HEADER HYDROLASE 21-MAR-16 5G0M TITLE BETA-GLUCURONIDASE WITH AN ACTIVITY-BASED PROBE (N-ACYL CYCLOPHELLITOL TITLE 2 AZIRIDINE) BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-GLUCURONIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.31; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACIDOBACTERIUM CAPSULATUM; SOURCE 3 ORGANISM_TAXID: 33075; SOURCE 4 ATCC: 51196; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: GOLD; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET-28A KEYWDS HYDROLASE, GH79, BETA-GLUCURONIDASE, ACTIVITY-BASED PROBE, RETAINING KEYWDS 2 ENZYME EXPDTA X-RAY DIFFRACTION AUTHOR Y.JIN,L.WU,J.B.JIANG,H.S.OVERKLEEFT,G.J.DAVIES REVDAT 2 22-MAY-19 5G0M 1 REMARK LINK REVDAT 1 12-APR-17 5G0M 0 JRNL AUTH Y.JIN,L.WU,J.B.JIANG,H.S.OVERKLEEFT,G.J.DAVIES JRNL TITL THE STRUCTURE OF A BACTERIA BETA-GLUCURONIDASE IN GH79 JRNL TITL 2 FAMILY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 43578 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2278 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3176 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE SET COUNT : 151 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3430 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 244 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.115 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.511 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3568 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3260 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4863 ; 1.812 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7490 ; 1.066 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 458 ; 6.331 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 156 ;33.713 ;23.654 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 500 ;13.558 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;14.712 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 521 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4156 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 846 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1832 ; 1.583 ; 1.759 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1831 ; 1.579 ; 1.758 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2290 ; 2.385 ; 2.631 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2291 ; 2.385 ; 2.631 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1736 ; 2.226 ; 1.982 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1733 ; 2.213 ; 1.978 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2574 ; 3.441 ; 2.883 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4058 ; 4.860 ;14.512 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4059 ; 4.870 ;14.526 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 5G0M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1290066525. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92002 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45856 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 66.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 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) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 3VO0 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7 UL 4.5 MG/ML PROTEIN STOCK IS REMARK 280 MIXED WITH 0.5 UL PRECIPITANT COMPOSED OF 1 M NAH2PO4:K2HPO4 = REMARK 280 0.5:9.5 (V/V) AT 20 DEGREE., PH 8.6, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 75.37000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.40500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 75.37000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.40500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.8 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 114.89134 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 