HEADER HYDROLASE 19-SEP-07 2VCB TITLE FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX TITLE 2 WITH PUGNAC COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-N-ACETYLGLUCOSAMINIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 26-916; COMPND 5 EC: 3.2.1.50; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS; SOURCE 3 ORGANISM_TAXID: 1502; SOURCE 4 ATCC: 13124; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS MUCOPOLYSACCHARIDOSIS, ALPHA-N-ACETYLGLUCOSAMINIDASE, FAMILY 89 KEYWDS 2 GLYCOSIDE HYDROLASE, HYDROLASE, GH89, NAGLU, PUGNAC, SANFILIPPO KEYWDS 3 DISEASE EXPDTA X-RAY DIFFRACTION AUTHOR E.FICKO-BLEAN,K.A.STUBBS,O.BERG,D.J.VOCADLO,A.B.BORASTON REVDAT 6 08-MAY-24 2VCB 1 REMARK LINK REVDAT 5 24-AUG-11 2VCB 1 REMARK HETSYN VERSN REVDAT 4 24-FEB-09 2VCB 1 VERSN REVDAT 3 27-MAY-08 2VCB 1 JRNL REMARK REVDAT 2 13-MAY-08 2VCB 1 JRNL REMARK REVDAT 1 18-MAR-08 2VCB 0 JRNL AUTH E.FICKO-BLEAN,K.A.STUBBS,O.NEMIROVSKY,D.J.VOCADLO, JRNL AUTH 2 A.B.BORASTON JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHT INTO THE BASIS OF JRNL TITL 2 MUCOPOLYSACCHARIDOSIS IIIB. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 6560 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18443291 JRNL DOI 10.1073/PNAS.0711491105 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 50811 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2688 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3734 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 209 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7149 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 332 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.52000 REMARK 3 B22 (A**2) : 1.52000 REMARK 3 B33 (A**2) : -2.29000 REMARK 3 B12 (A**2) : 0.76000 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): 0.285 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.222 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.169 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.833 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7236 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9794 ; 1.125 ; 1.932 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 881 ; 5.684 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 384 ;37.341 ;25.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1187 ;16.030 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;19.084 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1002 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5677 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3430 ; 0.189 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4947 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 424 ; 0.148 ; 0.200 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): 