HEADER HYDROLASE 23-MAR-00 1EOK TITLE CRYSTAL STRUCTURE OF ENDO-BETA-N-ACETYLGLUCOSAMINIDASE F3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE F3; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.96; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ELIZABETHKINGIA MENINGOSEPTICA; SOURCE 3 ORGANISM_TAXID: 238; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PMAL KEYWDS ALPHA/BETA-BARREL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.A.WADDLING,T.H.PLUMMER JR.,A.L.TARENTINO,P.VAN ROEY REVDAT 3 07-FEB-24 1EOK 1 REMARK REVDAT 2 24-FEB-09 1EOK 1 VERSN REVDAT 1 27-JUL-00 1EOK 0 JRNL AUTH C.A.WADDLING,T.H.PLUMMER JR.,A.L.TARENTINO,P.VAN ROEY JRNL TITL STRUCTURAL BASIS FOR THE SUBSTRATE SPECIFICITY OF JRNL TITL 2 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE F(3). JRNL REF BIOCHEMISTRY V. 39 7878 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10891067 JRNL DOI 10.1021/BI0001731 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1549914.880 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 30477 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) : 0.172 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3079 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4374 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 438 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2172 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 286 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.10000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.10 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) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.850 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) : 1.030 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.390 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.800 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.420 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.57 REMARK 3 BSOL : 92.75 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_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EOK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAR-00. REMARK 100 THE DEPOSITION ID IS D_1000010771. 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 : 7.0 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2 M AMMONIUM SULPHATE, 4% MPD, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K 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 34.67500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.09000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.16500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.09000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.67500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.16500 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 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 ALA A 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 REMARK 465 LEU A 4 REMARK 465 ALA A 5 REMARK 465 GLY A 6 REMARK 465 SER A 7 REMARK 465 ASN A 290 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 ILE A 115 -66.66 -90.31 REMARK 500 GLU A 128 4.22 -173.71 REMARK 500 ASN A 180 70.86 34.02 REMARK 500 SER A 187 -154.53 -157.45 REMARK 500 SER A 212 45.30 -79.79 REMARK 500 ASN A 277 92.04 -161.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EOM RELATED DB: PDB REMARK 900 1EOM CONTAINS THE SAME PROTEIN COMPLEXED WITH A BIANTENNARY COMPLEX REMARK 900 OCTASACCHARIDE. DBREF 1EOK A 1 290 UNP P36913 EBA3_FLAME 40 329 SEQRES 1 A 290 ALA THR ALA LEU ALA GLY SER ASN GLY VAL CYS ILE ALA SEQRES 2 A 290 TYR TYR ILE THR ASP GLY ARG ASN PRO THR PHE LYS LEU SEQRES 3 A 290 LYS ASP ILE PRO ASP LYS VAL ASP MET VAL ILE LEU PHE SEQRES 4 A 290 GLY LEU LYS TYR TRP SER LEU GLN ASP THR THR LYS LEU SEQRES 5 A 290 PRO GLY GLY THR GLY MET MET GLY SER PHE LYS SER TYR SEQRES 6 A 290 LYS ASP LEU ASP THR GLN ILE ARG SER LEU GLN SER ARG SEQRES 7 A 290 GLY ILE LYS VAL LEU GLN ASN ILE ASP ASP ASP VAL SER SEQRES 8 A 290 TRP GLN SER SER LYS PRO GLY GLY PHE ALA SER ALA ALA SEQRES 9 A 290 ALA TYR GLY ASP ALA ILE LYS SER ILE VAL ILE ASP LYS SEQRES 10 A 290 TRP LYS LEU ASP GLY ILE SER LEU ASP ILE GLU HIS SER SEQRES 11 A 290 GLY ALA LYS PRO ASN PRO ILE PRO THR PHE PRO GLY TYR SEQRES 12 A 290 ALA ALA THR GLY TYR ASN GLY TRP TYR SER GLY SER MET SEQRES 13 A 290 ALA ALA THR PRO ALA PHE LEU ASN VAL ILE SER GLU LEU SEQRES 14 A 290 THR LYS TYR PHE GLY THR THR ALA PRO ASN ASN LYS GLN SEQRES 15 A 290 LEU GLN ILE ALA SER GLY ILE ASP VAL TYR ALA TRP ASN SEQRES 16 A 290 LYS ILE MET GLU ASN PHE ARG ASN ASN PHE ASN TYR ILE SEQRES 17 A 290 GLN LEU GLN SER TYR GLY ALA ASN VAL SER ARG THR GLN SEQRES 18 A 290 LEU MET MET ASN TYR ALA THR GLY THR ASN LYS ILE PRO SEQRES 19 A 290 ALA SER LYS MET VAL PHE GLY ALA TYR ALA GLU GLY GLY SEQRES 20 A 290 THR ASN GLN ALA ASN ASP VAL GLU VAL ALA LYS TRP THR SEQRES 21 A 290 PRO THR GLN GLY ALA LYS GLY GLY MET MET ILE TYR THR SEQRES 22 A 290 TYR ASN SER ASN VAL SER TYR ALA ASN ALA VAL ARG ASP SEQRES 23 A 290 ALA VAL LYS ASN HET SO4 A 700 5 HET SO4 A 701 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *286(H2 O) HELIX 1 1 LYS A 25 ILE A 29 5 5 HELIX 2 2 LYS A 42 ASP A 48 1 7 HELIX 3 3 THR A 56 GLY A 60 5 5 HELIX 4 4 SER A 64 SER A 77 1 14 HELIX 5 5 ASP A 89 SER A 94 5 6 HELIX 6 6 LYS A 96 PHE A 100 5 5 HELIX 7 7 SER A 102 ILE A 115 1 14 HELIX 8 8 GLY A 142 GLY A 147 1 6 HELIX 9 9 THR A 159 THR A 170 1 12 HELIX 10 10 ALA A 193 ARG A 202 1 10 HELIX 11 11 ASN A 216 THR A 230 1 15 HELIX 12 12 PRO A 234 SER A 236 5 3 HELIX 13 13 ASN A 249 TRP A 259 1 11 HELIX 14 14 THR A 273 SER A 276 5 4 HELIX 15 15 ASN A 277 LYS A 289 1 13 SHEET 1 A 9 VAL A 10 ILE A 16 0 SHEET 2 A 9 MET A 35 PHE A 39 1 O MET A 35 N ALA A 13 SHEET 3 A 9 LYS A 81 ASP A 87 1 O LYS A 81 N VAL A 36 SHEET 4 A 9 GLY A 122 ASP A 126 1 O GLY A 122 N GLN A 84 SHEET 5 A 9 GLN A 182 SER A 187 1 O GLN A 182 N ILE A 123 SHEET 6 A 9 TYR A 207 LEU A 210 1 O TYR A 207 N ILE A 185 SHEET 7 A 9 MET A 238 ALA A 242 1 O VAL A 239 N LEU A 210 SHEET 8 A 9 GLY A 268 ILE A 271 1 O GLY A 268 N PHE A 240 SHEET 9 A 9 VAL A 10 ILE A 16 1 O VAL A 10 N MET A 269 CISPEP 1 ASN A 135 PRO A 136 0 0.56 CISPEP 2 TYR A 272 THR A 273 0 0.71 SITE 1 AC1 8 GLY A 54 SER A 64 TYR A 65 LYS A 133 SITE 2 AC1 8 HOH A 381 HOH A 405 HOH A 530 HOH A 615 SITE 1 AC2 4 LYS A 63 HIS A 129 SER A 130 HOH A 408 CRYST1 69.350 118.330 40.180 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 0.014420 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008451 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024888 0.00000