75.15828 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 PHE A 3 REMARK 465 ALA A 4 REMARK 465 ARG A 5 REMARK 465 GLY A 6 REMARK 465 GLY A 7 REMARK 465 LEU A 8 REMARK 465 ALA A 9 REMARK 465 GLN A 10 REMARK 465 THR A 11 REMARK 465 ALA A 12 REMARK 465 SER A 13 REMARK 465 GLN A 14 REMARK 465 THR A 15 REMARK 465 THR A 16 REMARK 465 SER A 17 REMARK 465 SER A 18 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 21 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 92 CE NZ REMARK 470 GLU A 98 CG CD OE1 OE2 REMARK 470 TYR A 178 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 179 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 250 CG OD1 OD2 REMARK 470 HIS A 456 CB CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 459 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 287 CD GLU A 287 OE2 0.092 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 204 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 385 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 385 NE - CZ - NH2 ANGL. DEV. = -3.3 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 ARG A 179 -37.72 -38.83 REMARK 500 TRP A 223 -56.97 -120.13 REMARK 500 VAL A 299 -63.28 -127.69 REMARK 500 SER A 457 119.68 -34.46 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 1476 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1477 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE J13 A 1478 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5G0Q RELATED DB: PDB REMARK 900 BETA-GLUCURONIDASE WITH AN ACTIVITY-BASED PROBE (N- ALKYL REMARK 900 CYCLOPHELLITOL AZIRIDINE) BOUND DBREF 5G0M A 1 475 UNP C1F2K5 C1F2K5_ACIC5 1 475 SEQRES 1 A 475 MET ALA PHE ALA ARG GLY GLY LEU ALA GLN THR ALA SER SEQRES 2 A 475 GLN THR THR SER SER PRO VAL ARG VAL GLY LEU SER VAL SEQRES 3 A 475 ASP ALA SER ALA LEU GLY HIS THR ILE PRO PRO ASP TYR SEQRES 4 A 475 THR GLY LEU SER TYR GLU GLN ALA GLN MET ALA ASN PRO SEQRES 5 A 475 ASN TYR PHE SER GLY ALA ASN THR GLN LEU ALA GLY PHE SEQRES 6 A 475 LEU ARG THR LEU GLY ARG GLN GLY VAL LEU ARG ILE GLY SEQRES 7 A 475 GLY ASN THR SER GLU TYR THR PHE TRP ASN ARG HIS ALA SEQRES 8 A 475 LYS PRO THR ALA ALA ASP GLU HIS LEU ALA ALA GLY PRO SEQRES 9 A 475 ASP LYS GLY HIS HIS ALA ALA ALA ARG GLU VAL ILE THR SEQRES 10 A 475 PRO GLU ALA VAL ASN ASN LEU SER GLU PHE LEU ASP LYS SEQRES 11 A 475 THR GLY TRP LYS LEU ILE TYR GLY LEU ASN LEU GLY LYS SEQRES 12 A 475 GLY THR PRO GLU ASN ALA ALA ASP GLU ALA ALA TYR VAL SEQRES 13 A 475 MET GLU THR ILE GLY ALA ASP ARG LEU LEU ALA PHE GLN SEQRES 14 A 475 LEU GLY ASN GLU PRO ASP LEU PHE TYR ARG ASN GLY ILE SEQRES 15 A 475 ARG PRO ALA SER TYR ASP PHE ALA ALA TYR ALA GLY ASP SEQRES 16 A 475 TRP GLN ARG PHE PHE THR ALA ILE ARG LYS ARG VAL PRO SEQRES 17 A 475 ASN ALA PRO PHE ALA GLY PRO ASP THR ALA TYR ASN THR SEQRES 18 A 475 LYS TRP LEU VAL PRO PHE ALA ASP LYS PHE LYS HIS ASP SEQRES 19 A 475 VAL LYS PHE ILE SER SER HIS TYR TYR ALA GLU GLY PRO SEQRES 20 A 475 PRO THR ASP PRO SER MET THR ILE GLU ARG LEU MET LYS SEQRES 21 A 475 PRO ASN PRO ARG LEU LEU GLY GLU THR ALA GLY LEU LYS SEQRES 22 A 475 GLN VAL GLU ALA ASP THR GLY LEU PRO PHE ARG LEU THR SEQRES 23 A 475 GLU THR ASN SER CYS TYR GLN GLY GLY LYS GLN GLY VAL SEQRES 24 A 475 SER ASP THR PHE ALA ALA ALA LEU TRP ALA GLY ASP LEU SEQRES 25 A 475 MET TYR GLN GLN ALA ALA ALA GLY SER THR GLY ILE ASN SEQRES 26 A 475 PHE HIS GLY GLY GLY TYR GLY TRP TYR THR PRO VAL ALA SEQRES 27 A 475 GLY THR PRO GLU ASP GLY PHE ILE ALA ARG PRO GLU TYR SEQRES 28 A 475 TYR GLY MET LEU LEU PHE ALA GLN ALA GLY ALA GLY GLN SEQRES 29 A 475 LEU LEU GLY ALA LYS LEU THR ASP ASN SER ALA ALA PRO SEQRES 30 A 475 LEU LEU THR ALA TYR ALA LEU ARG GLY THR ASP GLY ARG SEQRES 31 A 475 THR ARG ILE ALA LEU PHE ASN LYS ASN LEU ASP ALA ASP SEQRES 32 A 475 VAL GLU VAL ALA ILE