41 ; 0.201 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.066 ; 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): 4470 ; 0.416 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6965 ; 0.738 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3249 ; 0.962 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2828 ; 1.517 ; 4.500 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 : 1.40 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 2VCB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1290033880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 113.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL 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 : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53561 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 29.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 200 DATA REDUNDANCY : 2.610 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 84.15567 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 168.31133 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 126.23350 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 210.38917 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.07783 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 VAL A 164 REMARK 465 GLY A 855 REMARK 465 LEU A 911 REMARK 465 GLY A 912 REMARK 465 GLU A 913 REMARK 465 ASN A 914 REMARK 465 GLU A 915 REMARK 465 SER A 916 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 ILE A 910 CA C O CB CG1 CG2 CD1 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ILE A 910 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 31 OE2 REMARK 480 ASP A 125 CB CG OD1 OD2 REMARK 480 ARG A 144 CZ NH1 NH2 REMARK 480 LYS A 155 CG CD REMARK 480 THR A 157 CG2 REMARK 480 GLU A 163 CB CG CD OE1 OE2 REMARK 480 LYS A 165 CB CG CD CE NZ REMARK 480 LYS A 166 CB CG CD CE NZ REMARK 480 ARG A 209 CG CD NE CZ NH1 NH2 REMARK 480 ASP A 213 OD1 OD2 REMARK 480 LYS A 274 CG CD CE NZ REMARK 480 GLU A 277 CB CG CD OE1 OE2 REMARK 480 GLN A 423 NE2 REMARK 480 GLU A 424 OE2 REMARK 480 GLU A 448 CG CD OE1 OE2 REMARK 480 GLU A 463 CD OE1 OE2 REMARK 480 ASN A 524 ND2 REMARK 480 LYS A 642 CG CD REMARK 480 TRP A 685 CB CG CD1 CD2 NE1 CE2 CE3 REMARK 480 TRP A 685 CZ2 CZ3 CH2 REMARK 480 LYS A 706 CD CE NZ REMARK 480 ASN A 742 CG OD1 ND2 REMARK 480 ASN A 748 CB CG OD1 ND2 REMARK 480 GLU A 750 CB CG CD OE1 OE2 REMARK 480 LYS A 751 CB CG CD CE NZ REMARK 480 GLU A 835 CD OE1 OE2 REMARK 480 ALA A 851 CB REMARK 480 LYS A 858 CB CG CD CE NZ REMARK 480 ALA A 859 CB REMARK 480 ASN A 861 OD1 ND2 REMARK 480 LYS A 909 CB CG CD CE NZ 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 ND2 ASN A 524 O HOH A 2210 1.76 REMARK 500 OE1 GLN A 664 OAR