HEADER ISOMERASE 18-MAR-09 3GNX TITLE STRUCTURE OF DEHYDRATED D-XYLOSE ISOMERASE FROM STREPTOMYCES TITLE 2 RUBIGINOSUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE ISOMERASE; COMPND 3 CHAIN: A, E; COMPND 4 EC: 5.3.1.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS; SOURCE 3 ORGANISM_TAXID: 1929 KEYWDS PROTEIN D-XYLOSE ISOMERASE GLUCOSE DEHYDRATED, CARBOHYDRATE KEYWDS 2 METABOLISM, CYTOPLASM, ISOMERASE, MAGNESIUM, METAL-BINDING, PENTOSE KEYWDS 3 SHUNT, XYLOSE METABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR F.GRAMICCIA,M.SCHILTZ REVDAT 3 01-NOV-23 3GNX 1 HETSYN REVDAT 2 29-JUL-20 3GNX 1 COMPND REMARK HETNAM SITE REVDAT 1 23-MAR-10 3GNX 0 JRNL AUTH F.GRAMICCIA,C.BESNARD,M.SCHILTZ JRNL TITL DEHYDRATION-INDUCED STRUCTURAL PHASE TRANSITION IN CRYSTALS JRNL TITL 2 OF D-XYLOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 51870 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2771 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3689 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 174 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6062 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : 0.24000 REMARK 3 B33 (A**2) : 0.06000 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): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.592 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6224 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8424 ; 1.615 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 768 ; 5.645 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 336 ;34.401 ;23.095 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 976 ;15.249 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 68 ;20.119 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 874 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4958 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2557 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4236 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 342 ; 0.150 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.135 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 203 ; 0.159 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 37 ; 0.169 ; 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): 3909 ; 1.397 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6050 ; 2.110 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2598 ; 1.744 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2374 ; 2.736 ; 3.000 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 3GNX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052096. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : MULTILAYER OPTICS REMARK 200 OPTICS : XENOCS MULTILAYER OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : STOE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51870 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 94.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1XIG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6MM TRIS-HCL, 33MG/ML CRYSTALLINE REMARK 280 SUSPENSION, 0.91M AMMONIUM SULFATE, 1MM MAGNESIUM SULFATE REMARK 280 (HAMPTON RESEARCH LTD.); SOAKED IN XYLITOL SOLUTION, PH 7.0, REMARK 280 TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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 -X+1/2,Y+1/2,-Z 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 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 -1.000000 0.000000 0.000000 49.42650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.82500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.42650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.82500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 33150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -154.