SER GLY VAL ALA SER PRO SER GLY SEQRES 33 A 475 THR VAL LEU ARG LEU GLU ALA PRO ARG ALA ASP ASP THR SEQRES 34 A 475 THR ASP VAL THR PHE GLY GLY ALA PRO VAL GLY ALA SER SEQRES 35 A 475 GLY SER TRP SER PRO LEU VAL GLN GLU TYR VAL PRO GLY SEQRES 36 A 475 HIS SER GLY GLN PHE VAL LEU HIS MET ARG LYS ALA SER SEQRES 37 A 475 GLY ALA LEU LEU GLU PHE ALA HET PO4 A1476 5 HET PO4 A1477 5 HET J13 A1478 25 HETNAM PO4 PHOSPHATE ION HETNAM J13 (1S,2R,3R,4S,6S)-6-[(8-AZIDOOCTANOYL)AMINO]-2,3,4- HETNAM 2 J13 TRIHYDROXYCYCLOHEXANE-1-CARBOXYLATE FORMUL 2 PO4 2(O4 P 3-) FORMUL 4 J13 C15 H26 N4 O7 FORMUL 5 HOH *244(H2 O) HELIX 1 1 ALA A 47 ASN A 51 5 5 HELIX 2 2 ASN A 59 GLY A 70 1 12 HELIX 3 3 GLY A 79 GLU A 83 5 5 HELIX 4 4 ALA A 96 LEU A 100 5 5 HELIX 5 5 THR A 117 GLY A 132 1 16 HELIX 6 6 THR A 145 GLY A 161 1 17 HELIX 7 7 GLU A 173 PHE A 177 5 5 HELIX 8 8 ASP A 188 VAL A 207 1 20 HELIX 9 9 TRP A 223 LYS A 232 1 10 HELIX 10 10 HIS A 233 VAL A 235 5 3 HELIX 11 11 THR A 254 MET A 259 1 6 HELIX 12 12 ASN A 262 GLY A 280 1 19 HELIX 13 13 THR A 302 GLY A 320 1 19 HELIX 14 14 ARG A 348 GLY A 361 1 14 HELIX 15 15 GLY A 440 SER A 444 5 5 SHEET 1 AA 2 THR A 433 PHE A 434 0 SHEET 2 AA 2 GLY A 416 GLU A 422 -1 O GLU A 422 N THR A 433 SHEET 1 AB 2 GLU A 451 TYR A 452 0 SHEET 2 AB 2 GLY A 416 GLU A 422 1 O VAL A 418 N GLU A 451 SHEET 1 AC10 GLY A 455 HIS A 456 0 SHEET 2 AC10 GLN A 459 MET A 464 -1 O GLN A 459 N HIS A 456 SHEET 3 AC10 VAL A 404 SER A 409 -1 O VAL A 404 N MET A 464 SHEET 4 AC10 VAL A 20 ILE A 35 1 O VAL A 20 N GLU A 405 SHEET 5 AC10 GLY A 363 THR A 371 -1 O GLY A 363 N ILE A 35 SHEET 6 AC10 LEU A 379 GLY A 386 -1 O ALA A 383 N LEU A 366 SHEET 7 AC10 THR A 391 ASN A 397 -1 O ARG A 392 N LEU A 384 SHEET 8 AC10 SER A 468 PHE A 474 -1 O SER A 468 N ASN A 397 SHEET 9 AC10 GLY A 416 GLU A 422 -1 O THR A 417 N GLU A 473 SHEET 10 AC10 THR A 433 PHE A 434 -1 O THR A 433 N GLU A 422 SHEET 1 AD10 GLY A 455 HIS A 456 0 SHEET 2 AD10 GLN A 459 MET A 464 -1 O GLN A 459 N HIS A 456 SHEET 3 AD10 VAL A 404 SER A 409 -1 O VAL A 404 N MET A 464 SHEET 4 AD10 VAL A 20 ILE A 35 1 O VAL A 20 N GLU A 405 SHEET 5 AD10 GLY A 363 THR A 371 -1 O GLY A 363 N ILE A 35 SHEET 6 AD10 LEU A 379 GLY A 386 -1 O ALA A 383 N LEU A 366 SHEET 7 AD10 THR A 391 ASN A 397 -1 O ARG A 392 N LEU A 384 SHEET 8 AD10 SER A 468 PHE A 474 -1 O SER A 468 N ASN A 397 SHEET 9 AD10 GLY A 416 GLU A 422 -1 O THR A 417 N GLU A 473 SHEET 10 AD10 GLU A 451 TYR A 452 1 O GLU A 451 N VAL A 418 SHEET 1 AE 8 LEU A 165 LEU A 170 0 SHEET 2 AE 8 LYS A 134 LEU A 139 1 O LEU A 135 N LEU A 166 SHEET 3 AE 8 VAL A 74 GLY A 78 1 O LEU A 75 N ILE A 136 SHEET 4 AE 8 GLY A 41 GLU A 45 1 O LEU A 42 N ARG A 76 SHEET 5 AE 8 ILE A 324 GLY A 328 1 O PHE A 326 N SER A 43 SHEET 6 AE 8 PHE A 283 ASN A 289 1 O LEU A 285 N ASN A 325 SHEET 7 AE 8 PHE A 237 TYR A 243 1 O ILE A 238 N ARG A 284 SHEET 8 AE 8 ALA A 213 THR A 217 1 O GLY A 214 N SER A 239 SHEET 1 AF 2 THR A 85 TRP A 87 0 SHEET 2 AF 2 GLU A 114 ILE A 116 1 O GLU A 114 N PHE A 86 SHEET 1 AG 2 VAL A 337 THR A 340 0 SHEET 2 AG 2 GLY A 344 ALA A 347 -1 O GLY A 344 N THR A 340 LINK OE2 GLU A 287 C2 J13 A1478 1555 1555 1.44 CISPEP 1 GLY A 214 PRO A 215 0 5.51 SITE 1 AC1 7 GLY A 103 PRO A 104 GLY A 330 TYR A 331 SITE 2 AC1 7 GLY A 332 HOH A2067 HOH A2069 SITE 1 AC2 3 TRP A 333 HOH A2168 HOH A2171 SITE 1 AC3 15 GLU A 45 GLY A 79 ASN A 80 ASP A 105 SITE 2 AC3 15 ASN A 172 GLU A 173 TYR A 243 PRO A 248 SITE 3 AC3 15 GLU A 287 TYR A 292 GLN A 293 GLY A 294 SITE 4 AC3 15 HIS A 327 TYR A 334 HOH A2053 CRYST1 150.740 44.810 83.270 90.00 115.50 90.00 C 1 2 1 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 0.006634 0.000000 0.003164 0.00000 SCALE2 0.000000 0.022316 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013305 0.00000 MASTER 361 0 3 15 36 0 7 6 0 0 0 37 END