OAN A 1911 1.99 REMARK 500 O PRO A 521 NH2 ARG A 550 2.13 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 THR A 157 OG1 - CB - CG2 ANGL. DEV. = 15.5 DEGREES REMARK 500 ASP A 213 CB - CG - OD1 ANGL. DEV. = -5.6 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 ASN A 62 -140.69 -126.69 REMARK 500 ASN A 126 56.09 38.43 REMARK 500 LEU A 298 135.64 110.93 REMARK 500 ASP A 539 98.83 -66.29 REMARK 500 ASP A 547 40.38 -154.51 REMARK 500 HIS A 564 -65.60 75.73 REMARK 500 ASN A 604 12.62 -150.39 REMARK 500 THR A 654 -89.45 -120.39 REMARK 500 TYR A 663 135.39 -178.32 REMARK 500 SER A 681 168.90 174.64 REMARK 500 TRP A 685 51.62 -103.08 REMARK 500 THR A 809 -101.49 -127.37 REMARK 500 TRP A 811 -62.77 74.98 REMARK 500 ASP A 818 -76.29 -95.23 REMARK 500 TYR A 837 -60.00 -128.89 REMARK 500 ALA A 857 165.95 178.34 REMARK 500 ASP A 879 -73.11 -100.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 847 GLY A 848 44.40 REMARK 500 ALA A 857 LYS A 858 -32.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2042 DISTANCE = 6.70 ANGSTROMS REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 OAN A 1911 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 CA A1912 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 48 O REMARK 620 2 ASP A 51 OD1 90.3 REMARK 620 3 ASP A 53 O 177.4 87.9 REMARK 620 4 THR A 56 O 91.7 139.4 88.5 REMARK 620 5 THR A 56 OG1 96.7 67.6 80.9 71.9 REMARK 620 6 ALA A 148 O 87.1 144.9 95.5 75.7 147.4 REMARK 620 7 GLU A 149 OE2 102.3 69.0 78.7 148.9 132.3 77.5 REMARK 620 N 1 2 3 4 5 6 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OAN A 1911 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1912 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VC9 RELATED DB: PDB REMARK 900 FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS IN REMARK 900 COMPLEX WITH 2-ACETAMIDO-1 ,2-DIDEOXYNOJIRMYCIN REMARK 900 RELATED ID: 2VCA RELATED DB: PDB REMARK 900 FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS IN REMARK 900 COMPLEX WITH BETA-N-ACETYL -D-GLUCOSAMINE REMARK 900 RELATED ID: 2VCC RELATED DB: PDB REMARK 900 FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS DBREF 2VCB A 26 916 UNP Q0TST1 Q0TST1_CLOP1 26 916 SEQRES 1 A 891 GLY VAL GLU ILE THR GLU GLY VAL THR VAL THR ALA LYS SEQRES 2 A 891 GLY ASN THR GLU GLY ASN THR ALA ASP LEU ALA ILE ASP SEQRES 3 A 891 GLY ASP LEU SER THR TYR TRP GLU SER SER ASN ASP TYR SEQRES 4 A 891 LYS TRP ILE GLU VAL ASP LEU GLY GLY ILE TYR GLU LEU SEQRES 5 A 891 SER LYS ILE GLU ILE PHE ASN LYS ASP GLU ALA VAL TYR SEQRES 6 A 891 LYS TYR ASN ILE TYR ALA SER GLU ASP GLY GLU ASN PHE SEQRES 7 A 891 ASN LYS ILE ALA TYR LYS ASN ASN ASP ASN VAL SER ASP SEQRES 8 A 891 SER ASN GLY ASN MET HIS THR ILE ASP ASN VAL ARG ALA SEQRES 9 A 891 GLY