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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 98.85300 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 87.65000 REMARK 350 BIOMT3 2 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 ASN A 2 REMARK 465 GLY A 388 REMARK 465 ASN E 2 REMARK 465 GLY E 388 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 NE ARG A 340 O HOH A 596 1.98 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 O GLU E 128 NH2 ARG E 331 3556 2.15 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 266 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 331 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 331 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG E 266 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG E 331 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG E 331 NE - CZ - NH2 ANGL. DEV. = -4.8 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 THR A 17 -74.36 -86.92 REMARK 500 PHE A 94 -26.21 -141.00 REMARK 500 GLU A 186 108.76 78.34 REMARK 500 ASN A 247 -163.39 -162.54 REMARK 500 LYS A 253 -171.70 -172.99 REMARK 500 ALA A 343 62.67 -151.56 REMARK 500 PHE A 357 -71.49 -152.45 REMARK 500 ALA A 386 47.20 -106.95 REMARK 500 THR E 17 -71.98 -84.46 REMARK 500 GLU E 186 106.74 74.97 REMARK 500 ASN E 247 -165.45 -167.54 REMARK 500 ASN E 250 78.70 -105.00 REMARK 500 ALA E 343 59.04 -152.95 REMARK 500 PHE E 357 -69.81 -149.86 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 MN A 391 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 102.3 REMARK 620 3 ASP A 245 OD2 95.2 96.5 REMARK 620 4 ASP A 287 OD2 162.1 92.3 93.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN E 391 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU E 181 OE2 REMARK 620 2 GLU E 217 OE1 99.2 REMARK 620 3 ASP E 245 OD2 91.4 103.4 REMARK 620 4 ASP E 287 OD2 164.8 93.3 94.0 REMARK 620 N 1 2 3 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN USED IN THE STUDY WAS DIRECTLY EXTRACTED FROM REMARK 999 STREPTOMYCES RUBIGINOSUS. AUTHOR BELIEVE THAT ARG 41 IS AN ERROR IN REMARK 999 THE DEPOSITED PRIMARY SEQUENCE IN DATABASE UNP P24300 XYLA_STRRU. DBREF 3GNX A 2 388 UNP P24300 XYLA_STRRU 2 388 DBREF 3GNX E 2 388 UNP P24300 XYLA_STRRU 2 388 SEQADV 3GNX GLN A 41 UNP P24300 ARG 41 SEE REMARK 999 SEQADV 3GNX GLN E 41 UNP P24300 ARG 41 SEE REMARK 999 SEQRES 1 A 387 ASN TYR GLN PRO THR PRO GLU ASP ARG PHE THR PHE GLY SEQRES 2 A 387 LEU TRP THR VAL GLY TRP GLN GLY ARG ASP PRO PHE GLY SEQRES 3 A 387 ASP ALA THR ARG ARG ALA LEU ASP PRO VAL GLU SER VAL SEQRES 4 A 387 GLN ARG LEU ALA GLU LEU GLY ALA HIS GLY VAL THR PHE SEQRES 5 A 387 HIS ASP ASP ASP LEU ILE PRO PHE GLY SER SER ASP SER SEQRES 6 A 387 GLU ARG GLU GLU HIS VAL LYS ARG PHE ARG GLN ALA LEU SEQRES 7 A 387 ASP ASP THR GLY MET LYS VAL PRO MET ALA THR THR ASN SEQRES 8 A 387 LEU PHE THR HIS PRO VAL PHE LYS ASP GLY GLY PHE THR SEQRES 9 A 387 ALA ASN ASP ARG ASP VAL ARG ARG TYR ALA LEU ARG LYS SEQRES 10 A 387 THR ILE ARG ASN ILE ASP LEU ALA VAL GLU LEU GLY ALA SEQRES 11 A 387 GLU THR TYR VAL ALA