PDB Short entry for 1C8X HEADER HYDROLASE 30-JUL-99 1C8X TITLE ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H, D130E MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.96; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES PLICATUS; SOURCE 3 ORGANISM_TAXID: 1922; 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)8-BARREL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.RAO,C.TAO,C.GUAN,P.VAN ROEY REVDAT 6 07-FEB-24 1C8X 1 REMARK REVDAT 5 03-NOV-21 1C8X 1 REMARK SEQADV REVDAT 4 04-OCT-17 1C8X 1 REMARK REVDAT 3 24-FEB-09 1C8X 1 VERSN REVDAT 2 29-APR-03 1C8X 1 JRNL REMARK MASTER REVDAT 1 26-NOV-99 1C8X 0 JRNL AUTH V.RAO,T.CUI,C.GUAN,P.VAN ROEY JRNL TITL MUTATIONS OF ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H ACTIVE SITE JRNL TITL 2 RESIDUES ASP130 AND GLU132: ACTIVITIES AND CONFORMATIONS. JRNL REF PROTEIN SCI. V. 8 2338 1999 JRNL REFN ISSN 0961-8368 JRNL PMID 10595536 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 14192 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2017 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 152 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.725 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1C8X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000009439. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 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) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14192 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07900 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 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 <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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG1000, 100 MM CACODYLATE, PH REMARK 280 6.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 27.60000 REMARK 290 SMTRY3 2 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 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 OD1 ASP A 186 O HOH A 548 2859 2.13 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 17 -4.36 -58.38 REMARK 500 ASN A 169 94.42 -59.66 REMARK 500 ILE A 170 148.35 -179.87 REMARK 500 ALA A 205 63.42 -63.56 REMARK 500 ASP A 247 -164.92 -111.32 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 PO4 A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EDT RELATED DB: PDB REMARK 900 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H, WILD TYPE REMARK 900 RELATED ID: 1C3F RELATED DB: PDB REMARK 900 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H, D130N MUTANT REMARK 900 RELATED ID: 1C8Y RELATED DB: PDB REMARK 900 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H, D130A MUTANT REMARK 900 RELATED ID: 1C90 RELATED DB: PDB REMARK 900 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H, E132Q MUTANT REMARK 900 RELATED ID: 1C91 RELATED DB: PDB REMARK 900 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H, E132D MUTANT REMARK 900 RELATED ID: 1C92 RELATED DB: PDB REMARK 900 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H, E132A MUTANT REMARK 900 RELATED ID: 1C93 RELATED DB: PDB REMARK 900 ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H, D130N/E132Q MUTANT DBREF 1C8X A 6 270 UNP P04067 EBAG_STRPL 48 312 SEQADV 1C8X GLU A 130 UNP P04067 ASP 172 ENGINEERED MUTATION SEQRES 1 A 265 LYS GLN GLY PRO THR