LYS ILE ARG ILE ASP VAL VAL GLN ASN SER ASN SER SEQRES 10 A 891 ASP ARG VAL ASN ILE ALA GLU ILE ASN VAL PHE GLY LYS SEQRES 11 A 891 ASN THR GLY GLU SER LEU PRO GLU VAL LYS LYS ILE ALA SEQRES 12 A 891 THR SER ASN PHE SER GLU THR PRO TRP ALA THR GLU TYR SEQRES 13 A 891 GLU LYS PHE ASN SER ASP SER ALA TYR ALA ASN GLU LYS SEQRES 14 A 891 THR LEU ASN GLU ILE LYS ASN LEU VAL GLY ARG VAL ILE SEQRES 15 A 891 GLY ARG GLU PHE LYS ASP LYS PHE ILE PHE GLU ILE ARG SEQRES 16 A 891 ASP GLN LEU ASN GLY ASN ASP VAL PHE GLU VAL SER ASP SEQRES 17 A 891 SER GLY ASP GLY LYS VAL LEU ILE LYS GLY ASN ASN GLY SEQRES 18 A 891 VAL SER LEU ALA SER GLY PHE ASN TYR TYR LEU LYS ASN SEQRES 19 A 891 TYR CYS ASN VAL SER TYR ASN PRO ILE MET GLY SER ASN SEQRES 20 A 891 LEU LYS MET PRO GLU THR MET PRO SER VAL GLY GLU ARG SEQRES 21 A 891 VAL VAL ILE ASP THR PRO TYR GLU HIS ARG TYR ALA LEU SEQRES 22 A 891 ASN PHE CYS THR TYR SER TYR THR MET SER PHE TRP ASP SEQRES 23 A 891 TRP ASP GLN TYR GLU GLU PHE LEU ASP TRP CYS ALA MET SEQRES 24 A 891 ASN GLY VAL ASN LEU VAL LEU ASP ILE ILE GLY GLN GLU SEQRES 25 A 891 GLU VAL LEU ARG ARG THR LEU ASN GLU PHE GLY TYR SER SEQRES 26 A 891 ASP GLU GLU VAL LYS GLU PHE ILE SER GLY PRO ALA TYR SEQRES 27 A 891 PHE ALA TRP PHE TYR MET GLN ASN MET THR GLY PHE GLY SEQRES 28 A 891 GLY PRO LEU PRO ASN ASP TRP PHE GLU GLN ARG ALA GLU SEQRES 29 A 891 LEU GLY ARG LYS MET HIS ASP ARG MET GLN SER PHE GLY SEQRES 30 A 891 ILE ASN PRO VAL LEU GLN GLY TYR SER GLY MET VAL PRO SEQRES 31 A 891 ARG ASP PHE LYS GLU LYS ASN GLN GLU ALA GLN THR ILE SEQRES 32 A 891 SER GLN GLY GLY TRP CYS GLY PHE ASP ARG PRO ASP MET SEQRES 33 A 891 LEU LYS THR TYR VAL ASN GLU GLY GLU ALA ASP TYR PHE SEQRES 34 A 891 GLN LYS VAL ALA ASP VAL PHE TYR GLU LYS GLN LYS GLU SEQRES 35 A 891 VAL PHE GLY ASP VAL THR ASN PHE TYR GLY VAL ASP PRO SEQRES 36 A 891 PHE HIS GLU GLY GLY ASN THR GLY ASP LEU ASP ASN GLY SEQRES 37 A 891 LYS ILE TYR GLU ILE ILE GLN ASN LYS MET ILE GLU HIS SEQRES 38 A 891 ASP ASN ASP ALA VAL TRP VAL ILE GLN ASN TRP GLN GLY SEQRES 39 A 891 ASN PRO SER ASN ASN LYS LEU GLU GLY LEU THR LYS LYS SEQRES 40 A 891 ASP GLN ALA MET VAL LEU ASP LEU PHE SER GLU VAL SER SEQRES 41 A 891 PRO ASP TRP ASN ARG LEU GLU GLU ARG ASP LEU PRO TRP SEQRES 42 A 891 ILE TRP ASN MET LEU HIS ASN PHE GLY GLY ARG MET GLY SEQRES 43 A 891 MET ASP ALA ALA PRO GLU LYS LEU ALA THR GLU ILE PRO SEQRES 44 A 891 LYS ALA LEU ALA ASN SER GLU HIS MET VAL GLY ILE GLY SEQRES 45 A 891 ILE THR PRO GLU ALA ILE ASN THR ASN PRO LEU ALA TYR SEQRES 46 A 891 GLU LEU LEU PHE ASP MET ALA TRP THR ARG ASP GLN ILE SEQRES 47 A 891 ASN PHE ARG THR TRP THR GLU ASP TYR ILE GLU ARG ARG SEQRES 48 A 891 TYR GLY LYS THR ASN LYS GLU ILE LEU GLU ALA TRP ASN SEQRES 49 A 891 ILE ILE LEU ASP THR