TRP GLY GLY ARG GLU GLY ALA GLU SEQRES 12 A 387 SER GLY GLY ALA LYS ASP VAL ARG ASP ALA LEU ASP ARG SEQRES 13 A 387 MET LYS GLU ALA PHE ASP LEU LEU GLY GLU TYR VAL THR SEQRES 14 A 387 SER GLN GLY TYR ASP ILE ARG PHE ALA ILE GLU PRO LYS SEQRES 15 A 387 PRO ASN GLU PRO ARG GLY ASP ILE LEU LEU PRO THR VAL SEQRES 16 A 387 GLY HIS ALA LEU ALA PHE ILE GLU ARG LEU GLU ARG PRO SEQRES 17 A 387 GLU LEU TYR GLY VAL ASN PRO GLU VAL GLY HIS GLU GLN SEQRES 18 A 387 MET ALA GLY LEU ASN PHE PRO HIS GLY ILE ALA GLN ALA SEQRES 19 A 387 LEU TRP ALA GLY LYS LEU PHE HIS ILE ASP LEU ASN GLY SEQRES 20 A 387 GLN ASN GLY ILE LYS TYR ASP GLN ASP LEU ARG PHE GLY SEQRES 21 A 387 ALA GLY ASP LEU ARG ALA ALA PHE TRP LEU VAL ASP LEU SEQRES 22 A 387 LEU GLU SER ALA GLY TYR SER GLY PRO ARG HIS PHE ASP SEQRES 23 A 387 PHE LYS PRO PRO ARG THR GLU ASP PHE ASP GLY VAL TRP SEQRES 24 A 387 ALA SER ALA ALA GLY CYS MET ARG ASN TYR LEU ILE LEU SEQRES 25 A 387 LYS GLU ARG ALA ALA ALA PHE ARG ALA ASP PRO GLU VAL SEQRES 26 A 387 GLN GLU ALA LEU ARG ALA SER ARG LEU ASP GLU LEU ALA SEQRES 27 A 387 ARG PRO THR ALA ALA ASP GLY LEU GLN ALA LEU LEU ASP SEQRES 28 A 387 ASP ARG SER ALA PHE GLU GLU PHE ASP VAL ASP ALA ALA SEQRES 29 A 387 ALA ALA ARG GLY MET ALA PHE GLU ARG LEU ASP GLN LEU SEQRES 30 A 387 ALA MET ASP HIS LEU LEU GLY ALA ARG GLY SEQRES 1 E 387 ASN TYR GLN PRO THR PRO GLU ASP ARG PHE THR PHE GLY SEQRES 2 E 387 LEU TRP THR VAL GLY TRP GLN GLY ARG ASP PRO PHE GLY SEQRES 3 E 387 ASP ALA THR ARG ARG ALA LEU ASP PRO VAL GLU SER VAL SEQRES 4 E 387 GLN ARG LEU ALA GLU LEU GLY ALA HIS GLY VAL THR PHE SEQRES 5 E 387 HIS ASP ASP ASP LEU ILE PRO PHE GLY SER SER ASP SER SEQRES 6 E 387 GLU ARG GLU GLU HIS VAL LYS ARG PHE ARG GLN ALA LEU SEQRES 7 E 387 ASP ASP THR GLY MET LYS VAL PRO MET ALA THR THR ASN SEQRES 8 E 387 LEU PHE THR HIS PRO VAL PHE LYS ASP GLY GLY PHE THR SEQRES 9 E 387 ALA ASN ASP ARG ASP VAL ARG ARG TYR ALA LEU ARG LYS SEQRES 10 E 387 THR ILE ARG ASN ILE ASP LEU ALA VAL GLU LEU GLY ALA SEQRES 11 E 387 GLU THR TYR VAL ALA TRP GLY GLY ARG GLU GLY ALA GLU SEQRES 12 E 387 SER GLY GLY ALA LYS ASP VAL ARG ASP ALA LEU ASP ARG SEQRES 13 E 387 MET LYS GLU ALA PHE ASP LEU LEU GLY GLU TYR VAL THR SEQRES 14 E 387 SER GLN GLY TYR ASP ILE ARG PHE ALA ILE GLU PRO LYS SEQRES 15 E 387 PRO ASN GLU PRO ARG GLY ASP ILE LEU LEU PRO THR VAL SEQRES 16 E 387 GLY HIS ALA LEU ALA PHE ILE GLU ARG LEU GLU ARG PRO SEQRES 17 E 387 GLU LEU TYR GLY VAL ASN PRO GLU VAL GLY HIS GLU GLN SEQRES 18 E 387 MET ALA GLY LEU ASN PHE PRO HIS GLY ILE ALA GLN ALA SEQRES 19 E 387 LEU TRP ALA GLY LYS LEU PHE HIS ILE ASP LEU ASN GLY SEQRES 20 E 387 GLN ASN GLY ILE LYS TYR ASP GLN ASP LEU ARG PHE GLY SEQRES 21 E 387 ALA GLY ASP LEU ARG ALA ALA PHE TRP LEU VAL ASP LEU SEQRES 22 E 387 LEU GLU SER ALA GLY TYR SER GLY PRO ARG HIS PHE ASP SEQRES 23 E 387 PHE LYS PRO PRO ARG THR GLU ASP PHE ASP GLY VAL TRP SEQRES 24 E 387 ALA SER ALA ALA GLY CYS MET ARG ASN TYR LEU ILE LEU SEQRES 25 E 387 LYS GLU ARG ALA ALA ALA PHE ARG ALA ASP PRO GLU VAL SEQRES 26 E 387 GLN GLU ALA LEU ARG ALA SER ARG LEU ASP GLU LEU ALA SEQRES 27 E 387 ARG PRO THR ALA ALA ASP GLY LEU GLN ALA LEU LEU ASP SEQRES 28 E 387 ASP ARG SER ALA PHE GLU GLU PHE ASP VAL ASP ALA ALA SEQRES 29 E 387 ALA ALA ARG GLY MET ALA PHE GLU ARG LEU ASP GLN LEU SEQRES 30 E 387 ALA MET ASP HIS LEU LEU GLY ALA ARG GLY HET XYL A 389 10 HET MN A 390 1 HET MN A 391 1 HET