HEADER HYDROLASE 24-JUN-05 2CWR TITLE CRYSTAL STRUCTURE OF CHITIN BIDING DOMAIN OF CHITINASE FROM PYROCOCCUS TITLE 2 FURIOSUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CHITIN-BINDING DOMAIN; COMPND 5 EC: 3.2.1.14; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 GENE: PF1233; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CHITINASE, CHITIN-BINDING DOMAIN, PYROCOCCUS FURIOSUS, ENDOGLUCANASE, KEYWDS 2 CHITIN, HYPERTHERMOPHILIC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.UEGAKI,T.NAKAMURA,K.ISHIKAWA,H.MATSUMURA REVDAT 4 13-MAR-24 2CWR 1 SEQADV REVDAT 3 26-MAY-09 2CWR 1 JRNL REVDAT 2 24-FEB-09 2CWR 1 VERSN REVDAT 1 11-JUL-06 2CWR 0 JRNL AUTH T.NAKAMURA,S.MINE,Y.HAGIHARA,K.ISHIKAWA,T.IKEGAMI,K.UEGAKI JRNL TITL TERTIARY STRUCTURE AND CARBOHYDRATE RECOGNITION BY THE JRNL TITL 2 CHITIN-BINDING DOMAIN OF A HYPERTHERMOPHILIC CHITINASE FROM JRNL TITL 3 PYROCOCCUS FURIOSUS. JRNL REF J.MOL.BIOL. V. 381 670 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18582475 JRNL DOI 10.1016/J.JMB.2008.06.006 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1258850.710 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 11545 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 SET) : 0.194 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1186 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1483 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 165 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 738 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.57000 REMARK 3 B22 (A**2) : 3.57000 REMARK 3 B33 (A**2) : -7.13000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.560 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.590 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.680 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.930 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.700 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 39.95 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 : PROTEIN.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CWR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000024712. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BBS REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11986 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 14.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MAGNESIUM ACETATE, SODIUM REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 42.49650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.41350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.41350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 63.74475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.41350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.41350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.24825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.41350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.41350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 63.74475 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.41350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.41350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.24825 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 42.49650 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 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 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 256 REMARK 465 PRO A 257 REMARK 465 THR A 258 REMARK 465 THR A 259 REMARK 465 PRO A 260 REMARK 465 VAL A 261 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 5 O HOH A 118 2.18 REMARK 500 O HOH A 8 O HOH A 118 2.19 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 ASN A 316 98.87 -60.97 REMARK 500 ASN A 327 47.29 -107.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 2CWR A 258 358 UNP Q8U1H5 Q8U1H5_PYRFU 258 358 SEQADV 2CWR GLY A 256 UNP Q8U1H5 EXPRESSION TAG SEQADV 2CWR PRO A 257 UNP Q8U1H5 EXPRESSION TAG SEQRES 1 A 103 GLY PRO THR THR PRO VAL PRO VAL SER GLY SER LEU GLU SEQRES 2 A 103 VAL LYS VAL ASN ASP TRP GLY SER GLY ALA GLU TYR ASP SEQRES 3 A 103 VAL THR LEU ASN LEU ASP GLY GLN TYR ASP TRP THR VAL SEQRES 4 A 103 LYS VAL LYS LEU ALA PRO GLY ALA THR VAL GLY SER PHE SEQRES 5 A 103 TRP SER ALA ASN LYS GLN GLU GLY ASN GLY TYR VAL ILE SEQRES 6 A 103 PHE THR PRO VAL SER TRP ASN LYS GLY PRO THR ALA THR SEQRES 7 A 103 PHE GLY PHE ILE VAL ASN GLY PRO GLN GLY ASP LYS VAL SEQRES 8 A 103 GLU GLU ILE THR LEU GLU ILE ASN GLY GLN VAL ILE FORMUL 2 HOH *141(H2 O) SHEET 1 A 4 GLY A 265 ASP A 273 0 SHEET 2 A 4 GLY A 277 LEU A 286 -1 O THR A 283 N GLU A 268 SHEET 3 A 4 THR A 331 ASN A 339 -1 O ALA A 332 N LEU A 284 SHEET 4 A 4 THR A 303 TRP A 308 -1 N THR A 303 O ASN A 339 SHEET 1 B 5 ALA A 310 GLY A 315 0 SHEET 2 B 5 TYR A 318 PRO A 323 -1 O ILE A 320 N GLN A 313 SHEET 3 B 5 THR A 293 LEU A 298 -1 N VAL A 296 O VAL A 319 SHEET 4 B 5 VAL A 346 ILE A 353 -1 O GLU A 352 N THR A 293 SHEET 5 B 5 GLN A 356 VAL A 357 -1 O GLN A 356 N ILE A 353 CISPEP 1 GLY A 329 PRO A 330 0 0.01 CRYST1 48.827 48.827 84.993 90.00 90.00 90.00 P 43 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 0.020481 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020481 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011766 0.00000