ALA TYR LYS LYS ARG ASN ASP TYR SEQRES 50 A 891 TYR GLN GLY ALA ALA GLU SER ILE ILE ASN ALA ARG PRO SEQRES 51 A 891 GLY PHE GLY ILE LYS SER ALA SER THR TRP GLY HIS SER SEQRES 52 A 891 LYS ILE VAL TYR ASP LYS SER GLU PHE GLU LYS ALA ILE SEQRES 53 A 891 GLU ILE PHE ALA LYS ASN TYR ASP GLU PHE LYS ASP SER SEQRES 54 A 891 ASP ALA PHE LEU TYR ASP PHE ALA ASP ILE LEU LYS GLN SEQRES 55 A 891 LEU LEU ALA ASN SER ALA GLN GLU TYR TYR GLU VAL MET SEQRES 56 A 891 CYS ASN ALA TYR ASN ASN GLY ASN GLY GLU LYS PHE LYS SEQRES 57 A 891 PHE VAL SER GLY LYS PHE LEU GLU LEU ILE LYS LEU GLN SEQRES 58 A 891 GLU ARG VAL LEU SER THR ARG PRO GLU PHE LEU ILE GLY SEQRES 59 A 891 ASN TRP ILE GLU ASP ALA ARG THR MET LEU LYS ASP SER SEQRES 60 A 891 ASP ASP TRP THR LYS ASP LEU PHE GLU PHE ASN ALA ARG SEQRES 61 A 891 ALA LEU VAL THR THR TRP GLY SER ARG ASN ASN ALA ASP SEQRES 62 A 891 GLY GLY GLY LEU LYS ASP TYR SER ASN ARG GLN TRP SER SEQRES 63 A 891 GLY LEU THR GLU ASP TYR TYR TYR ALA ARG TRP GLU LYS SEQRES 64 A 891 TRP ILE ASN GLY LEU GLN ALA GLU LEU ASP GLY GLY ALA SEQRES 65 A 891 LYS ALA PRO ASN ILE ASP TRP PHE LYS MET GLU TYR ASP SEQRES 66 A 891 TRP VAL ASN LYS LYS SER ASP THR ASP LYS LEU TYR PRO SEQRES 67 A 891 THR GLU ALA SER ASN GLU ASN LEU GLY GLU LEU ALA LYS SEQRES 68 A 891 ILE ALA MET GLU SER TYR SER VAL THR ASN MET ASP LYS SEQRES 69 A 891 ILE LEU GLY GLU ASN GLU SER HET OAN A1911 25 HET CA A1912 1 HETNAM OAN O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N- HETNAM 2 OAN PHENYLCARBAMATE HETNAM CA CALCIUM ION HETSYN OAN PUGNAC FORMUL 2 OAN C15 H19 N3 O7 FORMUL 3 CA CA 2+ FORMUL 4 HOH *332(H2 O) HELIX 1 1 THR A 45 ILE A 50 5 6 HELIX 2 2 ASN A 171 GLU A 174 5 4 HELIX 3 3 THR A 175 ASP A 187 1 13 HELIX 4 4 ASP A 187 ILE A 207 1 21 HELIX 5 5 GLY A 208 ASP A 213 5 6 HELIX 6 6 ASN A 245 CYS A 261 1 17 HELIX 7 7 CYS A 301 THR A 306 1 6 HELIX 8 8 ASP A 311 ASN A 325 1 15 HELIX 9 9 GLY A 335 ASN A 345 1 11 HELIX 10 10 GLU A 346 GLY A 348 5 3 HELIX 11 11 SER A 350 ILE A 358 1 9 HELIX 12 12 TYR A 363 MET A 369 1 7 HELIX 13 13 ASP A 382 GLY A 402 1 21 HELIX 14 14 ASP A 417 ASN A 422 1 6 HELIX 15 15 ASP A 452 GLY A 470 1 19 HELIX 16 16 ASP A 491 ASP A 507 1 17 HELIX 17 17 SER A 522 GLU A 527 1 6 HELIX 18 18 LYS A 531 ASP A 533 5 3 HELIX 19 19 TRP A 548 GLU A 553 1 6 HELIX 20 20 ALA A 575 ASN A 589 1 15 HELIX 21 21 ASN A 606 MET A 616 1 11 HELIX 22 22 ALA A 617 THR A 619 5 3 HELIX 23 23 ASN A 624 GLY A 638 1 15 HELIX 24 24 ASN A 641 THR A 654 1 14 HELIX 25 25 SER A 669 ALA A 673 5 5 HELIX 26 26 ASP A 693 ASN A 707 1 15 HELIX 27 27 ASN A 707 LYS A 712 1 6 HELIX 28 28 SER A 714 ASN A 746 1 33 HELIX 29 29 GLY A 749 SER A 771 1 23 HELIX 30 30 THR A 772 PHE A 776 5 5 HELIX 31 31 LEU A 777 MET A 788 1 12 HELIX 32 32 ASP