XYL E 389 10 HET MN E 390 1 HET MN E 391 1 HETNAM XYL XYLITOL HETNAM MN MANGANESE (II) ION HETSYN XYL D-XYLITOL FORMUL 3 XYL 2(C5 H12 O5) FORMUL 4 MN 4(MN 2+) FORMUL 9 HOH *430(H2 O) HELIX 1 1 THR A 6 ASP A 9 5 4 HELIX 2 2 LEU A 15 GLY A 19 1 5 HELIX 3 3 ASP A 35 GLY A 47 1 13 HELIX 4 4 ASP A 55 ILE A 59 1 5 HELIX 5 5 SER A 64 GLY A 83 1 20 HELIX 6 6 HIS A 96 LYS A 100 5 5 HELIX 7 7 ASP A 108 GLY A 130 1 23 HELIX 8 8 SER A 145 LYS A 149 5 5 HELIX 9 9 ASP A 150 GLY A 173 1 24 HELIX 10 10 THR A 195 GLU A 204 1 10 HELIX 11 11 ARG A 208 GLU A 210 5 3 HELIX 12 12 GLU A 217 MET A 223 1 7 HELIX 13 13 ASN A 227 ALA A 238 1 12 HELIX 14 14 ASP A 264 ALA A 278 1 15 HELIX 15 15 ASP A 295 ASP A 323 1 29 HELIX 16 16 ASP A 323 SER A 333 1 11 HELIX 17 17 ARG A 334 ARG A 340 1 7 HELIX 18 18 GLY A 346 ASP A 353 1 8 HELIX 19 19 ARG A 354 PHE A 357 5 4 HELIX 20 20 ASP A 361 ARG A 368 1 8 HELIX 21 21 ALA A 371 LEU A 384 1 14 HELIX 22 22 THR E 6 ASP E 9 5 4 HELIX 23 23 LEU E 15 GLY E 19 1 5 HELIX 24 24 ASP E 35 GLY E 47 1 13 HELIX 25 25 HIS E 54 ILE E 59 1 6 HELIX 26 26 SER E 64 GLY E 83 1 20 HELIX 27 27 HIS E 96 LYS E 100 5 5 HELIX 28 28 ASP E 108 GLY E 130 1 23 HELIX 29 29 ASP E 150 GLY E 173 1 24 HELIX 30 30 THR E 195 GLU E 204 1 10 HELIX 31 31 ARG E 208 GLU E 210 5 3 HELIX 32 32 GLU E 217 MET E 223 1 7 HELIX 33 33 ASN E 227 ALA E 238 1 12 HELIX 34 34 ASP E 264 GLY E 279 1 16 HELIX 35 35 ASP E 295 ASP E 323 1 29 HELIX 36 36 ASP E 323 SER E 333 1 11 HELIX 37 37 ARG E 334 ARG E 340 1 7 HELIX 38 38 GLY E 346 ASP E 353 1 8 HELIX 39 39 ARG E 354 PHE E 357 5 4 HELIX 40 40 ASP E 361 ARG E 368 1 8 HELIX 41 41 ALA E 371 LEU E 384 1 14 SHEET 1 A 8 TYR A 212 VAL A 214 0 SHEET 2 A 8 ARG A 177 ILE A 180 1 N ILE A 180 O GLY A 213 SHEET 3 A 8 THR A 133 ALA A 136 1 N TYR A 134 O ARG A 177 SHEET 4 A 8 LYS A 85 THR A 90 1 N ALA A 89 O VAL A 135 SHEET 5 A 8 GLY A 50 HIS A 54 1 N VAL A 51 O LYS A 85 SHEET 6 A 8 PHE A 11 GLY A 14 1 N PHE A 13 O THR A 52 SHEET 7 A 8 ARG A 284 PHE A 286 1 O PHE A 286 N THR A 12 SHEET 8 A 8 ASP A 245 LEU A 246 1 N LEU A 246 O HIS A 285 SHEET 1 B 2 GLY A 142 ALA A 143 0 SHEET 2 B 2 ASP A 190 ILE A 191 -1 O ASP A 190 N ALA A 143 SHEET 1 C 4 GLY E 50 THR E 52 0 SHEET 2 C 4 PHE E 11 GLY E 14 1 N PHE E 13 O THR E 52 SHEET 3 C 4 ARG E 284 PHE E 286 1 O PHE E 286 N THR E 12 SHEET 4 C 4 ASP E 245 LEU E 246 1 N LEU E 246 O HIS E 285 SHEET 1 D 4 MET E 88 THR E 90 0 SHEET 2 D 4 THR E 133 TRP E 137 1 O VAL E 135 N ALA E 89 SHEET 3 D 4 ARG E 177 GLU E 181 1 O GLU E 181 N ALA E 136 SHEET 4 D 4 TYR E 212 VAL E 214 1 O GLY E 213 N ILE E 180 SHEET 1 E 2 GLY E 142 ALA E 143 0 SHEET 2 E 2 ASP E 190 ILE E 191 -1 O ASP E 190 N ALA E 143 LINK OE2 GLU A 181 MN MN A 391 1555 1555 2.08 LINK OE1 GLU A 217 MN MN A 391 1555 1555 2.17 LINK OD2 ASP A 245 MN MN A 391 1555 1555 2.17 LINK OD2 ASP A 287 MN MN A 391 1555 1555 2.18 LINK OE2 GLU E 181 MN MN E 391 1555 1555 2.13 LINK OE1 GLU E 217 MN MN E 391 1555 1555 2.17 LINK OD2 ASP E 245 MN MN E 391 1555 1555 2.18 LINK OD2 ASP E 287 MN MN E 391 1555 1555 2.22 LINK O1 XYL E 389 MN MN E 390 1555 1555 1.60 CISPEP 1 GLU A 186 PRO A 187 0 13.54 CISPEP 2 GLU E 186 PRO E 187 0 15.31 CRYST1 98.853 87.650 94.531 90.00 90.00 90.00 P 21 21 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 0.010116 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011409 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010579 0.00000