU LEU CYS ALA MODRES 2CGL MSE A 19 MET SELENOMETHIONINE MODRES 2CGL MSE A 111 MET SELENOMETHIONINE MODRES 2CGL MSE A 160 MET SELENOMETHIONINE MODRES 2CGL MSE A 172 MET SELENOMETHIONINE MODRES 2CGL MSE A 263 MET SELENOMETHIONINE MODRES 2CGL MSE A 298 MET SELENOMETHIONINE MODRES 2CGL MSE A 345 MET SELENOMETHIONINE MODRES 2CGL MSE A 356 MET SELENOMETHIONINE MODRES 2CGL MSE A 439 MET SELENOMETHIONINE HET MSE A 19 8 HET MSE A 111 8 HET MSE A 160 8 HET MSE A 172 8 HET MSE A 263 8 HET MSE A 298 8 HET MSE A 345 8 HET MSE A 356 8 HET MSE A 439 8 HET LFR A1481 12 HET ADP A1482 27 HET PO3 A1483 4 HETNAM MSE SELENOMETHIONINE HETNAM LFR BETA-L-FRUCTOFURANOSE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM PO3 PHOSPHITE ION FORMUL 1 MSE 9(C5 H11 N O2 SE) FORMUL 2 LFR C6 H12 O6 FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 PO3 O3 P 3- FORMUL 5 HOH *192(H2 O) HELIX 1 1 ASP A 52 ALA A 70 1 19 HELIX 2 2 ASP A 104 ASN A 108 5 5 HELIX 3 3 GLY A 109 GLY A 119 1 11 HELIX 4 4 GLY A 119 GLY A 128 1 10 HELIX 5 5 ASN A 135 GLN A 147 1 13 HELIX 6 6 PRO A 148 ILE A 154 5 7 HELIX 7 7 MSE A 160 GLY A 170 1 11 HELIX 8 8 GLU A 175 THR A 180 1 6 HELIX 9 9 THR A 181 GLN A 183 5 3 HELIX 10 10 ASP A 193 GLY A 201 1 9 HELIX 11 11 ASN A 203 PHE A 207 5 5 HELIX 12 12 HIS A 236 SER A 245 1 10 HELIX 13 13 ASN A 273 ASN A 280 1 8 HELIX 14 14 GLY A 286 ARG A 290 5 5 HELIX 15 15 LEU A 300 ARG A 310 1 11 HELIX 16 16 ASP A 314 GLN A 323 1 10 HELIX 17 17 ASP A 336 ILE A 340 5 5 HELIX 18 18 GLU A 344 MSE A 356 1 13 HELIX 19 19 SER A 363 GLY A 391 1 29 HELIX 20 20 GLY A 401 GLN A 405 5 5 HELIX 21 21 ASN A 406 GLY A 418 1 13 HELIX 22 22 GLU A 427 LEU A 441 1 15 HELIX 23 23 ASN A 446 THR A 456 1 11 HELIX 24 24 SER A 469 SER A 480 1 12 SHEET 1 AA 6 SER A 29 ASN A 39 0 SHEET 2 AA 6 SER A 15 GLU A 24 -1 O GLY A 16 N PHE A 38 SHEET 3 AA 6 ARG A 4 LEU A 11 -1 O ARG A 4 N TYR A 23 SHEET 4 AA 6 ILE A 74 THR A 81 1 N ASP A 75 O ASN A 5 SHEET 5 AA 6 GLU A 227 VAL A 231 1 O PRO A 229 N ILE A 77 SHEET 6 AA 6 VAL A 216 ILE A 221 -1 N ILE A 217 O VAL A 230 SHEET 1 AB 2 HIS A 43 GLN A 45 0 SHEET 2 AB 2 TYR A 48 THR A 50 -1 O TYR A 48 N GLN A 45 SHEET 1 AC 3 ARG A 95 VAL A 96 0 SHEET 2 AC 3 PHE A 86 LEU A 89 -1 O LEU A 88 N VAL A 96 SHEET 3 AC 3 HIS A 156 LEU A 159 -1 O HIS A 156 N LEU A 89 SHEET 1 AD 7 THR A 282 GLU A 284 0 SHEET 2 AD 7 TYR A 291 ILE A 297 -1 O ARG A 292 N GLU A 284 SHEET 3 AD 7 SER A 261 SER A 267 -1 O SER A 261 N ILE A 297 SHEET 4 AD 7 ALA A 252 SER A 257 -1 O TYR A 254 N GLY A 264 SHEET 5 AD 7 GLN A 396 VAL A 400 1 O GLN A 396 N ALA A 253 SHEET 6 AD 7 ARG A 420 ALA A 423 1 O ARG A 420 N LEU A 397 SHEET 7 AD 7 THR A 461 PHE A 463 -1 O THR A 461 N ALA A 423 SSBOND 1 CYS A 68 CYS A 222 1555 1555 2.03 LINK C VAL A 18 N MSE A 19 1555 1555 1.32 LINK C MSE A 19 N LEU A 20 1555 1555 1.32 LINK C LEU A 110 N MSE A 111 1555 1555 1.33 LINK C MSE A 111 N ALA A 112 1555 1555 1.33 LINK C LEU A 159 N MSE A 160 1555 1555 1.33 LINK C MSE A 160 N PRO A 161 1555 1555 1.35 LINK C LYS A 171 N MSE A 172 1555 1555 1.33 LINK C MSE A 172 N ASN A 173 1555 1555 1.33 LINK C LEU A 262 N MSE A 263 1555 1555 1.34 LINK C MSE A 263 N GLY A 264 1555 1555 1.32 LINK C ILE A 297 N MSE A 298 1555 1555 1.33 LINK C MSE A 298 N GLY A 299 1555 1555 1.33 LINK C GLU A 344 N MSE A 345 1555 1555 1.34 LINK C MSE A 345 N CYS A 346 1555 1555 1.34 LINK C GLU A 355 N MSE A 356 1555 1555 1.33 LINK C MSE A 356 N ALA A 357 1555 1555 1.34 LINK C LEU A 438 N MSE A 439 1555 1555 1.33 LINK C MSE A 439 N THR A 440 1555 1555 1.33 LINK O1B ADP A1482 P PO3 A1483 1555 1555 1.71 CISPEP 1 GLY A 424 PRO A 425 0 0.85 CRYST1 50.781 50.966 158.102 90.00 90.00 90.00 P 21 21 21 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 0.019692 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019621 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006325 0.00000 MASTER 377 0 12 24 18 0 0 6 0 0 0 38 END