A 793 VAL A 808 1 16 HELIX 33 33 SER A 813 ASP A 818 1 6 HELIX 34 34 GLY A 832 TYR A 837 1 6 HELIX 35 35 TYR A 837 ASP A 854 1 18 HELIX 36 36 ASP A 863 ASN A 873 1 11 HELIX 37 37 ASN A 890 TYR A 902 1 13 SHEET 1 AA 5 THR A 34 ALA A 37 0 SHEET 2 AA 5 TRP A 66 PHE A 83 -1 O GLU A 68 N THR A 36 SHEET 3 AA 5 ASN A 120 ASN A 139 -1 O ASN A 120 N ILE A 82 SHEET 4 AA 5 TYR A 90 SER A 97 -1 O LYS A 91 N GLN A 138 SHEET 5 AA 5 ASN A 104 LYS A 109 -1 O ASN A 104 N ALA A 96 SHEET 1 AB 3 THR A 34 ALA A 37 0 SHEET 2 AB 3 TRP A 66 PHE A 83 -1 O GLU A 68 N THR A 36 SHEET 3 AB 3 GLU A 149 ASN A 156 -1 O GLU A 149 N PHE A 83 SHEET 1 AC 2 TRP A 58 GLU A 59 0 SHEET 2 AC 2 ASN A 146 ILE A 147 -1 O ILE A 147 N TRP A 58 SHEET 1 AD 4 PHE A 215 ILE A 219 0 SHEET 2 AD 4 VAL A 239 GLY A 243 1 O VAL A 239 N ILE A 216 SHEET 3 AD 4 VAL A 228 ASP A 233 -1 O GLU A 230 N LYS A 242 SHEET 4 AD 4 VAL A 286 ASP A 289 -1 O VAL A 286 N VAL A 231 SHEET 1 AE 9 HIS A 294 ALA A 297 0 SHEET 2 AE 9 MET A 593 ILE A 598 1 O VAL A 594 N HIS A 294 SHEET 3 AE 9 TRP A 558 MET A 562 1 O TRP A 558 N VAL A 594 SHEET 4 AE 9 ALA A 535 ASP A 539 1 O VAL A 537 N ILE A 559 SHEET 5 AE 9 VAL A 511 ASN A 516 1 O TRP A 512 N MET A 536 SHEET 6 AE 9 PHE A 475 GLY A 477 1 O TYR A 476 N VAL A 513 SHEET 7 AE 9 ASN A 404 GLN A 408 1 O LEU A 407 N GLY A 477 SHEET 8 AE 9 LEU A 329 LEU A 331 1 O VAL A 330 N VAL A 406 SHEET 9 AE 9 HIS A 294 ALA A 297 1 O ALA A 297 N LEU A 331 SHEET 1 AF 3 MET A 413 VAL A 414 0 SHEET 2 AF 3 ASP A 440 LEU A 442 -1 O ASP A 440 N VAL A 414 SHEET 3 AF 3 THR A 427 ILE A 428 -1 O ILE A 428 N MET A 441 SHEET 1 AG 2 GLY A 432 TRP A 433 0 SHEET 2 AG 2 PHE A 436 ASP A 437 -1 O PHE A 436 N TRP A 433 LINK O LEU A 48 CA CA A1912 1555 1555 2.14 LINK OD1 ASP A 51 CA CA A1912 1555 1555 2.36 LINK O ASP A 53 CA CA A1912 1555 1555 2.32 LINK O THR A 56 CA CA A1912 1555 1555 2.38 LINK OG1 THR A 56 CA CA A1912 1555 1555 2.67 LINK O ALA A 148 CA CA A1912 1555 1555 2.37 LINK OE2 GLU A 149 CA CA A1912 1555 1555 2.41 CISPEP 1 GLY A 26 VAL A 27 0 12.54 CISPEP 2 GLU A 42 GLY A 43 0 -6.94 CISPEP 3 GLU A 42 GLY A 43 0 -4.35 CISPEP 4 GLY A 377 PRO A 378 0 2.49 CISPEP 5 ASN A 520 PRO A 521 0 1.76 CISPEP 6 ASN A 748 GLY A 749 0 7.67 SITE 1 AC1 16 ASN A 299 CYS A 301 TYR A 305 TRP A 366 SITE 2 AC1 16 MET A 369 HIS A 482 GLU A 483 TRP A 517 SITE 3 AC1 16 LEU A 540 PHE A 566 GLU A 601 GLN A 664 SITE 4 AC1 16 LEU A 822 TYR A 825 HOH A2137 HOH A2338 SITE 1 AC2 6 LEU A 48 ASP A 51 ASP A 53 THR A 56 SITE 2 AC2 6 ALA A 148 GLU A 149 CRYST1 90.704 90.704 252.467 90.00 90.00 120.00 P 61 6 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 0.011025 0.006365 0.000000 0.00000 SCALE2 0.000000 0.012730 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003961 0.00000