SER VAL ALA TYR VAL GLU VAL ASN SEQRES 2 A 265 ASN ASN SER MET LEU ASN VAL GLY LYS TYR THR LEU ALA SEQRES 3 A 265 ASP GLY GLY GLY ASN ALA PHE ASP VAL ALA VAL ILE PHE SEQRES 4 A 265 ALA ALA ASN ILE ASN TYR ASP THR GLY THR LYS THR ALA SEQRES 5 A 265 TYR LEU HIS PHE ASN GLU ASN VAL GLN ARG VAL LEU ASP SEQRES 6 A 265 ASN ALA VAL THR GLN ILE ARG PRO LEU GLN GLN GLN GLY SEQRES 7 A 265 ILE LYS VAL LEU LEU SER VAL LEU GLY ASN HIS GLN GLY SEQRES 8 A 265 ALA GLY PHE ALA ASN PHE PRO SER GLN GLN ALA ALA SER SEQRES 9 A 265 ALA PHE ALA LYS GLN LEU SER ASP ALA VAL ALA LYS TYR SEQRES 10 A 265 GLY LEU ASP GLY VAL ASP PHE GLU ASP GLU TYR ALA GLU SEQRES 11 A 265 TYR GLY ASN ASN GLY THR ALA GLN PRO ASN ASP SER SER SEQRES 12 A 265 PHE VAL HIS LEU VAL THR ALA LEU ARG ALA ASN MET PRO SEQRES 13 A 265 ASP LYS ILE ILE SER LEU TYR ASN ILE GLY PRO ALA ALA SEQRES 14 A 265 SER ARG LEU SER TYR GLY GLY VAL ASP VAL SER ASP LYS SEQRES 15 A 265 PHE ASP TYR ALA TRP ASN PRO TYR TYR GLY THR TRP GLN SEQRES 16 A 265 VAL PRO GLY ILE ALA LEU PRO LYS ALA GLN LEU SER PRO SEQRES 17 A 265 ALA ALA VAL GLU ILE GLY ARG THR SER ARG SER THR VAL SEQRES 18 A 265 ALA ASP LEU ALA ARG ARG THR VAL ASP GLU GLY TYR GLY SEQRES 19 A 265 VAL TYR LEU THR TYR ASN LEU ASP GLY GLY ASP ARG THR SEQRES 20 A 265 ALA ASP VAL SER ALA PHE THR ARG GLU LEU TYR GLY SER SEQRES 21 A 265 GLU ALA VAL ARG THR HET PO4 A 500 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *152(H2 O) HELIX 1 1 SER A 21 GLY A 26 5 6 HELIX 2 2 ASN A 62 ASN A 71 1 10 HELIX 3 3 ASN A 71 ILE A 76 1 6 HELIX 4 4 ILE A 76 GLN A 82 1 7 HELIX 5 5 SER A 104 TYR A 122 1 19 HELIX 6 6 GLY A 137 THR A 141 5 5 HELIX 7 7 SER A 147 MET A 160 1 14 HELIX 8 8 PRO A 172 ARG A 176 5 5 HELIX 9 9 SER A 185 PHE A 188 5 4 HELIX 10 10 PRO A 207 ALA A 209 5 3 HELIX 11 11 SER A 222 GLY A 237 1 16 HELIX 12 12 ARG A 251 GLY A 264 1 14 SHEET 1 A10 LEU A 211 SER A 212 0 SHEET 2 A10 TYR A 190 TRP A 192 1 O ALA A 191 N SER A 212 SHEET 3 A10 ILE A 164 TYR A 168 1 O ILE A 165 N TYR A 190 SHEET 4 A10 GLY A 126 GLU A 130 1 O VAL A 127 N SER A 166 SHEET 5 A10 LYS A 85 GLY A 92 1 O VAL A 86 N GLY A 126 SHEET 6 A10 VAL A 40 ASP A 51 1 N ALA A 41 O LYS A 85 SHEET 7 A10 THR A 10 GLU A 16 1 O SER A 11 N VAL A 40 SHEET 8 A10 VAL A 240 TYR A 244 1 O TYR A 241 N VAL A 12 SHEET 9 A10 ALA A 214 GLU A 217 1 O ALA A 214 N LEU A 242 SHEET 10 A10 THR A 198 TRP A 199 1 O THR A 198 N ALA A 215 SHEET 1 A1 7 LEU A 211 SER A 212 0 SHEET 2 A1 7 TYR A 190 TRP A 192 1 O ALA A 191 N SER A 212 SHEET 3 A1 7 ILE A 164 TYR A 168 1 O ILE A 165 N TYR A 190 SHEET 4 A1 7 GLY A 126 GLU A 130 1 O VAL A 127 N SER A 166 SHEET 5 A1 7 LYS A 85 GLY A 92 1 O VAL A 86 N GLY A 126 SHEET 6 A1 7 VAL A 40 ASP A 51 1 N ALA A 41 O LYS A 85 SHEET 7 A1 7 THR A 56 HIS A 60 -1 O THR A 56 N ASP A 51 SHEET 1 B 2 TYR A 28 LEU A 30 0 SHEET 2 B 2 ALA A 267 ARG A 269 -1 N VAL A 268 O THR A 29 SHEET 1 C 2 SER A 178 TYR A 179 0 SHEET 2 C 2 VAL A 182 ASP A 183 -1 O VAL A 182 N TYR A 179 CISPEP 1 PHE A 44 ALA A 45 0 0.01 SITE 1 AC1 5 TYR A 14 GLU A 16 PHE A 44 TYR A 196 SITE 2 AC1 5 TYR A 244 CRYST1 44.200 55.200 46.200 90.00 103.80 90.00 P 1 21 1 2 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 0.022624 0.000000 0.005557 0.00000 SCALE2 0.000000 0.018116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022288 0.00000